Projects: bioconductor: phyloseq
https://packages.ecosyste.ms/registries/bioconductor.org/packages/phyloseq
Handling and analysis of high-throughput microbiome census data
2 versions
Latest release: almost 3 years ago
20 dependent packages
628,327 downloads total
Science Score: 75/100
Starting Score: 100 points
Bonuses:
Penalties:
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Non-science indicators
1 non-scientific terms found
Very Likely Science (75)
Papers Mentioning phyloseq 1,702
10.1186/s40168-019-0705-7
Microbial indicators of environmental perturbations in coral reef ecosystemsCited by: 109
Author(s): Bettina Glasl, David G. Bourne, Pedro R. Frade, Torsten Thomas, Britta Schaffelke, Nicole S. Webster
Software Mentions: 6
Published: over 7 years ago
10.1371/journal.pone.0248030
Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiomeCited by: 22
Author(s): Heidi M.-L. Wipf, Devin Coleman‐Derr
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pone.0235159
Zooplankton biogeographic boundaries in the California Current System as determined from metabarcodingCited by: 13
Author(s): Kathleen J. Pitz, Jinchen Guo, Shannon B. Johnson, Tracy L. Campbell, Haibin Zhang, Robert C. Vrijenhoek, Francisco P. Chávez, Jonathan B. Geller
Software Mentions: 6
Published: about 6 years ago
10.1186/s40168-018-0449-9
The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive toolCited by: 113
Author(s): Jo De Vrieze, Ameet J. Pinto, William T. Sloan, Umer Zeeshan Ijaz
Software Mentions: 6
Published: over 8 years ago
10.1371/journal.pone.0236574
Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of KenyaCited by: 11
Author(s): Edward Nderitu Karanja, Andreas Fließbach, Noah Adamtey, Anne Kelly Kambura, Martha W. Musyoka, Komi K. M. Fiaboe, Romano Mwirichia
Software Mentions: 6
Published: about 6 years ago
10.1371/journal.pone.0251136
Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional studyCited by: 7
Author(s): Martijn G H Sanders, Tamar Nijsten, Joost Verlouw, Robert Kraaij, Luba M. Pardo
Software Mentions: 6
Published: over 5 years ago
10.1098/rspb.2019.0804
Anthropogenic remediation of heavy metals selects against natural microbial remediationCited by: 11
Author(s): Elze Hesse, Daniel Padfield, Florian Bayer, Eleanor M. van Veen, Christopher G. Bryan, Angus Buckling
Software Mentions: 6
Published: over 7 years ago
10.1002/ece3.3638
Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (<i>Sus scrofa</i>)Cited by: 54
Author(s): Michael S. Robeson, Kamil Khanipov, George Golovko, Samantha M. Wisely, Michael D. White, Michael J. Bodenchuck, Timothy J. Smyser, Yuriy Fofanov, Noah Fierer, Antoinette J. Piaggio
Software Mentions: 6
Published: almost 9 years ago
10.3390/microorganisms8101566
The Prokaryotic Microbiome of Acropora digitifera is Stable under Short-Term Artificial Light PollutionCited by: 6
Author(s): Jake Ivan P. Baquiran, Michael Angelou L. Nada, Celine Luisa D. Campos, Sherry Lyn G. Sayco, Patrick C. Cabaitan, Yaeli Rosenberg, Inbal Ayalon, Oren Levy, Cecilia Conaco
Software Mentions: 6
Published: almost 6 years ago
10.7717/peerj.12135
Biogeography rather than substrate type determines bacterial colonization dynamics of marine plasticsCited by: 9
Author(s): Ashley K. Coons, Kathrin Busch, Mark Lenz, Ute Hentschel, Erik Borchert
Software Mentions: 6
Published: about 5 years ago
10.3390/microorganisms6030068
Cloacal and Ocular Microbiota of the Endangered Australian Northern QuollCited by: 2
Author(s): Catherine Burke, Delaney Burnard, Adam Polkinghorne, Jonathan K. Webb, Wilhelmina M. Huston
Software Mentions: 6
Published: about 8 years ago
10.1002/ece3.7171
Identification of novel bacterial biomarkers to detect bird scavenging by invasive ratsCited by: 3
Author(s): Carly R. Muletz‐Wolz, Erin E. Wilson Rankin, Sarah McGrath‐Blaser, Madhvi X. Venkatraman, Jesús E. Maldonado, Daniel S. Gruner, Robert C. Fleischer
Software Mentions: 6
Published: over 5 years ago
10.1186/s40104-021-00580-4
Convergence of the turkey gut microbiota following cohabitation under commercial settingsCited by: 1
Author(s): Elizabeth A. Miller, Brittanie Winfield, Bonnie Weber, Cristian Flores-Figueroa, Jeannette Muñoz-Aguayo, Jared Huisinga, Timothy J. Johnson
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pone.0204317
Association of metformin administration with gut microbiome dysbiosis in healthy volunteersCited by: 85
Author(s): Ilze Elbere, Ineta Kalniņa, Ivars Silamiķelis, Ilze Konrāde, Linda Zaharenko, Kristine Sekace, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Dita Gudrā, Valdis Pīrāgs, Jānis Kloviņš
Software Mentions: 6
Published: almost 8 years ago
10.1128/mSphere.00798-19
Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral TherapyCited by: 37
Author(s): Medini K. Annavajhala, Sobia Khan, Sean B. Sullivan, Jainil P. Shah, Lauren Pass, Karolina Kister, Heather Kunen, Victor Chiang, Gwennaëlle Monnot, Christopher L. Ricupero, Rebecca A. Mazur, Peter Gordon, Annemieke de Jong, Sunil Wadhwa, Michael T. Yin, Ryan T. Demmer, Anne‐Catrin Uhlemann
Software Mentions: 6
Published: over 6 years ago
10.3390/microorganisms9030492
The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort StudyCited by: 11
Author(s): Barry Linnane, Aaron M. Walsh, Calum J. Walsh, Fiona Crispie, Órla O’Sullivan, Paul D. Cotter, Michael McDermott, J. A. A. Renwick, Paul McNally
Software Mentions: 6
Published: over 5 years ago
10.1002/ece3.5361
Drivers and patterns of microbial community assembly in a Lyme disease vectorCited by: 30
Author(s): Lisa I. Couper, Jessica Y. Kwan, Joyce Ma, Andrea Swei
Software Mentions: 6
Published: over 7 years ago
10.1371/journal.pone.0187612
Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of LactobacillusCited by: 39
Author(s): Jocelyn M. Wessels, Julie Lajoie, Danielle Vitali, Kenneth Omollo, Joshua Kimani, Julius Oyugi, Juliana Cheruiyot, Murungaru Kimani, Joseph Maina Mungai, Maureen Akolo, Jennifer C. Stearns, Michael G. Surette, Keith R. Fowke, Charu Kaushic
Software Mentions: 6
Published: almost 9 years ago
10.1128/mSphere.00455-21
A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial DecompositionCited by: 9
Author(s): Heather L. Deel, Alexandra L. Emmons, Jennifer Kiely, Franklin E. Damann, David Carter, Aaron M. Lynne, Rob Knight, Zhenjiang Xu, Sibyl R. Bucheli, Jessica L. Metcalf
Software Mentions: 6
Published: about 5 years ago
10.3389/fmicb.2018.00674
Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy CropCited by: 38
Author(s): Késia Silva Lourenço, Noriko A. Cassman, Agata Pijl, Johannes A. van Veen, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 6
Published: over 8 years ago
10.3389/fmicb.2016.00399
Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial CommunitiesCited by: 21
Author(s): Megan A. Rúa, Emily Wilson, S. D. Steele, Arielle R. Munters, Jason D. Hoeksema, A. Carolin Frank
Software Mentions: 6
Published: over 10 years ago
10.1186/s40168-019-0639-0
Rare gut microbiota associated with breeding success, hormone metabolites and ovarian cycle phase in the critically endangered eastern black rhinoCited by: 61
Author(s): Rachael E. Antwis, Katie L. Edwards, Bryony Unwin, Susan L. Walker, Susanne Shultz
Software Mentions: 6
Published: over 7 years ago
10.3390/ph14070635
Probiotic Bacteria with High Alpha-Gal Content Protect Zebrafish against MycobacteriosisCited by: 10
Author(s): Iván Pacheco, Sandra Díaz-Sánchez, Marinela Contreras, Margarita Villar, Alejandro Cabezas-Cruz, Christian Gortázar, José de la Fuente
Software Mentions: 6
Published: about 5 years ago
10.3390/microorganisms8121978
Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanoroseaCited by: 8
Author(s): Bruno Francesco Rodrigues de Oliveira, Isabelle Rodrigues Lopes, Anna Luiza Bauer Canellas, Guilherme Muricy, Alan D. W. Dobson, Marinella Silva Laport
Software Mentions: 6
Published: almost 6 years ago
10.1242/dmm.041947
Temporal evolution of the microbiome, immune system, and epigenome with disease progression in ALS miceCited by: 44
Author(s): Claudia Figueroa‐Romero, Kai Guo, Benjamin J. Murdock, Ximena Paez-Colasante, Christine M. Bassis, Kristen A. Mikhail, Kristen D. Raue, Matthew C. Evans, Ghislaine F. Taubman, Andrew J. McDermott, Phillipe D. O’Brien, Masha G. Savelieff, Junguk Hur, Eva L. Feldman
Software Mentions: 6
Published: over 7 years ago
10.3389/fmicb.2021.592725
Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest BiomeCited by: 13
Author(s): Henry Joseph Oduor Ogola, Ramganesh Selvarajan, Memory Tekere
Software Mentions: 6
Published: over 5 years ago
10.3390/microorganisms8071004
Relationship between the Oral and Vaginal Microbiota of South African Adolescents with High Prevalence of Bacterial VaginosisCited by: 11
Author(s): Christina Balle, Rachel Esra, Enock Havyarimana, Shameem Z. Jaumdally, Katie Lennard, Iyaloo N. Konstantinus, Shaun Barnabas, Anna‐Ursula Happel, Katherine Gill, Tanya Pidwell, Jairam R. Lingappa, Hoyam Gamieldien, Linda‐Gail Bekker, Jo‐Ann S. Passmore, Heather B. Jaspan
Software Mentions: 6
Published: about 6 years ago
10.1007/s00248-020-01656-w
Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh ElevationsCited by: 2
Author(s): Edisa García Hernández, Matty P. Berg, A. Raoul Van Oosten, Christian Smit, Joana Falcão Salles
Software Mentions: 6
Published: over 5 years ago
10.1038/s42003-021-01712-2
Feedback mechanisms stabilise degraded turf algal systems at a CO2 seep siteCited by: 10
Author(s): Ben P. Harvey, Ro Allen, Sylvain Agostini, Linn Hoffmann, Koetsu Kon, Tina C. Summerfield, Shigeki Wada, Jason M. Hall-Spencer
Software Mentions: 6
Published: over 5 years ago
10.1111/1751-7915.13450
Environmental filtering increases with elevation for the assembly of gut microbiota in wild pikasCited by: 47
Author(s): Huan Li, Rui Zhou, Jun Zhu, Xiaodan Huang, Jiapeng Qu
Software Mentions: 6
Published: over 7 years ago
10.3390/microorganisms9051060
Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North AmericaCited by: 42
Author(s): Keisha Harrison, Chris Curtin
Software Mentions: 6
Published: over 5 years ago
10.1111/1751-7915.13323
Diet and diet‐associated bacteria shape early microbiome development in Yellowtail Kingfish (<i>Seriola lalandi</i>)Cited by: 56
Author(s): Jackson Wilkes Walburn, Bernd Wemheuer, Torsten Thomas, Elizabeth Copeland, Wayne A. O’Connor, Mark A. Booth, D. Stewart Fielder, Suhelen Egan
Software Mentions: 6
Published: almost 8 years ago
10.18632/aging.103168
Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosisCited by: 103
Author(s): Jianquan He, Shuaimei Xu, Bangzhou Zhang, Chuanxing Xiao, Zhangran Chen, Fuyou Si, Jifan Fu, Xiaobo Lin, Guohua Zheng, Guangchuang Yu, Jian Chen
Software Mentions: 6
Published: over 6 years ago
10.1186/s12862-021-01773-1
Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distanceCited by: 5
Author(s): Jiří Reif, Lucie Schmiedová, Jakub Kreisinger, Tomáš Albrecht, Jiří Reif, Tomasz S. Osiejuk, Radka Reifová
Software Mentions: 6
Published: over 5 years ago
10.3390/microorganisms8020279
Diversity of Bacterial Biosynthetic Genes in Maritime AntarcticaCited by: 9
Author(s): Adriana Rego, António G G Sousa, João P. Santos, Francisco Pascoal, João Canário, Pedro N. Leão, Catarina Magalhães
Software Mentions: 6
Published: over 6 years ago
10.3390/microorganisms8030368
Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk MicrobiotaCited by: 8
Author(s): Alexandre J.K. Ouamba, Gisèle LaPointe, Simon Dufour, Denis Roy
Software Mentions: 6
Published: over 6 years ago
10.1126/sciadv.abg5016
High-salt diet mediates interplay between NK cells and gut microbiota to induce potent tumor immunityCited by: 48
Author(s): Zaigham Abbas Rizvi, Rajdeep Dalal, Srikanth Sadhu, Yashwant Kumar, Sunil Kumar, Sonu Kumar Gupta, Manas Ranjan Tripathy, Deepak Kumar Rathore, Amit Awasthi
Software Mentions: 6
Published: about 5 years ago
10.1186/s40168-017-0314-2
A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysisCited by: 61
Author(s): Fiona Whelan, Michael G. Surette
Software Mentions: 6
Published: about 9 years ago
10.3390/microorganisms8071015
Gut Microbiota and Dietary Intake of Normal-Weight and Overweight Filipino ChildrenCited by: 16
Author(s): Maria Julia Golloso-Gubat, Quinten R Ducarmon, Robby Carlo A. Tan, Romy D. Zwittink, Ed J. Kuijper, Jacus S. Nacis, Noelle Lyn C Santos
Software Mentions: 6
Published: about 6 years ago
10.3390/microorganisms8070982
Microbial Diversity Associated with Gwell, a Traditional French Mesophilic Fermented Milk Inoculated with a Natural StarterCited by: 10
Author(s): Lucas von Gastrow, Marie‐Noëlle Madec, Victoria Chuat, S. Lubac, Clémence Morinière, Sébastien Lê, Sylvain Santoni, Delphine Sicard, Florence Valence
Software Mentions: 6
Published: about 6 years ago
10.3390/cells8060517
Fecal Microbiota Transplantation Controls Murine Chronic Intestinal Inflammation by Modulating Immune Cell Functions and Gut Microbiota CompositionCited by: 46
Author(s): Claudia Burrello, Maria Rita Giuffrè, Angeli Dominique Macandog, Angélica Díaz‐Basabe, Fulvia Milena Cribiù, Gianluca Lopez, Francesca Borgo, Luigi Nezi, Flavio Caprioli, Maurizio Vecchi, Federica Facciotti
Software Mentions: 6
Published: over 7 years ago
10.1038/s41423-021-00647-2
The microbiota is dispensable for the early stages of peripheral regulatory T cell induction within mesenteric lymph nodesCited by: 16
Author(s): Carolin Wiechers, Mangge Zou, Eric Galvez, Michael Beckstette, Maria F. Ebel, Till Strowig, Jochen Huehn, Joern Pezoldt
Software Mentions: 6
Published: over 5 years ago
10.3389/fmicb.2017.01379
Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis)Cited by: 25
Author(s): Obed Hernández‐Gómez, Jason T. Hoverman, Rod N. Williams
Software Mentions: 6
Published: about 9 years ago
10.1016/j.xcrm.2020.100077
Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational StudyCited by: 108
Author(s): Cristina Alcon-Giner, Matthew J. Dalby, Shabhonam Caim, Jennifer Ketskemety, Alexander Shaw, Kathleen Sim, Melissa A. Lawson, Raymond Kiu, Charlotte Leclaire, Lisa Chalklen, Magdalena Kujawska, Suparna Mitra, Fahmina Fardus‐Reid, Gusztav Belteki, Katherine McColl, Jonathan R. Swann, J. Simon Kroll, Paul Clarke, Lindsay J. Hall
Software Mentions: 6
Published: about 6 years ago
10.3390/microorganisms9010076
Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected MicroplasticsCited by: 44
Author(s): Katharina Kesy, Matthias Labrenz, Brittan S. Scales, Bernd Kreikemeyer, Sonja Oberbeckmann
Software Mentions: 6
Published: over 5 years ago
10.3390/microorganisms7100473
Rapid Bacterial Community Changes during Vermicomposting of Grape Marc Derived from Red WinemakingCited by: 18
Author(s): María Gómez-Brandòn, Manuel Aira, Allison R. Kolbe, Nariane de Andrade, Marcos Pérez‐Losada, Jorge Domínguez
Software Mentions: 6
Published: almost 7 years ago
10.1371/journal.pone.0239681
The Znt7-null mutation has sex dependent effects on the gut microbiota and goblet cell population in the mouse colonCited by: 3
Author(s): Mary E. Kable, Niknaz Riazati, Catherine P. Kirschke, Junli Zhao, Surapun Tepaamorndech, Liping Huang
Software Mentions: 6
Published: almost 6 years ago
10.3390/ijms22115981
Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal TractCited by: 8
Author(s): Adrian Low, Melissa Soh, Sou Miyake, Vanessa Zhi Jie Aw, Jian Feng, Adeline Wong, Henning Seedorf
Software Mentions: 6
Published: over 5 years ago
10.3390/nu13030807
Transient Effect of Infant Formula Supplementation on the Intestinal MicrobiotaCited by: 6
Author(s): Ning Chin, Gema Méndez-Lagares, Diana H. Taft, Victoria Laleau, Hung T. Kieu, Narayan Nicole, Susan B. Roberts, David A. Mills, Dennis J. Hartigan-O’Connor, Valerie J. Flaherman
Software Mentions: 6
Published: over 5 years ago
10.7554/eLife.21887
A phylogenetic transform enhances analysis of compositional microbiota dataCited by: 239
Author(s): Justin D. Silverman, Alex D. Washburne, Sayan Mukherjee, Lawrence A. David
Software Mentions: 6
Published: over 9 years ago
10.3390/ijms21176283
Differential Profiles of Gut Microbiota and Metabolites Associated with Host Shift of Plutella xylostellaCited by: 22
Author(s): Fei‐Ying Yang, Hafiz Sohaib Ahmed Saqib, Junhui Chen, Qian‐Qian Ruan, Liette Vasseur, Weiyi He, Minsheng You
Software Mentions: 6
Published: about 6 years ago
10.3390/jof7080607
The Diplodia Tip Blight Pathogen Sphaeropsis sapinea Is the Most Common Fungus in Scots Pines’ Mycobiome, Irrespective of Health Status—A Case Study from GermanyCited by: 12
Author(s): Kathrin Blumenstein, Johanna Bußkamp, Gitta Jutta Langer, Ewald Langer, Eeva Terhonen
Software Mentions: 6
Published: about 5 years ago
10.1007/s00784-020-03613-w
Limited antimicrobial efficacy of oral care antiseptics in microcosm biofilms and phenotypic adaptation of bacteria upon repeated exposureCited by: 22
Author(s): Sophia R. Schwarz, Stefanie Hirsch, Andreas Hiergeist, Christian Kirschneck, Denise Muehler, Karl‐Anton Hiller, Tim Maisch, Ali Al‐Ahmad, André Gessner, Wolfgang Buchalla, Fabian Cieplik
Software Mentions: 6
Published: almost 6 years ago
10.3389/fmicb.2016.02064
Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming SystemCited by: 177
Author(s): Manoeli Lupatini, G.W. Korthals, Mattias de Hollander, Thierry Janssens, Eiko E. Kuramae
Software Mentions: 6
Published: over 9 years ago
10.3389/fmicb.2021.675693
Nitrogen Fertilization and Native C4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic CommunitiesCited by: 10
Author(s): Jialin Hu, Jonathan D. Richwine, Patrick D. Keyser, Lidong Li, Fei Yao, Sindhu Jagadamma, Jennifer M. DeBruyn
Software Mentions: 6
Published: about 5 years ago
10.1002/brb3.2259
Changes in the gut microbiome associated with infliximab in patients with bipolar disorderCited by: 3
Author(s): Aadil Bharwani, Jake C. Szamosi, Valerie H. Taylor, Yena Lee, Asem Bala, Rodrigo B. Mansur, Mehala Subramaniapillai, Michael G. Surette, Roger S. McIntyre
Software Mentions: 6
Published: over 5 years ago
10.1186/s42523-020-00057-1
Skin microbiome of beluga whales: spatial, temporal, and health-related dynamicsCited by: 12
Author(s): Amy M. Van Cise, Paul R. Wade, Caroline E. C. Goertz, Kathleen A. Burek‐Huntington, Kim M. Parsons, Tonya M. Clauss, Roderick C. Hobbs, Amy Apprill
Software Mentions: 6
Published: almost 6 years ago
10.1186/s13068-020-01855-0
Lignin intermediates lead to phenyl acid formation and microbial community shifts in meso- and thermophilic batch reactorsCited by: 7
Author(s): Eva Maria Prem, Mira Mutschlechner, Blaž Stres, Paul Illmer, Andreas Otto Wagner
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pone.0237272
Passenger-surface microbiome interactions in the subway of Mexico CityCited by: 10
Author(s): Daniela Vargas-Robles, Carolina Gonzalez-Cedillo, Apolinar M. Hernández, Luis David Alcaraz, Mariana Peimbert
Software Mentions: 6
Published: about 6 years ago
10.1038/s41396-021-00987-x
Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and GammaproteobacteriaCited by: 14
Author(s): François Thomas, Nolwen Le Duff, Ting-Di Wu, Aurélie Cébron, Stéphane Uroz, Pascal Riera, Cédric Leroux, Gwenn Tanguy, Erwan Legeay, Jean‐Luc Guerquin‐Kern
Software Mentions: 6
Published: over 5 years ago
10.3390/microorganisms7120596
Dietary Saccharomyces cerevisiae boulardii CNCM I-1079 Positively Affects Performance and Intestinal Ecosystem in Broilers during a Campylobacter jejuni InfectionCited by: 22
Author(s): Francesca Romana Massacci, Carmela Lovito, Silvia Tofani, Michele Tentellini, Domenica Anna Genovese, Alessia Arcangela Pia De Leo, Paola Papa, Chiara Francesca Magistrali, Elisabetta Manuali, Massimo Trabalza‐Marinucci, Livia Moscati, Claudio Forte
Software Mentions: 6
Published: almost 7 years ago
10.1038/s41396-020-00844-3
Soil microbial legacies differ following drying-rewetting and freezing-thawing cyclesCited by: 45
Author(s): Annelein Meisner, L. Basten Snoek, Joseph Nesme, Elizabeth Dent, Samuel Jacquiod, Aimée T. Classen, Anders Priemé
Software Mentions: 6
Published: over 5 years ago
10.1002/ece3.6934
Mechanisms governing avian phylosymbiosis: Genetic dissimilarity based on neutral and MHC regions exhibits little relationship with gut microbiome distributions of Galápagos mockingbirdsCited by: 7
Author(s): Ramona Fleischer, Alice Risely, Paquita E. A. Hoeck, Lukas F. Keller, Simone Sommer
Software Mentions: 6
Published: almost 6 years ago
10.1038/s41396-021-00895-0
Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasetsCited by: 22
Author(s): Danièle De Luca, Roberta Piredda, Diana Sarno, Wiebe H. C. F. Kooistra
Software Mentions: 6
Published: over 5 years ago
10.3389/fmicb.2021.642197
Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of LifeCited by: 25
Author(s): Modupe Coker, Hannah E. Laue, Anne G. Hoen, Margaret Hilliard, Erika Dade, Zhigang Li, Thomas J. Palys, Hilary G. Morrison, Emily Baker, Margaret R. Karagas, Juliette C. Madan
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pone.0195534
Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysisCited by: 34
Author(s): Daniel Hagenfeld, Raphael Koch, Sebastian Jünemann, Karola Prior, Inga Harks, Peter Eickholz, Thomas Hoffmann, Ti‐Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Benjamin Ehmke, Dag Harmsen
Software Mentions: 6
Published: over 8 years ago
10.1186/s40168-019-0711-9
Bacterial alkylquinolone signaling contributes to structuring microbial communities in the oceanCited by: 22
Author(s): Kristen E. Whalen, Jamie W. Becker, Anna M. Schrecengost, Yongjie Gao, Nicole Giannetti, Elizabeth L. Harvey
Software Mentions: 6
Published: over 7 years ago
10.1038/s42003-019-0610-4
Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structureCited by: 4
Author(s): Francisco J. A. Nascimento, Martin Dahl, Diana Deyanova, Liberatus D. Lyimo, Holly M. Bik, Taruna Schuelke, Tiago José Pereira, Mats Björk, Simon Creer, Martin Gullström
Software Mentions: 6
Published: almost 7 years ago
10.1186/s42523-020-00044-6
An observational field study of the cloacal microbiota in adult laying hens with and without access to an outdoor rangeCited by: 9
Author(s): Janneke Schreuder, Francisca C. Velkers, Ruth Bouwstra, Nancy Beerens, J.A. Stegeman, Willem F. de Boer, Pim van Hooft, A.R.W. Elbers, Alex Bossers, Stephanie D. Jurburg
Software Mentions: 6
Published: about 6 years ago
10.1002/ece3.3597
Gut microbiota composition is associated with environmental landscape in honey beesCited by: 94
Author(s): Julia C. Jones, Carmelo Fruciano, Falk Hildebrand, Hasan Al Toufalilia, Nicholas J. Balfour, Peer Bork, Philipp Engel, Francis L. W. Ratnieks, William O. Hughes
Software Mentions: 6
Published: almost 9 years ago
10.1128/mSystems.00540-20
Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic ResolutionCited by: 29
Author(s): Sean K. Bay, Melodie A. McGeoch, Osnat Gillor, Nimrod Wieler, David J. Palmer, D. James Baker, Steven L. Chown, Chris Greening
Software Mentions: 6
Published: about 6 years ago
10.1186/s13073-018-0586-6
Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancersCited by: 96
Author(s): Vanessa L. Hale, Patricio Jeraldo, Jun Chen, Michael B. Mundy, Jingwen Yao, Sambhawa Priya, Gary Keeney, Kelly Lyke, Jason M. Ridlon, Bryan A. White, Amy J. French, Stephen N. Thibodeau, Christian Diener, Osbaldo Reséndis-Antonio, Jaime Gransee, Tumpa Dutta, Xuan Mai Petterson, Jaeyun Sung, Ran Blekhman, Lisa A. Boardman, David W. Larson, Heidi Nelson, Nicholas Chia
Software Mentions: 6
Published: almost 8 years ago
10.3389/fmicb.2021.623799
Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic ManagementCited by: 11
Author(s): Ahmad Nuruddin Khoiri, Supapon Cheevadhanarak, Jiraporn Jirakkakul, Sudarat Dulsawat, Peerada Prommeenate, Anuwat Tachaleat, Kanthida Kusonmano, Songsak Wattanachaisaereekul, Sawannee Sutheeworapong
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-021-92405-7
Microplastics accumulate fungal pathogens in terrestrial ecosystemsCited by: 73
Author(s): Gerasimos Gkoutselis, Stephan Rohrbach, Janno Harjes, Martin Obst, Andreas Brachmann, Marcus A. Horn, Gerhard Rambold
Software Mentions: 6
Published: about 5 years ago
10.1038/s41598-021-93468-2
Integrative biology defines novel biomarkers of resistance to strongylid infection in horsesCited by: 5
Author(s): Guillaume Sallé, Cécile Canlet, Jacques Cortet, Christine Koch, Joshua Malsa, Fabrice Reigner, Mickaël Riou, Noémie Perrot, Alexandra Blanchard, Núria Mach
Software Mentions: 6
Published: about 5 years ago
10.3389/fnut.2019.00045
What's Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE StudyCited by: 135
Author(s): Kimberly A. Lackey, Janet E. Williams, Courtney L. Meehan, Jessica A. Zachek, Elizabeth D. Benda, William J. Price, James A. Foster, Daniel Sellen, Elizabeth Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela Gindola K, Linda J. Kvist, Gloria E. Otoo, Cristina García-Carral, Esther Jiménez, Lorena Ruíz, Juan M. Rodríguez, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Michelle K. McGuire
Software Mentions: 6
Published: over 7 years ago
10.3389/fnmol.2021.723317
Dynamic Changes in the Levels of Amyloid-β42 Species in the Brain and Periphery of APP/PS1 Mice and Their Significance for Alzheimer’s DiseaseCited by: 13
Author(s): Liding Zhang, Changwen Yang, Yanqing Li, Shiqi Niu, Xiaohan Liang, Zhihong Zhang, Qi Luo, Haiming Luo
Software Mentions: 6
Published: about 5 years ago
10.1038/s41598-021-92007-3
Validity and safety of ID-JPL934 in lower gastrointestinal symptom improvementCited by: 4
Author(s): Cheol Min Shin, Yoon Jin Choi, Dong Hoon Lee, Jin Seok Moon, Tae Yoon Kim, Yoon Keun Kim, Won Hee Lee, Hyuk Yoon, Young Soo Park, Nayoung Kim
Software Mentions: 6
Published: about 5 years ago
10.1038/s41598-021-92042-0
Socioeconomic position links circulatory microbiota differences with biological ageCited by: 12
Author(s): Hannah Craven, Dagmara McGuinness, Sarah Buchanan, Norman Galbraith, David McGuinness, Brian Jones, Emilie Combet, Denise Mafra, Peter Bergman, Anne Ellaway, Peter Stenvinkel, Umer Zeeshan Ijaz, Paul G. Shiels
Software Mentions: 6
Published: over 5 years ago
10.3389/fmicb.2020.01528
Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid InfestationCited by: 7
Author(s): Nicholas C. Dove, Timothy J. Rogers, Christy Leppanen, Daniel Simberloff, James A. Fordyce, Veronica A. Brown, Anthony V. LeBude, Thomas G. Ranney, Melissa Cregger
Software Mentions: 6
Published: about 6 years ago
10.1038/s41598-021-87365-x
Comparison of Argentinean microbiota with other geographical populations reveals different taxonomic and functional signatures associated with obesityCited by: 5
Author(s): Susana Pesoa, Néstor D. Portela, Eduardo Aguilar Fernández, Osvaldo Elbarcha, Martín Gotteland, Fabien Magne
Software Mentions: 6
Published: over 5 years ago
10.3389/fmicb.2021.659918
Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host SpeciesCited by: 12
Author(s): Alice Risely, Mark A. F. Gillingham, Arnaud Béchet, Stefan Dominik Brändel, Alexander Christoph Heni, Marco Heurich, Sebastian Menke, Marta B. Manser, Marco Tschapka, . Wasimuddin, Simone Sommer
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-021-85460-7
Early socialization and environmental enrichment of lactating piglets affects the caecal microbiota and metabolomic response after weaningCited by: 7
Author(s): Mireia Saladrigas-García, Matilde D’Angelo, Heng-Lun Ko, Sara Traserra, Pau Nolis, Yuliaxis Ramayo-Caldas, Josep María Folch, P. Vergara, Pol Llonch, José Francisco Pérez, S. M. Martín‐Orúe
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-021-82573-x
Composition and acquisition of the microbiome in solitary, ground-nesting alkali beesCited by: 19
Author(s): Karen M. Kapheim, Makenna M. Johnson, Maggi Jolley
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-021-82379-x
Evidence for strong environmental control on bacterial microbiomes of Antarctic springtailsCited by: 5
Author(s): Chiara Leo, Francesco Nardi, Claudio Cucini, Francesco Frati, Peter Convey, James T. Weedon, Dick Roelofs, Antonio Carapelli
Software Mentions: 6
Published: over 5 years ago
10.3389/fmicb.2020.586437
Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut LumenCited by: 13
Author(s): Mohamed Kamal Abdelhamid, Narciso M. Quijada, Monika Dzieciol, Tamas Hatfaludi, Ivana Bilić, Evelyne Selberherr, Dieter Liebhart, Claudia Heß, Michael Heß, Surya Paudel
Software Mentions: 6
Published: almost 6 years ago
10.1038/s41598-020-80568-8
Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic PeninsulaCited by: 15
Author(s): Nicole Trefault, Rodrigo De la Iglesia, Mario Moreno-Pino, Adriana Lopes dos Santos, Catherine Gérikas Ribeiro, Génesis Parada-Pozo, Antonia Cristi, Dominique Marie, Daniel Vaulot
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-020-60929-z
Chronic disturbance modulates symbiont (Symbiodiniaceae) beta diversity on a coral reefCited by: 11
Author(s): Danielle C. Claar, Kristina L. Tietjen, Kieran Cox, Ruth D. Gates, Julia K. Baum
Software Mentions: 6
Published: over 6 years ago
10.1038/s41598-019-54098-x
Obesity during pregnancy results in maternal intestinal inflammation, placental hypoxia, and alters fetal glucose metabolism at mid-gestationCited by: 48
Author(s): Jessica G. Wallace, Christian J. Bellissimo, Erica Yeo, Yu Xia, Jim Petrik, Michael G. Surette, Dawn M. E. Bowdish, Deborah M. Sloboda
Software Mentions: 6
Published: almost 7 years ago
10.1038/s41598-019-52148-y
Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural SoilCited by: 64
Author(s): Vanessa Brisson, Jennifer E. Schmidt, Trent Northen, John P. Vogel, Amélie C. M. Gaudin
Software Mentions: 6
Published: almost 7 years ago
10.1038/s41598-019-50839-0
Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structuresCited by: 36
Author(s): Prashant Singh, Sylvain Santoni, Audrey Weber, Patrice This, Jean‐Pierre Péros
Software Mentions: 6
Published: almost 7 years ago
10.3389/fmicb.2018.00387
The Intestinal Mycobiota in Wild Zebrafish Comprises Mainly Dothideomycetes While Saccharomycetes Predominate in Their Laboratory-Reared CounterpartsCited by: 23
Author(s): Prabhugouda Siriyappagouder, Viswanath Kiron, Jep Lokesh, Moger Rajeish, Martina Kopp, Jorge M. O. Fernandes
Software Mentions: 6
Published: over 8 years ago
10.3389/fmicb.2020.526545
Nutrients and Pharmaceuticals Structure Bacterial Core Communities in Urban and Montane Stream BiofilmsCited by: 4
Author(s): Elizabeth M. Ogata, Michelle A. Baker, Emma J. Rosi, Trevor B. Smart, Donald Long, Zachary T. Aanderud
Software Mentions: 6
Published: almost 6 years ago
10.3389/fmicb.2020.574110
Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal PathogensCited by: 28
Author(s): Itzel A. Solís-García, Oscar Ceballos-Luna, Elvis Marian Cortazar-Murillo, Damaris Desgarennes, Edith Garay‐Serrano, Violeta Patiño-Conde, Edgar Guevara-Avendaño, Alfonso Méndez-Bravo, Frédérique Reverchon
Software Mentions: 6
Published: over 5 years ago
10.3390/insects11040217
Host Plants Influence the Symbiont Diversity of Eriosomatinae (Hemiptera: Aphididae)Cited by: 14
Author(s): Tingting Xu, Li‐Yun Jiang, Jing Chen, Ge‐Xia Qiao
Software Mentions: 6
Published: over 6 years ago
10.1080/19490976.2021.1874815
Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layerCited by: 33
Author(s): Kellyanne Duncan, Kelly Carey-Ewend, Shipra Vaishnava
Software Mentions: 6
Published: over 5 years ago
10.3389/fmicb.2019.02278
Assessment of Artificial and Natural Transport Mechanisms of Ice Nucleating Particles in an Alpine Ski Resort in Obergurgl, AustriaCited by: 4
Author(s): Philipp Baloh, Nora Els, Robert O. David, Catherine Larose, Karin Whitmore, Birgit Sattler, Hinrich Grothe
Software Mentions: 6
Published: almost 7 years ago
10.3389/fmicb.2020.01451
Bacterial and Fungal Dynamics During the Fermentation Process of Sesotho, a Traditional Beer of Southern AfricaCited by: 19
Author(s): Errol D. Cason, Bokang John Mahlomaholo, Matšepo M. Taole, George Ooko Abong, Jan‐G Vermeulen, Olga de Smidt, Marcele Vermeulen, Laurinda Steyn, Ángel Valverde, Bennie C. Viljoen
Software Mentions: 6
Published: about 6 years ago
10.1080/19490976.2021.1902771
The intestinal microbiota and metabolites in patients with anorexia nervosaCited by: 44
Author(s): Petra Procházková, Radka Roubalová, Jiří Dvořák, Jakub Kreisinger, Martin Hill, Helena Tlaskalová‐Hogenová, Petra Tomášová, Helena Pelantová, M Cermáková, Marek Kuzma, Josef Bulant, Martin Bilej, Kvido Smitka, Alena Lambertová, Petra Holanová, Hana Papežová
Software Mentions: 6
Published: over 5 years ago
10.1080/19490976.2020.1814120
Analysis of 16S rRNA genes reveals reduced Fusobacterial community diversity when translocating from saliva to GI sitesCited by: 10
Author(s): Miles Richardson, Ji‐Chang Ren, Mara Roxana Rubinstein, Jamila A Taylor, Richard A. Friedman, Bo Shen, Yiping W. Han
Software Mentions: 6
Published: almost 6 years ago