Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: qiime

https://packages.ecosyste.ms/registries/pypi.org/packages/qiime

Quantitative Insights Into Microbial Ecology
4 versions
Latest release: over 9 years ago
199 downloads last month

Papers Mentioning qiime 157

10.3389/fmicb.2017.02619
Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats
Cited by: 10
Author(s): Mercedes Berlanga, Montserrat Palau, Ricardo Guerrero
Software Mentions: 3
Published: over 6 years ago
10.1111/imm.13158
Depletion of Foxp3 <sup>+</sup> regulatory T cells is accompanied by an increase in the relative abundance of Firmicutes in the murine gut microbiome
Cited by: 21
Author(s): Jan Kehrmann, Laura Effenberg, C. Matthias Wilk, Davina Schoemer, Nhi Ngo Thi Phuong, Alexandra Adamczyk, Eva Pastille, René Scholtysik, Ludger Klein-Hitpaß, Robert Klopfleisch, Astrid M. Westendorf, Jan Buer
Software Mentions: 2
Published: almost 5 years ago
10.3390/ani10020259
Targeted-Release Organic Acids and Essential Oils Improve Performance and Digestive Function in Broilers under a Necrotic Enteritis Challenge
Cited by: 34
Author(s): Nedra Abdelli, José Francisco Pérez, E. Vilarrasa, Irene Cabeza Luna, Diego Melo-Durán, Matilde D’Angelo, David Solà-Oriol
Software Mentions: 2
Published: over 4 years ago
10.1186/s12915-021-01070-9
An engineered genetic circuit for lactose intolerance alleviation
Cited by: 2
Author(s): Mingyue Cheng, Zhangyu Cheng, Yiyan Yu, Wangjie Liu, Ruihao Li, Zhenyi Guo, Jiyue Qin, Zhi Zeng, Dong Lin, Yufeng Mo, Chunxiu Pan, Yuanhao Liang, Jinman Li, Yigang Tong, Yunjun Yan, Yi Zhan, Kang Ning
Software Mentions: 2
Published: about 3 years ago
10.1186/1472-6831-14-157
Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant and periodontal sites
Cited by: 43
Author(s): Simone Schaumann, Ingmar Staufenbiel, Ralph Scherer, Markus B. Schilhabel, Andreas Winkel, Sascha Nico Stumpp, Jörg Eberhard, Meike Stiesch
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12890-017-0512-5
The lung microbiome in patients with pneumocystosis
Cited by: 10
Author(s): Jan Kehrmann, B. Veckollari, Dirk Schmidt, Oliver Schildgen, Verena Schildgen, Nicholas Wagner, Michael Zeschnigk, Ludger Klein-Hitpaß, Oliver Witzke, Jan Buer, Jörg Steinmann
Software Mentions: 2
Published: almost 7 years ago
10.1111/2041-210X.12416
High‐throughput monitoring of wild bee diversity and abundance via mitogenomics
Cited by: 115
Author(s): Min Tang, Chloe J. Hardman, Yinqiu Ji, Guanliang Meng, Shanlin Liu, Meihua Tan, Shenzhou Yang, Ellen D. Moss, Jingxin Wang, Chunyan Yang, Catharine Bruce, Timothy D. Nevard, Simon G. Potts, Xin Zhou, Douglas W. Yu
Software Mentions: 2
Published: about 9 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
10.1111/1751-7915.12733
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
10.1099/mgen.0.000028
Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics
Cited by: 5
Author(s): Katy J. Califf, Paul Keim, David M. Wagner, Jason W. Sahl
Software Mentions: 2
Published: about 9 years ago
10.3390/microorganisms8122015
Essential Oils as Alternative Biocides for the Preservation of Waterlogged Archaeological Wood
Cited by: 18
Author(s): Federica Antonelli, Marco Bartolini, Marie-Laure Plissonnier, Alfonso Esposito, Giulia Galotta, Sandra Ricci, Barbara Davidde Petriaggi, Cristian Pedone, Antonella Di Giovanni, Silvano Piazza, Francesca Guerrieri, Manuela Romagnoli
Software Mentions: 2
Published: almost 4 years ago
10.3390/vetsci8060096
Different Non-Structural Carbohydrates/Crude Proteins (NCS/CP) Ratios in Diet Shape the Gastrointestinal Microbiota of Water Buffalo
Cited by: 1
Author(s): Rubina Paradiso, Giorgia Borriello, Sergio Bolletti Censi, Angela Salzano, Roberta Cimmino, Giorgio Galiero, Giovanna Fusco, Esterina De Carlo, Giuseppe Campanile
Software Mentions: 2
Published: over 3 years ago
10.3390/v10090496
Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters
Cited by: 22
Author(s): Yanze Li, Pascal Hingamp, Hiroyasu Watai, Hisashi Endo, Takashi Yoshida, Hiroyuki Ogata
Software Mentions: 2
Published: about 6 years ago
10.7717/peerj.494
RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
Cited by: 125
Author(s): Henning Seedorf, Sandra Kittelmann, Gemma Henderson, Peter H. Janssen
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0253133
Effects of cat ownership on the gut microbiota of owners
Cited by: 7
Author(s): Guankui Du, Hairong Huang, Qiwei Zhu, Ying Li
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2021.726384
Influence of Climate on Soil and Wine Bacterial Diversity on a Vineyard in a Non-traditional Wine Region in Argentina
Cited by: 4
Author(s): Gabriel Alejandro Rivas, Andrea Cecilia Guillade, Liliana Semorile, Lucrecia Delfederico
Software Mentions: 2
Published: about 3 years ago
10.3389/fmicb.2020.614278
Characterization of Microbial Dynamics and Volatile Metabolome Changes During Fermentation of Chambourcin Hybrid Grapes From Two Pennsylvania Regions
Cited by: 10
Author(s): Hung Li Wang, Helene Hopfer, Darrell Cockburn, Josephine Wee
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2021.599664
Compositional Differences in the Oral Microbiome of E-cigarette Users
Cited by: 16
Author(s): Jessica Chopyk, C.M. Bojanowski, John H. Shin, A. Moshensky, Ana Lucía Fuentes, Saniya S Bonde, Dagni Chuki, David T. Pride, Laura E. Crotty Alexander
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2021.671699
The Effect of Radiation on the Gut Bacteriome of Aedes albopictus
Cited by: 1
Author(s): Dongjing Zhang, Shi Chen, Adly M. M. Abd-Alla, Kostas Bourtzis
Software Mentions: 2
Published: about 3 years ago
10.3389/fmicb.2019.01350
Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria
Cited by: 32
Author(s): Defei Liu, Huanjun Sun, Hongwu Ma
Software Mentions: 2
Published: over 5 years ago
10.3389/fmicb.2018.03091
Combination of Clostridium butyricum and Corn Bran Optimized Intestinal Microbial Fermentation Using a Weaned Pig Model
Cited by: 19
Author(s): Jie Zhang, Sun Jian, Xiyue Chen, Cunxi Nie, Jinbiao Zhao, Wanyi Guan, Li-Hui Lei, Ting He, Yiqiang Chen, Lee J Johnston, Jinshan Zhao
Software Mentions: 2
Published: almost 6 years ago
10.3389/fmicb.2020.01671
Metagenomic Characterization of Indoor Dust Bacterial and Fungal Microbiota in Homes of Asthma and Non-asthma Patients Using Next Generation Sequencing
Cited by: 18
Author(s): Jean‐Pierre Gangneux, Mohamed Sassi, Pierre Lemire, Pierre Le Cann
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2020.01335
Breast-Milk Microbiota Linked to Celiac Disease Development in Children: A Pilot Study From the PreventCD Cohort
Cited by: 22
Author(s): Alfonso Benı́tez-Páez, Marta Olivares, Hania Szajewska, Małgorzata Pieścik-Lech, Isabel Polanco, Gemma Castillejo, M. Del Carmen Nunez, Carmen Ribes-Koninckx, Ilma Rita Korponay-Szabó, Sibylle Koletzko, C. Meijer, M. Luisa Mearin, Yolanda Sanz
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2020.576061
Gut Microbiota Variation With Short-Term Intake of Ginger Juice on Human Health
Cited by: 16
Author(s): Xiaolong Wang, Dan Zhang, Haiqiang Jiang, Shuo Zhang, Xiaogang Pang, Shijie Gao, Huimin Zhang, Shanyu Zhang, Qin Xiao, Liyuan Chen, Shengqi Wang, Dongmei Qi, Yunlun Li
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2020.00716
Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida)
Cited by: 35
Author(s): Georg Steinert, Kathrin Busch, Kristina Bayer, Sahar Kodami, Pedro Martínez Arbizu, Michelle Kelly, Sadie Mills, Dirk Erpenbeck, Martin Dohrmann, Gert Wörheide, Ute Hentschel, Peter J. Schupp
Software Mentions: 2
Published: over 4 years ago
10.1111/gbi.12316
A combined lipidomic and 16S <scp>rRNA</scp> gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column
Cited by: 49
Author(s): Martina Sollai, Laura Villanueva, Ellen C. Hopmans, Gert‐Jan Reichart, Jaap S. Sinninghe Damsté
Software Mentions: 2
Published: almost 6 years ago
10.1186/s42523-021-00124-1
High royal jelly production does not impact the gut microbiome of honey bees
Cited by: 1
Author(s): Megan E Damico, Olav Rueppell, Zack Shaffer, Bin Han, Kasie Raymann
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.ppat.1007381
Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization
Cited by: 52
Author(s): Caitlin C. Murdoch, Scott T. Espenschied, Molly A. Matty, Olaf Mueller, David M. Tobin, John F. Rawls
Software Mentions: 2
Published: over 5 years ago
10.1186/s12284-016-0111-8
Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition
Cited by: 64
Author(s): Matthew R. Shenton, Chie Iwamoto, Nori Kurata, Kazuho Ikeo
Software Mentions: 2
Published: about 8 years ago
10.1038/s41598-019-56741-z
Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments
Cited by: 27
Author(s): Alex Gobbi, Ifigeneia Kyrkou, Elisa Filippi, Lea Ellegaard-Jensen, Lars Hestbjerg Hansen
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-020-60622-1
Effect of iron and magnesium addition on population dynamics and high value product of microalgae grown in anaerobic liquid digestate
Cited by: 16
Author(s): Hande Ermiş, Ünzile Güven-Gülhan, Tunahan Çakır, Mahmut Altınbaş
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms20092137
High-Amylose Maize, Potato, and Butyrylated Starch Modulate Large Intestinal Fermentation, Microbial Composition, and Oncogenic miRNA Expression in Rats Fed A High-Protein Meat Diet
Cited by: 29
Author(s): Tina Skau Nielsen, Zach Bendiks, Bo Thomsen, Matthew Wright, Peter Kappel Theil, Benjamin L. Scherer, Maria L. Marco
Software Mentions: 2
Published: over 5 years ago
10.3390/nu12061628
Nutritional Composition and Microbial Communities of Two Non-alcoholic Traditional Fermented Beverages from Zambia: A Study of Mabisi and Munkoyo
Cited by: 20
Author(s): Justin Chileshe, Joost van den Heuvel, Ray Handema, Bas J. Zwaan, Elise F. Talsma, Sijmen E. Schoustra
Software Mentions: 2
Published: over 4 years ago
10.1016/j.psj.2021.101224
Effects of dicopper oxide and copper sulfate on growth performance and gut microbiota in broilers
Cited by: 17
Author(s): Asal Forouzandeh, Laia Blavi, Nedra Abdelli, Diego Melo-Durán, Àlvar Martínez Vidal, María Martín Rodríguez, Alessandra Monteiro, José Francisco Pérez, Laila Darwich, David Solà-Oriol
Software Mentions: 1
Published: about 3 years ago
10.3389/fvets.2019.00026
Effects of Dietary Supplementation With Enterococcus faecium and Clostridium butyricum, Either Alone or in Combination, on Growth and Fecal Microbiota Composition of Post-weaning Pigs at a Commercial Farm
Cited by: 27
Author(s): Yoshibumi Sato, Yasutoshi Kuroki, Koichiro Oka, Motomichi Takahashi, Shengbin Rao, Shin Sukegawa, Tadao Fujimura
Software Mentions: 1
Published: over 5 years ago
10.3389/fmicb.2016.00789
Bacterial and Fungal Microbiota Changes Distinguish C. difficile Infection from Other Forms of Diarrhea: Results of a Prospective Inpatient Study
Cited by: 48
Author(s): William Sangster, John P. Hegarty, Kathleen M. Schieffer, Justin Wright, Jada Hackman, David R. Toole, Regina Lamendella, David B. Stewart
Software Mentions: 1
Published: over 8 years ago
10.3389/fmicb.2018.01372
Dynamic and Assembly of Epiphyte and Endophyte Lactic Acid Bacteria During the Life Cycle of Origanum vulgare L.
Cited by: 38
Author(s): Erica Pontonio, Raffaella Di Cagno, Waed Tarraf, Pasquale Filannino, Giuseppe De Mastro, Marco Gobbetti
Software Mentions: 1
Published: about 6 years ago
10.3389/fmicb.2020.01522
Defining Culture Conditions for the Hidden Nitrite-Oxidizing Bacterium Nitrolancea
Cited by: 26
Author(s): Eva Spieck, Katharina Saß, Sabine Keuter, Sophia Hirschmann, Michael Spohn, Daniela Indenbirken, Linnea F. M. Kop, Sebastian Lücker, Alejandra Giaveno
Software Mentions: 1
Published: about 4 years ago
10.3389/fmicb.2021.621310
Predictive Metagenomic Analysis of Autoimmune Disease Identifies Robust Autoimmunity and Disease Specific Microbial Signatures
Cited by: 17
Author(s): Angelina Volkova, Kelly V. Ruggles
Software Mentions: 1
Published: over 3 years ago
10.3389/fcimb.2021.719542
Intestinal Microbiota Play an Important Role in the Treatment of Type I Diabetes in Mice With BefA Protein
Cited by: 3
Author(s): Qin Qi, Yan Chen, Yongbo Li, Jing Wei, Xiaoting Zhou, Fuyin Le, Hong Hu, Tingtao Chen
Software Mentions: 1
Published: about 3 years ago
10.1111/1462-2920.13038
An analysis of<i>P</i><i>seudomonas</i>genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota
Cited by: 30
Author(s): Tim H. Mauchline, D. Chedom-Fotso, Govind Chandra, Toby Samuels, N. Greenaway, Andreas Backhaus, V. E. Mcmillan, Gail Canning, Stephen J. Powers, K. E. Hammond‐Kosack, P. R. Hirsch, Ian M. Clark, Zia Mehrabi, Joshua David Roworth, James N. Burnell, Jacob G. Malone
Software Mentions: 1
Published: almost 9 years ago
10.3390/diagnostics11081324
Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience
Cited by: 19
Author(s): Eungyung Lee, Suhyun Park, Sunwoo Um, Seunghoon Kim, Jaewoong Lee, Jinho Jang, Hyoung-oh Jeong, Jonghyun Shin, JiHoon Kang, Semin Lee, Tae-Sung Jeong
Software Mentions: 1
Published: about 3 years ago
10.3390/cancers12092672
The Pancreatic Microbiome is Associated with Carcinogenesis and Worse Prognosis in Males and Smokers
Cited by: 37
Author(s): Jaideep Chakladar, Selena Z. Kuo, Grant Castaneda, Wei Tse Li, Aditi Gnanasekar, Michael Yu, Eric Y. Chang, Xiao Qi Wang, Weg M. Ongkeko
Software Mentions: 1
Published: about 4 years ago
10.7717/peerj.7683
Effect of radiotherapy on the gut microbiome in pediatric cancer patients: a pilot study
Cited by: 18
Author(s): Nourhan Sahly, Ahmed Moustafa, Mohamed S. Zaghloul, Tamer Z. Salem
Software Mentions: 1
Published: almost 5 years ago
10.1128/mSystems.00642-21
Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome
Cited by: 6
Author(s): Alexander K. Umbach, Ashley A. Stegelmeier, Josh D. Neufeld
Software Mentions: 1
Published: about 3 years ago
10.1038/s41396-021-00937-7
Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life
Cited by: 106
Author(s): Naoki Tsukuda, Kana Yahagi, Takeo Hara, Yozo Watanabe, Hoshitaka Matsumoto, Hiroshi Mori, Koichi Higashi, Hirokazu Tsuji, Satoshi Matsumoto, Ken Kurokawa, Takahiro Matsuki
Software Mentions: 1
Published: over 3 years ago
10.1186/s13071-019-3287-0
Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory
Cited by: 18
Author(s): Jewelna Akorli, Philomena Asor Namaali, Godwin Williams Ametsi, Richardson Kwesi Egyirifa, Nana Adjoa Pels
Software Mentions: 1
Published: over 5 years ago
10.1002/mbo3.802
Bioturbation of peanut worms <i>Sipunculus nudus</i> on the composition of prokaryotic communities in a tidal flat as revealed by 16S rRNA gene sequences
Cited by: 12
Author(s): Junwei Li, Ruiping Hu, Yong Guo, Suwen Chen, Xiaoyong Xie, Jianguang Qin, Zhenhua Ma, Cheng Zhu, Surui Pei
Software Mentions: 1
Published: over 5 years ago
10.1111/1751-7915.13511
Root‐tip cutting and uniconazole treatment improve the colonization rate of <i>Tuber indicum</i> on <i>Pinus armandii</i> seedlings in the greenhouse
Cited by: 7
Author(s): Xin Li, Lei Ye, Xiaoping Zhu, Hao Tan, Qiang Li
Software Mentions: 1
Published: over 4 years ago
10.1111/1751-7915.12756
Unravelling biocomplexity of electroactive biofilms for producing hydrogen from biomass
Cited by: 22
Author(s): Alex J. Lewis, Maria Fernanda Campa, Terry C. Hazen, Abhijeet P. Borole
Software Mentions: 1
Published: about 7 years ago
10.1186/s12917-021-02969-9
Data analysis workflow for the detection of canine vector-borne pathogens using 16 S rRNA Next-Generation Sequencing
Cited by: 1
Author(s): Elton J. R. Vasconcelos, Chayan Roy, Joseph Geiger, Kristina M. Oney, Melody Koo, Shuo Ren, Brian B. Oakley, Pedro Diniz
Software Mentions: 1
Published: about 3 years ago
10.1111/1751-7915.12128
Microbial response to single‐cell protein production and brewery wastewater treatment
Cited by: 34
Author(s): Jackson Z. Lee, Andrew Logan, S. L. Terry, John R. Spear
Software Mentions: 1
Published: over 10 years ago
10.3390/md18020124
Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors
Cited by: 19
Author(s): Ipsita Mohanty, Sheila Podell, Jason S. Biggs, Neha Garg, Eric E. Allen, Vinayak Agarwal
Software Mentions: 1
Published: over 4 years ago
10.3390/ijms221910858
Flaxseed Powder Attenuates Non-Alcoholic Steatohepatitis via Modulation of Gut Microbiota and Bile Acid Metabolism through Gut–Liver Axis
Cited by: 14
Author(s): Chao Yang, Min Wan, Dengfeng Xu, Da Pan, Hui Xia, Ligang Yang, Guiju Sun
Software Mentions: 1
Published: almost 3 years ago
10.3390/nu12020551
Safety Assessment of Bacteroides Uniformis CECT 7771, a Symbiont of the Gut Microbiota in Infants
Cited by: 25
Author(s): Eva M. Gómez del Pulgar, Alfonso Benı́tez-Páez, Yolanda Sanz
Software Mentions: 1
Published: over 4 years ago
10.1038/srep09470
Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis
Cited by: 83
Author(s): Awawing A. Andongma, Lun Wan, Yongcheng Dong, Ping Li, Nicolas Desneux, Jennifer A. White, Changying Niu
Software Mentions: 1
Published: over 9 years ago
10.1038/srep19083
The Impact of Dietary Energy Intake Early in Life on the Colonic Microbiota of Adult Mice
Cited by: 18
Author(s): Jinyu Xu, Jeffrey D. Galley, Michael T. Bailey, Jennifer M. Thomas‐Ahner, Steven K. Clinton, Susan Olivo‐Marston
Software Mentions: 1
Published: over 8 years ago