Xie, Fei Xu, Lei Wang, Yue Mao, Shengyong
Published in
mSystems
The cecum serves as an additional fermentation site for ruminants, but it lacks buffering capacity and has a relatively simple epithelial structure compared to the rumen. The role of high-grain (HG) diets in manipulating the rumen microbiome has been well elucidated, yet the microbial response to such diets in the cecum and the subsequent microbe-h...
Armstrong, George Martino, Cameron Rahman, Gibraan Gonzalez, Antonio Vázquez-Baeza, Yoshiki Mishne, Gal Knight, Rob
Published in
mSystems
Microbiome data are sparse and high dimensional, so effective visualization of these data requires dimensionality reduction. To date, the most commonly used method for dimensionality reduction in the microbiome is calculation of between-sample microbial differences (beta diversity), followed by principal-coordinate analysis (PCoA). Uniform Manifold...
Leclerc, Marion Bedu-Ferrari, Cassandre Etienne-Mesmin, Lucie Mariadassou, Mahendra Lebreuilly, Lucie Tran, Seav-Ly Brazeau, Laurence Mayeur, Camille Delmas, Julien Rué, Olivier
...
Published in
mSystems
The disruption of gut microbiota homeostasis has been associated with numerous diseases and with a disproportionate inflammatory response, including overproduction of nitric oxide (NO) in the intestinal lumen. However, the influence of NO on the human gut microbiota has not been well characterized yet. We used in vitro fermentation systems inoculat...
Koch, Rachel A Herr, Joshua R
Published in
mSystems
During mycoparasitism, a fungus-the host-is parasitized by another fungus-the mycoparasite. The genetic underpinnings of these relationships have been best characterized in ascomycete fungi. However, within basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mus...
Gaulke, Christopher A Schmeltzer, Emily R Dasenko, Mark Tyler, Brett M Vega Thurber, Rebecca Sharpton, Thomas J
Published in
mSystems
Shotgun metagenomic sequencing has transformed our understanding of microbial community ecology. However, preparing metagenomic libraries for high-throughput DNA sequencing remains a costly, labor-intensive, and time-consuming procedure, which in turn limits the utility of metagenomes. Several library preparation procedures have recently been devel...
Mantri, Shrikant S Negri, Timo Sales-Ortells, Helena Angelov, Angel Peter, Silke Neidhardt, Harald Oelmann, Yvonne Ziemert, Nadine
Published in
mSystems
Discovery of novel antibiotics is crucial for combating rapidly spreading antimicrobial resistance and new infectious diseases. Most of the clinically used antibiotics are natural products-secondary metabolites produced by soil microbes that can be cultured in the lab. Rediscovery of these secondary metabolites during discovery expeditions costs bo...
Beach, Natalie K Myers, Kevin S Owen, Brian R Seib, Matt Donohue, Timothy J Noguera, Daniel R
Published in
mSystems
Microorganisms must respond to environmental changes to survive, often by controlling transcription initiation. Intermittent aeration during wastewater treatment presents a cyclically changing environment to which microorganisms must react. We used an intermittently aerated bioreactor performing partial nitritation and anammox (PNA) to investigate ...
Chowdhury, Sounak Khakzad, Hamed Bergdahl, Gizem Ertürk Lood, Rolf Ekstrom, Simon Linke, Dirk Malmström, Lars Happonen, Lotta Malmström, Johan
Published in
mSystems
Streptococcus pyogenes is known to cause both mucosal and systemic infections in humans. In this study, we used a combination of quantitative and structural mass spectrometry techniques to determine the composition and structure of the interaction network formed between human plasma proteins and the surfaces of different S. pyogenes serotypes. Quan...
Dziuba, Marina Riese, Cornelius N Borgert, Lion Wittchen, Manuel Busche, Tobias Kalinowski, Jörn Uebe, René Schüler, Dirk
Published in
mSystems
Magnetosomes are complex membrane organelles synthesized by magnetotactic bacteria (MTB) for navigation in the Earth's magnetic field. In the alphaproteobacterium Magnetospirillum gryphiswaldense, all steps of magnetosome formation are tightly controlled by >30 specific genes arranged in several gene clusters. However, the transcriptional organizat...
Roda-Garcia, Juan J Haro-Moreno, Jose M Huschet, Lukas A Rodriguez-Valera, Francisco López-Pérez, Mario
Published in
mSystems
The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship betwe...
