cran: PERMANOVA | Projects | Ecosyste.ms: Papers

10.1186/s40168-021-01044-7

Characterization of the public transit air microbiome and resistome reveals geographical specificity
Cited by: 20
Author(s): Marcus H. Y. Leung, Xinzhao Tong, Kari Oline Bøifot, Daniela Bezdan, Daniel Butler, David Danko, Jostein Gohli, D. C. Green, Mark Hernandez, Frank J. Kelly, Shawn Levy, Gabriella Mason-Buck, Marina Nieto-Caballero, Denise Syndercombe‐Court, Klas I. Udekwu, Brian P. Young, Christopher E. Mason, Marius Dybwad, P. K. H. Lee
Software Mentions: 7
Published: over 3 years ago

10.1186/s40793-020-0353-3

Unravelling the effects of tropical land use conversion on the soil microbiome
Cited by: 35
Author(s): Dirk Hölscher, Dominik Schneider, Anja Meryandini, Rolf Daniel
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0255012

Hierarchical modelling of immunoglobulin coated bacteria in dogs with chronic enteropathy shows reduction in coating with disease remission but marked inter-individual and treatment-response variability
Cited by: 0
Author(s): Lina María Martínez-López, Alexis Perez‐Gonzalez, Elizabeth A. Washington, Andrew Woodward, Alexandra J. Roth‐Schulze, Julien Dandrieux, Thurid Johnstone, Nathalee Prakash, Aaron R. Jex, Caroline Mansfield
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-017-15220-z

Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals
Cited by: 28
Author(s): Marlène Chiarello, Sébastien Villéger, Corinne Bouvier, Jean‐Christophe Auguet, Thierry Bouvier
Software Mentions: 7
Published: about 7 years ago

10.7717/peerj.9493

Microbial and chemical dynamics of a toxic dinoflagellate bloom
Cited by: 9
Author(s): Nastassia V. Patin, Emily R. Brown, Gabriella Chebli, Claire Garfield, Julia Kubanek, Frank J. Stewart
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2018.01073

Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function
Cited by: 28
Author(s): Jacob W. Bledsoe, Geoffrey C. Waldbieser, Kelly S. Swanson, Brian Peterson, Brian C. Small
Software Mentions: 7
Published: over 6 years ago

10.1111/eva.12531

Egg size and the adaptive capacity of early life history traits in Chinook salmon (Oncorhynchus tshawytscha )
Cited by: 21
Author(s): Michael W. Thorn, Yolanda E. Morbey
Software Mentions: 7
Published: about 7 years ago

10.1186/s40168-017-0280-8

Human presence impacts fungal diversity of inflated lunar/Mars analog habitat
Cited by: 23
Author(s): Adriana Blachowicz, Teresa Mayer, Mina Bashir, Thomas R. Pieber, Pablo de León, Kasthuri Venkateswaran
Software Mentions: 7
Published: over 7 years ago

10.1002/ece3.5025

Spatiotemporal variability in the structure of seagrass meadows and associated macrofaunal assemblages in southwest England (UK): Using citizen science to benchmark ecological pattern
Cited by: 7
Author(s): Dan A. Smale, Graham Epstein, Mark Parry, Martin J. Attrill
Software Mentions: 7
Published: over 5 years ago

10.1186/s40168-015-0116-3

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities
Cited by: 151
Author(s): Aleksandra Checinska, Alexander J. Probst, Parag Vaishampayan, James R. White, Deepika Kumar, В. П. Степанов, George E. Fox, R. Henrik Nilsson, Duane L. Pierson, Jay L. Perry, Kasthuri Venkateswaran
Software Mentions: 7
Published: about 9 years ago

10.1186/s13059-020-02144-7

1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding
Cited by: 32
Author(s): Toby Wilkinson, Daniel Korir, Moses Ogugo, Robert D. Stewart, Mick Watson, Edith Paxton, John P. Goopy, Christelle Robert
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-018-21197-0

Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones
Cited by: 14
Author(s): Erick Cardenas, Luis H. Orellana, Konstantinos T. Konstantinidis, William W. Mohn
Software Mentions: 7
Published: almost 7 years ago

10.1128/mBio.03701-20

Inter- and Intra-Annual Bacterioplankton Community Patterns in a Deepwater Sub-Arctic Region: Persistent High Background Abundance of Putative Oil Degraders
Cited by: 8
Author(s): Angelina Angelova, Barbara Berx, Eileen Bresnan, Samantha B. Joye, Andrew Free, Tony Gutiérrez
Software Mentions: 7
Published: over 3 years ago

10.1128/mSphere.00670-20

Natural Infection with Giardia Is Associated with Altered Community Structure of the Human and Canine Gut Microbiome
Cited by: 26
Author(s): Alexander S. F. Berry, Keegan S. Johnson, Rene Martins, Megan C. Sullivan, Camila Farias Amorim, Alexandra Putre, Aiysha Scott, Shuai Wang, Brianna Lindsay, Robert N. Baldassano, Thomas J. Nolan, Daniel P. Beiting
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0197697

Agricultural matrices affect ground ant assemblage composition inside forest fragments
Cited by: 13
Author(s): Diego Santana Assis, Iracenir Andrade dos Santos, Flávio Nunes Ramos, Katty Elena Barrios-Rojas, Jonathan Majer, Evaldo F. Vilela
Software Mentions: 7
Published: over 6 years ago

10.1128/mSphere.00169-17

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
Cited by: 52
Author(s): Alexandra M. Linz, Benjamin C. Crary, Ashley Shade, Sarah M. Owens, Jack A. Gilbert, Rob Knight, Katherine D. McMahon
Software Mentions: 7
Published: over 7 years ago

10.1111/gcb.15302

Stream microbial communities and ecosystem functioning show complex responses to multiple stressors in wastewater
Cited by: 44
Author(s): Francis J. Burdon, Yaohui Bai, Marta Reyes, Manu Tamminen, Philipp Staudacher, Simon Mangold, Heinz Singer, Katja Räsänen, Adriano Joss, Scott D. Tiegs, Jukka Jokela, Rik I.L. Eggen, Christian Stamm
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0233943

Effects of parity, blood progesterone, and non-steroidal anti-inflammatory treatment on the dynamics of the uterine microbiota of healthy postpartum dairy cows
Cited by: 17
Author(s): Osvaldo Bogado Pascottini, J. F. W. Sprícigo, Sabrina J. Van Schyndel, B. Mion, Joyce D. Rousseau, J. Scott Weese, S.J. LeBlanc
Software Mentions: 7
Published: almost 4 years ago

10.1093/gigascience/giaa022

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
Cited by: 28
Author(s): Haris Zafeiropoulos, Ha Quoc Viet, Katerina Vasileiadou, Antonis Potirakis, Christos Arvanitidis, Pantelis Topalis, Christina Pavloudi, Evangelos Pafilis
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2019.00281

Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean
Cited by: 36
Author(s): Jackie Zorz, Ciara Willis, A. Comeau, Morgan G. I. Langille, Catherine L. Johnson, William K. W. Li, Julie LaRoche
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-020-70318-1

The role of seagrass vegetation and local environmental conditions in shaping benthic bacterial and macroinvertebrate communities in a tropical coastal lagoon
Cited by: 25
Author(s): Zahra Hassan Ali Alsaffar, John K. Pearman, J. Cúrdia, Joanne I. Ellis, María Ll. Calleja, Pedro Ruiz-Compean, Florian Roth, Rodrigo Villalobos, Burton H. Jones, Xosé Anxelu G. Morán, Susana Carvalho
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2021.601901

The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons
Cited by: 0
Author(s): Kristina Baker, Colleen T. E. Kellogg, J. W. McClelland, Kenneth H. Dunton, Byron C. Crump
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0250344

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome
Cited by: 13
Author(s): Arnon Gal, Patrick C. Barko, Patrick J. Biggs, Kristene Gedye, Anne C. Midwinter, David A. Williams, Richard K. Burchell, P. Pazzi
Software Mentions: 7
Published: over 3 years ago

10.3390/microorganisms9030557

The Composition and Diversity of the Gut Microbiota in Children Is Modifiable by the Household Dogs: Impact of a Canine-Specific Probiotic
Cited by: 10
Author(s): Carlos Gómez-Gallego, Mira Forsgren, Marta Selma‐Royo, Merja Nermes, María Carmen Collado, Seppo Salminen, Shea Beasley, Erika Isolauri
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-017-16353-x

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs
Cited by: 85
Author(s): Ana Carolina M. Junqueira, Aakrosh Ratan, Enzo Acerbi, Daniela I. Drautz–Moses, Balakrishnan N. V. Premkrishnan, Paul Igor Costea, Bodo Linz, Rikky W. Purbojati, Daniel F. Paulo, Nicolas E. Gaultier, Poorani Subramanian, Nur A. Hasan, Rita R. Colwell, Peer Bork, Ana Maria Lima de Azeredo-Espin, Donald A. Bryant, Stephan C. Schuster
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0246932

Distribution and diversity of mosquitoes and Oropouche-like virus infection rates in an Amazonian rural settlement
Cited by: 10
Author(s): Jordam William Pereira-Silva, Claudia María Ríos-Velásquez, Gervilane Ribeiro de Lima, Eric Fabrício Marialva, Heliana Christy Matos Belchior, Sérgio Luíz Bessa Luz, Felipe Gomes Naveca, Felipe Arley Costa Pessoa
Software Mentions: 7
Published: almost 4 years ago

10.1186/s40168-021-01013-0

animalcules: interactive microbiome analytics and visualization in R
Cited by: 16
Author(s): Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segrè, Stefano Monti, W. Evan Johnson
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2019.02621

Influence of Various Processing Parameters on the Microbial Community Dynamics, Metabolomic Profiles, and Cup Quality During Wet Coffee Processing
Cited by: 31
Author(s): Sophia Jiyuan Zhang, Florac De Bruyn, Vasileios Pothakos, Gonzalo F Contreras, Z. Y. Cai, Cyril Moccand, Stefan Weckx, Luc De Vuyst
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0202212

Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons)
Cited by: 8
Author(s): Marius Wenzel, Alex Douglas, Stuart B. Piertney
Software Mentions: 7
Published: about 6 years ago

10.1128/mBio.03601-20

Ketogenic Diets Induced Glucose Intolerance and Lipid Accumulation in Mice with Alterations in Gut Microbiota and Metabolites
Cited by: 15
Author(s): Yue Li, Yifan Yang, Jing Zhang, Tianyi Jiang, Ziyi Zhang, Zhiyi Wang, Mengxue Gong, Liping Zhao, Chenhong Zhang
Software Mentions: 7
Published: over 3 years ago

10.1186/s40168-021-01025-w

Protists as main indicators and determinants of plant performance
Cited by: 51
Author(s): Sai Guo, Wu Xiong, Xinnan Hang, Zhilei Gao, Zixuan Jiao, Hongjun Liu, Yani Mo, Nan Zhang, George A. Kowalchuk, Rong Li, Stefan Geisen
Software Mentions: 7
Published: over 3 years ago

10.7717/peerj.6687

A longitudinal study of the faecal microbiome and metabolome of periparturient mares
Cited by: 11
Author(s): Shebl E. Salem, Rachael Hough, Chris Probert, Thomas W. Maddox, Philipp Antczak, Julian M. Ketley, Nicola Williams, Sarah J. Stoneham, Debra Archer
Software Mentions: 7
Published: over 5 years ago

10.1186/s40168-016-0167-0

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation
Cited by: 28
Author(s): Teresa Mayer, Adriana Blachowicz, Alexander J. Probst, Parag Vaishampayan, Aleksandra Checinska, Tiffany M. Swarmer, Pablo de León, Kasthuri Venkateswaran
Software Mentions: 7
Published: over 8 years ago

10.1128/mSystems.00066-18

Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers
Cited by: 53
Author(s): Robert Danczak, Michael D. Johnston, Chris Kenah, Michael T. Slattery, Michael J. Wilkins
Software Mentions: 7
Published: about 6 years ago

10.7717/peerj.10836

Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry
Cited by: 9
Author(s): Kerri L. Steenwerth, Ian Arthur Morelan, Ruby J. Stahel, Rosa Figueroa‐Balderas, Dario Cantu, Jungmin Lee, Ron C. Runnebaum, Amisha T. Poret-Peterson
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-020-63565-9

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
Cited by: 36
Author(s): Bryan Nguyen, Elaine W. Shen, Janina Seemann, Adrienne M. S. Correa, James L. O’Donnell, Andrew H. Altieri, Nancy Knowlton, Keith A. Crandall, Scott P. Egan, W. Owen McMillan, Matthieu Leray
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2020.566619

Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers
Cited by: 13
Author(s): Anita Dame-Korevaar, Jannigje G. Kers, Jeanet van der Goot, Francisca C. Velkers, Daniela Ceccarelli, Dik Mevius, Arjan Stegeman, E.A.J. Fischer
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0218636

Characterizing the postmortem human bone microbiome from surface-decomposed remains
Cited by: 23
Author(s): Alexandra L. Emmons, Amy Z. Mundorff, Sarah W. Keenan, Jonathan Davoren, Janna M. Andronowski, David Carter, Jennifer M. DeBruyn
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0245626

Diversity of microbial communities and soil nutrients in sugarcane rhizosphere soil under water soluble fertilizer
Cited by: 20
Author(s): Huan Niu, Ziqin Pang, Nyumah Fallah, Yongmei Zhou, Caifang Zhang, Chaohua Hu, Wenxiong Lin, Zhaonian Yuan
Software Mentions: 7
Published: almost 4 years ago

10.1111/ele.12878

Ecological selection of siderophore‐producing microbial taxa in response to heavy metal contamination
Cited by: 90
Author(s): Elze Hesse, Siobhán O’Brien, Nicolas Tromas, Florian Bayer, Adela M. Luján, Eleanor M. van Veen, Dave Hodgson, Angus Buckling
Software Mentions: 7
Published: about 7 years ago

10.1002/ece3.5188

Invasive species removal increases species and phylogenetic diversity of wetland plant communities
Cited by: 12
Author(s): Shane C. Lishawa, Beth A. Lawrence, Dennis A. Albert, Daniel J. Larkin, Nancy C. Tuchman
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-018-29373-y

Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota
Cited by: 25
Author(s): Turan Demircan, Guvanch Ovezmyradov, Berna Yıldırım, İlknur Keskin, Ayşe Elif İlhan, Ece Cana Fesçioğlu, Gürkan Öztürk, Süleyman Yıldırım
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2019.02037

Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon
Cited by: 41
Author(s): S. R. Gupta, Jep Lokesh, Yousri Abdelhafiz, Prabhugouda Siriyappagouder, Ronan Pierre, Mette Sørensen, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 7
Published: about 5 years ago

10.3390/genes10070484

Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback
Cited by: 25
Author(s): Robert A Steury, Mark Currey, William A. Cresko, Brendan J. M. Bohannan
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2018.02404

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia
Cited by: 11
Author(s): Martina Prazeres
Software Mentions: 7
Published: about 6 years ago

10.1186/s40168-020-00869-y

Topography of the respiratory tract bacterial microbiota in cattle
Cited by: 36
Author(s): Christopher McMullen, Trevor W. Alexander, Renaud Léguillette, Matthew L. Workentine, Edouard Timsit
Software Mentions: 7
Published: over 4 years ago

10.5808/GI.2019.17.1.e6

Statistical Analysis of Metagenomics Data
Cited by: 147
Author(s): M. Luz Calle
Software Mentions: 7
Published: over 5 years ago

10.1128/mBio.02723-20

Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development
Cited by: 17
Author(s): Kathleen Beilsmith, Matthew Perisin, Joy Bergelson
Software Mentions: 7
Published: over 3 years ago

10.1128/mBio.03396-20

Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes
Cited by: 21
Author(s): Rozlyn C.T. Boutin, Hind Sbihi, Ryan J. McLaughlin, Aria S. Hahn, Kishori M. Konwar, Rachelle Loo, Darlene Dai, Charisse Petersen, Fiona S. L. Brinkman, Geoffrey L. Winsor, Malcolm R. Sears, Theo J. Moraes, Allan B. Becker, Meghan B. Azad, Piush J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0227289

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach
Cited by: 27
Author(s): Aashish R. Jha, Justin Shmalberg, Jirayu Tanprasertsuk, Lee Ann M. Perry, Dan Massey, Ryan W. Honaker
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13059-021-02427-7

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
Cited by: 56
Author(s): Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L. P. Tytgat, Mireia Vallès-Colomer, Willem M. de Vos, Nicola Segata
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0155826

Elevational Distribution of Flightless Ground Beetles in the Tropical Rainforests of North-Eastern Australia
Cited by: 10
Author(s): Kyran M. Staunton, Akihiro Nakamura, Chris J. Burwell, Simon K. A. Robson, Stephen E. Williams
Software Mentions: 7
Published: over 8 years ago

10.1038/s41598-017-18435-2

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys
Cited by: 32
Author(s): Pål Trosvik, Eli Knispel Rueness, Eric J. de Muinck, Amera Moges, Addisu Mekonnen
Software Mentions: 7
Published: almost 7 years ago

10.1080/19490976.2020.1794466

Alterations of gut microbiota composition in neonates conceived by assisted reproductive technology and its relation to infant growth
Cited by: 6
Author(s): Qun Lü, Yuan Lin, Ting Chen, Hong Lv, Feiyang Diao, Cong Liu, Meijuan Peng, Xiufeng Ling, Hong Li, Yun Wang, Yongyue Wei, Jiangbo Du, Guangfu Jin, Yankai Xia, Hongxia Ma, Xingyin Liu, Hongbing Shen, Zhibin Hu
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2020.575625

Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar
Cited by: 9
Author(s): Karelle Rheault, Denis Lachance, Marie-Josée Morency, Évelyne Thiffault, Marie Guittonny, Nathalie Isabel, Christine Martineau, Armand Séguin
Software Mentions: 6
Published: almost 4 years ago

10.1186/s40168-020-00962-2

Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions
Cited by: 8
Author(s): Joshua M. Lyte, James Keane, Julia Eckenberger, Nicholas B. Anthony, Sandip Shrestha, Daya Marasini, Karrie M. Daniels, Valentina Caputi, Annie Donoghue, Mark Lyte
Software Mentions: 6
Published: almost 4 years ago

10.1111/1462-2920.14516

Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples
Cited by: 12
Author(s): Fabien Cholet, Umer Zeeshan Ijaz, Cindy J. Smith
Software Mentions: 6
Published: almost 6 years ago

10.7717/peerj.3674

Microbiome succession during ammonification in eelgrass bed sediments
Cited by: 21
Author(s): Cassandra L. Ettinger, Susan L. Williams, Jessica M. Abbott, John J. Stachowicz, Jonathan A. Eisen
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2016.00372

A Combination of Biochar–Mineral Complexes and Compost Improves Soil Bacterial Processes, Soil Quality, and Plant Properties
Cited by: 62
Author(s): Jun Ye, Rui Zhang, Shaun Nielsen, Stephen Joseph, Danfeng Huang, Torsten Thomas
Software Mentions: 6
Published: over 8 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 Biome
Cited by: 13
Author(s): Henry Joseph Oduor Ogola, Ramganesh Selvarajan, Memory Tekere
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-73083-3

Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs
Cited by: 12
Author(s): Hiu Wai Lee, Borja Esteve‐Altava, Arhat Abzhanov
Software Mentions: 6
Published: about 4 years ago

10.3390/nu13092983

Supplementation of 1-Kestose Modulates the Gut Microbiota Composition to Ameliorate Glucose Metabolism in Obesity-Prone Hosts
Cited by: 10
Author(s): Ayako Watanabe, Takumi Tochio, Yasuhiro Kadota, Motoki Takahashi, Yasuyuki Kitaura, H. Ishikawa, Takanori Yasutake, Masahiro Nakano, Hiroe Shinohara, Toru Kudo, Yuichiro Nishimoto, Yoshinori Mizuguchi, Akihito Endo, Yoshiharu Shimomura
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0244616

Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia
Cited by: 11
Author(s): Jan Niklas Macher, Martina Prazeres, Sarah Taudien, Jamaluddin Jompa, Aleksey Sadekov, Willem Renema
Software Mentions: 6
Published: almost 4 years ago

10.1128/mSystems.00100-17

Making It Last: Storage Time and Temperature Have Differential Impacts on Metabolite Profiles of Airway Samples from Cystic Fibrosis Patients
Cited by: 11
Author(s): Stephen Wandro, Lisa A. Carmody, Tara Gallagher, John J. LiPuma, Katrine Whiteson
Software Mentions: 6
Published: almost 7 years ago

10.1186/s13073-021-00844-8

The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries
Cited by: 21
Author(s): Caroline Young, Henry M. Wood, Ramakrishnan Ayloor Seshadri, Pham Van Nang, Carlos Vaccaro, Luis Contreras Melendez, Mayilvahanan Bose, Mai Van Doi, Tamara Alejandra Piñero, Camilo Tapia Valladares, Julieta Argüero, Alba Fuentes Balaguer, Kelsey N. Thompson, Yan Yan, Curtis Huttenhower, Philip Quirke
Software Mentions: 6
Published: almost 4 years ago

10.1128/mSystems.00043-17

The Skin Microbiome of Cohabiting Couples
Cited by: 86
Author(s): Ashley A. Ross, Andrew C. Doxey, Josh D. Neufeld
Software Mentions: 6
Published: about 7 years ago

10.3389/fmicb.2017.02222

Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients
Cited by: 126
Author(s): Jing Wang, Yang Wang, Xu Zhang, Jiaqi Liu, Qianpeng Zhang, Yu Zhao, Jinghua Peng, Qin Feng, Jianye Dai, Shujun Sun, Yuwu Zhao, Liping Zhao, Yongyu Zhang, Yiyang Hu, Menghui Zhang
Software Mentions: 6
Published: about 7 years ago

10.7717/peerj.5467

Unveiling community patterns and trophic niches of tropical and temperate ants using an integrative framework of field data, stable isotopes and fatty acids
Cited by: 17
Author(s): Félix Baumgarten Rosumek, Nico Blüthgen, Adrian Brückner, Florian Menzel, Gerhard Gebauer, Michael Heethoff
Software Mentions: 6
Published: over 6 years ago

10.3390/genes10070524

MODIMA, a Method for Multivariate Omnibus Distance Mediation Analysis, Allows for Integration of Multivariate Exposure–Mediator–Response Relationships
Cited by: 13
Author(s): Bashir Hamidi, Kristin Wallace, Alexander V. Alekseyenko
Software Mentions: 6
Published: over 5 years ago

10.1128/mSphere.01261-20

Predominance of Atopobium vaginae at Midtrimester: a Potential Indicator of Preterm Birth Risk in a Nigerian Cohort
Cited by: 13
Author(s): Nkechi Martina Odogwu, Jun Chen, Chinedum Amara Onebunne, Patricio Jeraldo, Lu Yang, Stephen Johnson, Funmilola A. Ayeni, Marina Walther-Antonio, Oladapo Olayemi, Nicholas Chia, Akinyinka Omigbodun
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-017-1359-z

Experimental design and quantitative analysis of microbial community multiomics
Cited by: 125
Author(s): Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan, Curtis Huttenhower
Software Mentions: 6
Published: almost 7 years ago

10.1128/mSphere.00843-20

Pseudomonas aeruginosa Volatilome Characteristics and Adaptations in Chronic Cystic Fibrosis Lung Infections
Cited by: 10
Author(s): Thomas J. Davis, Ava V. Karanjia, Charity N. Bhebhe, Sarah B. West, Matthew Richardson, Heather D. Bean
Software Mentions: 6
Published: about 4 years ago

10.7717/peerj.6674

Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂)
Cited by: 6
Author(s): Zhifei Li, Guangjun Wang, Kai Zhang, Wangbao Gong, Ermeng Yu, Jingjing Tian, Jun Xie, Deguang Yu
Software Mentions: 6
Published: over 5 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 rhino
Cited by: 61
Author(s): Rachael E. Antwis, Katie L. Edwards, Bryony Unwin, Susan L. Walker, Susanne Shultz
Software Mentions: 6
Published: almost 6 years ago

10.1534/g3.118.200017

Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the Nematode Caenorhabditis remanei
Cited by: 20
Author(s): Kristin L. Sikkink, Rose M. Reynolds, Catherine M. Ituarte, William A. Cresko, Patrick C. Phillips
Software Mentions: 6
Published: over 5 years ago

10.3389/fvets.2021.664318

Longitudinal Survey of Fecal Microbiota in Healthy Dogs Administered a Commercial Probiotic
Cited by: 3
Author(s): Susan Ciaravolo, Lina María Martínez-López, Richard Allcock, Andrew Woodward, Caroline Mansfield
Software Mentions: 6
Published: over 3 years ago

10.1128/mSystems.00097-18

Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?
Cited by: 108
Author(s): Florent Mazel, Katherine M. Davis, Andrew H. Loudon, Waldan K. Kwong, Mathieu Groussin, Laura Wegener Parfrey
Software Mentions: 6
Published: about 6 years ago

10.1186/s40168-019-0711-9

Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean
Cited 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 5 years ago

10.12688/f1000research.16680.1

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
Cited by: 105
Author(s): Gaurav S. Kandlikar, Zachary Gold, Madeline C. Cowen, Rachel S. Meyer, Amanda C. Freise, Nathan J. B. Kraft, Jordan Moberg Parker, Joshua Sprague, David J. Kushner, Emily Curd
Software Mentions: 6
Published: about 6 years ago

10.1186/s40168-021-01053-6

Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues
Cited by: 60
Author(s): Talisa Doering, Marlene Wall, Lalita Putchim, Tipwimon Rattanawongwan, Roman Schroeder, Ute Hentschel, Anna Krystyna Roik
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-020-1947-1

Assembly of hundreds of novel bacterial genomes from the chicken caecum
Cited by: 95
Author(s): Laura Glendinning, Robert D. Stewart, Mark J. Pallen, Kellie Watson, Mick Watson
Software Mentions: 6
Published: almost 5 years ago

10.1093/femsec/fiaa205

Effects of simulated drought on biological soil quality, microbial diversity and yields under long-term conventional and organic agriculture
Cited by: 23
Author(s): Dominika Kundel, Natacha Bodenhausen, Helene Bracht Jørgensen, Jaak Truu, Klaus Birkhofer, Katarina Hedlund, Paul Mäder, Andreas Fließbach
Software Mentions: 6
Published: about 4 years ago

10.1186/s40168-021-01144-4

Trophic level drives the host microbiome of soil invertebrates at a continental scale
Cited by: 14
Author(s): Dong Zhu, Manuel Delgado‐Baquerizo, Jing Ding, Michael R. Gillings, Yong‐Guan Zhu
Software Mentions: 6
Published: about 3 years ago

10.3389/fmicb.2019.00065

Comparison of Microbial Communities in the Sediments and Water Columns of Frozen Cryoconite Holes in the McMurdo Dry Valleys, Antarctica
Cited by: 29
Author(s): Pacifica Sommers, John L. Darcy, Dorota L. Porazinska, Eli M. S. Gendron, Andrew G. Fountain, Felix Jacob Zamora, Vincent Kim, Kaelin M. Cawley, Adam J. Solon, Lara Vimercati, Jenna Ryder, Steven K. Schmidt
Software Mentions: 6
Published: almost 6 years ago

10.3389/fmicb.2014.00358

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
Cited by: 239
Author(s): Ryan J. Williams, Adina Howe, Kirsten Hofmockel
Software Mentions: 6
Published: over 10 years ago

10.1128/mBio.03162-20

Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island
Cited by: 5
Author(s): Brad Griesenauer, Camila González-Beiras, Katherine R. Fortney, Huaiying Lin, Xiang Gao, Charmie Godornes, David E. Nelson, Barry P. Katz, Sheila A. Lukehart, Oriol Mitjà, Qunfeng Dong, Stanley M. Spinola
Software Mentions: 6
Published: over 3 years ago

10.3390/genes11111291

The Role of Salmonella Genomic Island 4 in Metal Tolerance of Salmonella enterica Serovar I 4,[5],12:i:- Pork Outbreak Isolate USDA15WA-1
Cited by: 13
Author(s): Bradley L. Bearson, Julian Trachsel, Daniel C. Shippy, Sathesh K Sivasankaran, B. J. Kerr, Crystal L. Loving, Brian W. Brunelle, Shelby M Curry, Nicholas K. Gabler, Shawn M. D. Bearson
Software Mentions: 6
Published: about 4 years ago

10.1128/mSphere.00798-19

Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy
Cited 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 4 years ago

10.1128/mSphere.00455-21

A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition
Cited 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 3 years ago

10.1186/s40793-020-00356-9

Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China
Cited by: 26
Author(s): Xiangming Tang, Guobo Xie, Kwang‐Tsao Shao, Yang Hu, Jian Cai, Chengrong Bai, Yi Gong, Guang Gao
Software Mentions: 6
Published: over 4 years ago

10.1186/s40168-020-00854-5

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria
Cited by: 52
Author(s): Xingxing Jian, Yinghong Zhu, Jian Ouyang, Yihui Wang, Qian Lei, Jiliang Xia, Yongjun Guan, Jingyu Zhang, Jiaojiao Guo, Yanjuan He, Jinuo Wang, Jian Li, Jingchao Lin, Mingming Su, Guancheng Li, Minghua Wu, Lugui Qiu, Juanjuan Xiang, Lu Xie, Jia Wang, Wen Zhou
Software Mentions: 6
Published: over 4 years ago

10.1128/mSphere.00393-21

Multidimensional Clinical Surveillance of Pseudomonas aeruginosa Reveals Complex Relationships between Isolate Source, Morphology, and Antimicrobial Resistance
Cited by: 3
Author(s): Laura J. Dunphy, Glynis L. Kolling, Matthew L. Jenior, Joanne Carroll, April E Attai, Farzad Farnoud, Amy J Mathers, Molly A. Hughes, Jason A. Papin
Software Mentions: 6
Published: about 3 years ago

10.1186/s13059-019-1908-8

Host-associated microbiomes are predicted by immune system complexity and climate
Cited by: 45
Author(s): Douglas C. Woodhams, Molly C. Bletz, C. Guilherme Becker, Hayden A. Bender, Daniel Buitrago-Rosas, Hannah Diebboll, Roger Huynh, Patrick J. Kearns, Jordan G. Kueneman, Emmi Kurosawa, Brandon LaBumbard, Casandra Lyons, Kerry McNally, Klaus Schliep, Nachiket Shankar, Amanda G. Tokash-Peters, Miguel Vences, Ross Whetstone
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0220953

COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems
Cited by: 67
Author(s): Mehrdad Hajibabaei, Teresita M. Porter, Michael Wright, Josip Rudar
Software Mentions: 6
Published: about 5 years ago

10.1111/1462-2920.15260

The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche‐driven microbial community assembly processes
Cited by: 11
Author(s): Alizée Le Moigne, Maciej Bartosiewicz, Gabriela Schaepman‐Strub, Samuel Abiven, Jakob Pernthaler
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-020-63173-7

Fungal community shifts in soils with varied cover crop treatments and edaphic properties
Cited by: 31
Author(s): Mara Cloutier, Ebony G. Murrell, Mary E. Barbercheck, Jason P. Kaye, Denise M. Finney, Irene García-González, Mary Ann Bruns
Software Mentions: 6
Published: over 4 years ago

10.1186/s13073-018-0586-6

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers
Cited 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: about 6 years ago

10.3389/fmicb.2018.02619

Stochastic and Deterministic Effects of a Moisture Gradient on Soil Microbial Communities in the McMurdo Dry Valleys of Antarctica
Cited by: 37
Author(s): Kevin C. Lee, Tancredi Caruso, Stephen Archer, Len N. Gillman, Maggie C. Y. Lau, S. Craig Cary, Charles K. Lee, Stephen B. Pointing
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-018-27322-3

Costs of injury for scent signalling in a strepsirrhine primate
Cited by: 18
Author(s): Rachel L. Harris, Marylène Boulet, Kathleen E. Grogan, Christine M. Drea
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2021.723682

Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon)
Cited by: 13
Author(s): Ying Zhu, Yudong Li, Hai-Qiong Yang, Ke He, Keyi Tang
Software Mentions: 6
Published: over 3 years ago

Projects: cran: PERMANOVA

Papers Mentioning PERMANOVA 6,292