Preprints (not yet peer-reviewed)

7 downloads
55 views

Hepatocellular carcinoma (HCC) is a kind of cancer with high incidence and often accompanied by intestinal flora imbalance. Many studies have shown that probiotics such as anthocyanins can regulate gut microbiome and improve disease. This study was designed to...

["Agricultural Science","Food Science and Technology","Microbiology"]
doi:10.7287/peerj.preprints.27429v1
36 downloads
99 views

Background Our team discovered that Prochlorococcus can take up glucose, in a process that changes the transcriptional pattern of several genes involved in glucose metabolization. We have also shown that glcH encodes a very high affinity glucose transporter, and...

["Ecology","Marine Biology","Microbiology","Molecular Biology","Biological Oceanography"]
doi:10.7287/peerj.preprints.27423v1
2,537 downloads
4,388 views
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, II, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation...

["Bioinformatics","Ecology","Microbiology","Data Science"]
doi:10.7287/peerj.preprints.27295v2
88 downloads
184 views

Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes...

["Ecology","Microbiology","Plant Science"]
doi:10.7287/peerj.preprints.27393v1
24 downloads
72 views

The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous...

["Agricultural Science","Biotechnology","Ecosystem Science","Microbiology","Environmental Contamination and Remediation"]
doi:10.7287/peerj.preprints.27391v1
48 downloads
112 views

Background. Necrotic enteritis (NE) is caused by type A strains of the bacterium Clostridium perfringens. Total global economic losses to the poultry industry due to NE is estimated to be over 2 billion dollars annually. Traditionally, NE has been effectively controlled...

["Agricultural Science","Biotechnology","Microbiology","Veterinary Medicine"]
doi:10.7287/peerj.preprints.27390v1
57 downloads
126 views

Neisseria meningitidis (Nm) and N. gonorrhoeae (Ng) are closely related pathogenic bacteria. Using those genes found across 20 Nm and 15 Ng genomes we find that Nm is 7x more diverse than Ng in their combined core genome. Both species have acquired the majority...

["Evolutionary Studies","Genetics","Genomics","Microbiology","Infectious Diseases"]
doi:10.7287/peerj.preprints.27382v1
25 downloads
63 views

We proposed a theoretical framework predicting mutualistic outcomes for the arbuscular mycorrhizal (AM) symbiosis based on host identity (crop versus wild). To test the framework, we grew two isolates of Rhizoglomus irregulare (commercial versus an isolate locally...

["Microbiology"]
doi:10.7287/peerj.preprints.27384v1
25 downloads
101 views

Introduction. Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded...

["Bioinformatics","Ecology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.27376v1
105 downloads
151 views

MicroRNAs (miRNAs) play an important role in plant resistance to pathogen infections. However, little is known about the role of miRNAs in banana Fusarium wilt, which is the most economically devastating disease in banana production. In the present study, we identified...

["Microbiology","Molecular Biology","Plant Science"]
doi:10.7287/peerj.preprints.27369v1
118 downloads
268 views

Background. Although pathogenic Gram-negative bacteria lack their own ubiquitination machinery, they have evolved or acquired virulence effectors that can manipulate the host ubiquitination process through structural and/or functional mimicry of host machinery....

["Bioinformatics","Computational Biology","Microbiology","Infectious Diseases","Data Mining and Machine Learning"]
doi:10.7287/peerj.preprints.27292v1
261 downloads
500 views

A productive biosphere and oxygenated atmosphere are defining features of Earth and are fundamentally linked. Here I argue that cellular metabolism imposes central constraints on the historical trajectories of biopsheric productivity and atmospheric oxygenation....

["Ecology","Evolutionary Studies","Microbiology","Biosphere Interactions","Biogeochemistry"]
doi:10.7287/peerj.preprints.27269v1
67 downloads
218 views

The gut microbiota has been shown to have an important influence on host health. Microbial composition of the gut microbiota is modulated by diet and human habits. The composition of human gut microbiota changes with age; and alterations in this composition may...

["Biotechnology","Genomics","Microbiology","Molecular Biology"]
doi:10.7287/peerj.preprints.27252v1
103 downloads
236 views

Background: It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into three clades, with the A group infecting a range of arthropods, the B group infecting nematode worms,...

["Evolutionary Studies","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.27242v1
108 downloads
118 views

The mechanisms underlying community dynamics, which govern the complicated biogeographical patterns of microbes, have long been a research hotspot in community ecology. However, the mixing of multiple ecological processes and the one-sidedness of analytical methods...

["Ecology","Microbiology"]
doi:10.7287/peerj.preprints.27223v1
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