Search Results - "Microbiome"

Microbiome definition re-visited: old concepts and new challenges by Berg, Gabriele, Rybakova, Daria, Fischer, Doreen, Cernava, Tomislav, Vergès, Marie-Christine Champomier, Charles, Trevor, Chen, Xiaoyulong, Cocolin, Luca, Eversole, Kellye, Corral, Gema Herrero, Kazou, Maria, Kinkel, Linda, Lange, Lene, Lima, Nelson, Loy, Alexander, Macklin, James A, Maguin, Emmanuelle, Mauchline, Tim, McClure, Ryan, Mitter, Birgit, Ryan, Matthew, Sarand, Inga, Smidt, Hauke, Schelkle, Bettina, Roume, Hugo, Kiran, G Seghal, Selvin, Joseph, Souza, Rafael Soares Correa de, van Overbeek, Leo, Singh, Brajesh K, Wagner, Michael, Walsh, Aaron, Sessitsch, Angela, Schloter, Michael

“…The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of…”
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VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses by Guo, Jiarong, Bolduc, Ben, Zayed, Ahmed A, Varsani, Arvind, Dominguez-Huerta, Guillermo, Delmont, Tom O, Pratama, Akbar Adjie, Gazitúa, M Consuelo, Vik, Dean, Sullivan, Matthew B, Roux, Simon

“…Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" in metagenomic/metatranscriptomic sequence datasets…”
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Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin by Bokulich, Nicholas A, Kaehler, Benjamin D, Rideout, Jai Ram, Dillon, Matthew, Bolyen, Evan, Knight, Rob, Huttley, Gavin A, Gregory Caporaso, J

“…Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. We present q2-feature-classifier (…”
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Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data by Davis, Nicole M, Proctor, Diana M, Holmes, Susan P, Relman, David A, Callahan, Benjamin J

“…The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants-DNA sequences not…”
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Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health by Oliphant, Kaitlyn, Allen-Vercoe, Emma

“…The human gut microbiome is a critical component of digestion, breaking down complex carbohydrates, proteins, and to a lesser extent fats that reach the lower…”
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Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis by Wu, Zhenhua, Huang, Shimeng, Li, Tiantian, Li, Na, Han, Dandan, Zhang, Bing, Xu, Zhenjiang Zech, Zhang, Shiyi, Pang, Jiaman, Wang, Shilan, Zhang, Guolong, Zhao, Jiangchao, Wang, Junjun

“…Abstract Background Alteration of the gut microbiota may contribute to the development of inflammatory bowel disease (IBD). Epigallocatechin-3-gallate (EGCG),…”
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MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis by Uritskiy, Gherman V, DiRuggiero, Jocelyne, Taylor, James

“…The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in…”
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VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences by Kieft, Kristopher, Zhou, Zhichao, Anantharaman, Karthik

“…Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral…”
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Review: microbial transformations of human bile acids by Guzior, Douglas V., Quinn, Robert A.

“…Abstract Bile acids play key roles in gut metabolism, cell signaling, and microbiome composition. While the liver is responsible for the production of primary…”
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Specialized metabolic functions of keystone taxa sustain soil microbiome stability by Xun, Weibing, Liu, Yunpeng, Li, Wei, Ren, Yi, Xiong, Wu, Xu, Zhihui, Zhang, Nan, Miao, Youzhi, Shen, Qirong, Zhang, Ruifu

“…The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic…”
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Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons by Chen, Weidong, Ren, Kexin, Isabwe, Alain, Chen, Huihuang, Liu, Min, Yang, Jun

“…The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the…”
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Microbial interactions within the plant holobiont by Hassani, M Amine, Durán, Paloma, Hacquard, Stéphane

“…Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other,…”
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Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir by Mo, Yuanyuan, Peng, Feng, Gao, Xiaofei, Xiao, Peng, Logares, Ramiro, Jeppesen, Erik, Ren, Kexin, Xue, Yuanyuan, Yang, Jun

“…Abstract Background Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem…”
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Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family by Lagkouvardos, Ilias, Lesker, Till R, Hitch, Thomas C A, Gálvez, Eric J C, Smit, Nathiana, Neuhaus, Klaus, Wang, Jun, Baines, John F, Abt, Birte, Stecher, Bärbel, Overmann, Jörg, Strowig, Till, Clavel, Thomas

“…Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had…”
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Normalization and microbial differential abundance strategies depend upon data characteristics by Weiss, Sophie, Xu, Zhenjiang Zech, Peddada, Shyamal, Amir, Amnon, Bittinger, Kyle, Gonzalez, Antonio, Lozupone, Catherine, Zaneveld, Jesse R, Vázquez-Baeza, Yoshiki, Birmingham, Amanda, Hyde, Embriette R, Knight, Rob

“…Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary…”
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Fecal microbiota transplantation protects rotenone-induced Parkinson's disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-brain axis by Zhao, Zhe, Ning, Jingwen, Bao, Xiu-Qi, Shang, Meiyu, Ma, Jingwei, Li, Gen, Zhang, Dan

“…Parkinson's disease (PD) is a prevalent neurodegenerative disorder, displaying not only well-known motor deficits but also gastrointestinal dysfunctions…”
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Gut microbiota dysbiosis contributes to the development of hypertension by Li, Jing, Zhao, Fangqing, Wang, Yidan, Chen, Junru, Tao, Jie, Tian, Gang, Wu, Shouling, Liu, Wenbin, Cui, Qinghua, Geng, Bin, Zhang, Weili, Weldon, Ryan, Auguste, Kelda, Yang, Lei, Liu, Xiaoyan, Chen, Li, Yang, Xinchun, Zhu, Baoli, Cai, Jun

“…Recently, the potential role of gut microbiome in metabolic diseases has been revealed, especially in cardiovascular diseases. Hypertension is one of the most…”
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METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks by Zhou, Zhichao, Tran, Patricia Q, Breister, Adam M, Liu, Yang, Kieft, Kristopher, Cowley, Elise S, Karaoz, Ulas, Anantharaman, Karthik

“…Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed…”
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Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization by Chen, Shuaimin, Waghmode, Tatoba R, Sun, Ruibo, Kuramae, Eiko E, Hu, Chunsheng, Liu, Binbin

“…Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant…”
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Disease-induced changes in plant microbiome assembly and functional adaptation by Gao, Min, Xiong, Chao, Gao, Cheng, Tsui, Clement K. M., Wang, Meng-Meng, Zhou, Xin, Zhang, Ai-Min, Cai, Lei

“…Abstract Background The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health…”
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