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Microbial taxonomy

Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States

Madison Goforth, Victoria Obergh, Richard Park, Martin Porchas, Kevin M. Crosby, John L. Jifon, Sadhana Ravishankar, Paul Brierley, Daniel L. Leskovar, Thomas A. Turini, Jonathan Schultheis, Timothy Coolong, Rhonda Miller, Hisashi Koiwa, Bhimanagouda S. Patil, Margarethe A. Cooper, Steven Huynh, Craig T. Parker, Wenjing Guan, Kerry K. Cooper

published 11 Apr 2024

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Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions

Rachel C. Harbeitner, Fabian Wittmers, Charmaine C. M. Yung, Charlotte A. Eckmann, Elisabeth Hehenberger, Marguerite Blum, David M. Needham, Alexandra Z. Worden

published 02 Apr 2024

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Investigating the relationship between microbial network features of giant kelp “seedbank” cultures and subsequent farm performance

Melisa G. Osborne, Ariel Levi Simons, Gary Molano, Bernadeth Tolentino, Anupam Singh, Gabriel J. Montecinos Arismendi, Filipe Alberto, Sergey V. Nuzhdin

published 27 Mar 2024

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Speeding genomic island discovery through systematic design of reference database composition

Steven L. Yu, Catherine M. Mageeney, Fatema Shormin, Noushin Ghaffari, Kelly P. Williams

published 13 Mar 2024

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The salivary microbiota of patients with acute lower respiratory tract infection–A multicenter cohort study

Matthew B. Rogers, Ashley Harner, Megan Buhay, Brian Firek, Barbara Methé, Alison Morris, Octavia M. Peck Palmer, Susan B. Promes, Robert L. Sherwin, Lauren Southerland, Alexandre R. Vieira, Sachin Yende, Michael J. Morowitz, David T. Huang

published 11 Jan 2024

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Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data

Moussa Sondo, Issa Wonni, Kadidia Koïta, Isabelle Rimbault, Mariam Barro, Charlotte Tollenaere, Lionel Moulin, Agnieszka Klonowska

published 30 Nov 2023

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Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf

Saja A. Fakhraldeen, Sakinah Al-Haddad, Nazima Habibi, Surendraraj Alagarsamy, Sabeena F. K. Habeebullah, Abdulmuhsen K. Ali, Walid M. Al-Zakri

published 16 Nov 2023

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Integrating current analyses of the breast cancer microbiome

Sidra Sohail, Michael B. Burns

published 12 Sep 2023

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MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome-assembled genomes

Wanxin Li, Lila Kari, Yaoliang Yu, Laura A. Hug

published 18 Aug 2023

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The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection

Ruijie Xu, Sreekumari Rajeev, Liliana C. M. Salvador

published 07 Apr 2023

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Quantification of diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media using 16S amplicon barcoding

Moussa Sondo, Issa Wonni, Agnieszka Klonowska, Kadidia Koïta, Lionel Moulin

published 06 Apr 2023

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Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach

Sandra Dérozier, Robert Bossy, Louise Deléger, Mouhamadou Ba, Estelle Chaix, Olivier Harlé, Valentin Loux, Hélène Falentin, Claire Nédellec

published 20 Jan 2023

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Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples

Katherine A. Maki, Brian Wolff, Leonardo Varuzza, Stefan J. Green, Jennifer J. Barb

published 13 Jan 2023

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