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Sara F Paver, Daniel Muratore, Ryan J Newton, Maureen L Coleman
Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages...
November 2018: MSystems
Benjamin Hillmann, Gabriel A Al-Ghalith, Robin R Shields-Cutler, Qiyun Zhu, Daryl M Gohl, Kenneth B Beckman, Rob Knight, Dan Knights
Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis...
November 2018: MSystems
Jingwei Cai, Robert G Nichols, Imhoi Koo, Zachary A Kalikow, Limin Zhang, Yuan Tian, Jingtao Zhang, Philip B Smith, Andrew D Patterson
The gut microbiota is susceptible to modulation by environmental stimuli and therefore can serve as a biological sensor. Recent evidence suggests that xenobiotics can disrupt the interaction between the microbiota and host. Here, we describe an approach that combines in vitro microbial incubation (isolated cecal contents from mice), flow cytometry, and mass spectrometry- and 1 H nuclear magnetic resonance (NMR)-based metabolomics to evaluate xenobiotic-induced microbial toxicity. Tempol, a stabilized free radical scavenger known to remodel the microbial community structure and function in vivo , was studied to assess its direct effect on the gut microbiota...
November 2018: MSystems
Shao K Huang, Kun T Ye, Wei F Huang, Bi H Ying, Xin Su, Li H Lin, Jiang H Li, Yan P Chen, Ji L Li, Xiu L Bao, Jian Z Hu
The gut microbiota plays an essential role in the health of bees. To elucidate the effect of feed and Nosema ceranae infection on the gut microbiota of honey bee (Apis cerana), we used 16S rRNA sequencing to survey the gut microbiota of honey bee workers fed with sugar water or beebread and inoculated with or without N. ceranae. The gut microbiota of A. cerana is dominated by Serratia , Snodgrassella , and Lactobacillus genera. The overall gut microbiota diversity was show to be significantly differential by feeding type...
November 2018: MSystems
Egle Cekanaviciute, Anne-Katrin Pröbstel, Anna Thomann, Tessel F Runia, Patrizia Casaccia, Ilana Katz Sand, Elizabeth Crabtree, Sneha Singh, John Morrissey, Patrick Barba, Refujia Gomez, Rob Knight, Sarkis Mazmanian, Jennifer Graves, Bruce A C Cree, Scott S Zamvil, Sergio E Baranzini
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by adaptive and innate immune system dysregulation. Recent work has revealed moderate alteration of gut microbial communities in subjects with MS and in experimental, induced models. However, a mechanistic understanding linking the observed changes in the microbiota and the presence of the disease is still missing. Chloroform-resistant, spore-forming bacteria, which primarily belong to the classes Bacilli and Clostridia in the phylum Firmicutes , have been shown to exhibit immunomodulatory properties in vitro and in vivo , but they have not yet been characterized in the context of human disease...
November 2018: MSystems
Leen Boesmans, Mireia Valles-Colomer, Jun Wang, Venessa Eeckhaut, Gwen Falony, Richard Ducatelle, Filip Van Immerseel, Jeroen Raes, Kristin Verbeke
Advances in gut microbiota research have triggered interest in developing colon butyrate producers as niche-specific next-generation probiotics, targeted at increasing colon butyrate production and countering disease-associated microbiota alterations. Crucial steps in the development of next-generation probiotics are the design of formulations with a reasonable shelf life as well as the safety demonstration of an intervention in healthy volunteers. One such potential next-generation butyrate-producing probiotic is Butyricicoccus pullicaecorum 25-3T , with demonstrated safety in in vitro as well as animal models...
November 2018: MSystems
Jeremiah J Minich, Greg Humphrey, Rodolfo A S Benitez, Jon Sanders, Austin Swafford, Eric E Allen, Rob Knight
Next-generation sequencing technologies have enabled many advances across biology, with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparation methods has largely remained unchanged. In this study, we developed a low-cost miniaturized (5-µl volume) high-throughput (384-sample) amplicon library preparation method with the Echo 550 acoustic liquid handler. Our method reduces costs of library preparation to $1...
November 2018: MSystems
Sean Ting-Shyang Wei, Yu-Wei Wu, Tzong-Huei Lee, Yi-Shiang Huang, Cheng-Yu Yang, Yi-Lung Chen, Yin-Ru Chiang
The 2,3- seco pathway, the pathway for anaerobic cholesterol degradation, has been established in the denitrifying betaproteobacterium Sterolibacterium denitrificans. However, knowledge of how microorganisms respond to cholesterol at the community level is elusive. Here, we applied mesocosm incubation and 16S rRNA sequencing to reveal that, in denitrifying sludge communities, three betaproteobacterial operational taxonomic units (OTUs) with low (94% to 95%) 16S rRNA sequence similarity to Stl. denitrificans are cholesterol degraders and members of the rare biosphere...
September 2018: MSystems
Florent Mazel, Katherine M Davis, Andrew Loudon, Waldan K Kwong, Mathieu Groussin, Laura Wegener Parfrey
Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature...
September 2018: MSystems
Lili Ren, Rongbao Zhang, Jian Rao, Yan Xiao, Zhao Zhang, Bin Yang, Depan Cao, Hui Zhong, Pu Ning, Ying Shang, Mingkun Li, Zhancheng Gao, Jianwei Wang
Alteration of the lung microbiome has been observed in several respiratory tract diseases. However, most previous studies were based on 16S ribosomal RNA and shotgun metagenome sequencing; the viability and functional activity of the microbiome, as well as its interaction with host immune systems, have not been well studied. To characterize the active lung microbiome and its associations with host immune response and clinical features, we applied metatranscriptome sequencing to bronchoalveolar lavage fluid (BALF) samples from 25 patients with chronic obstructive pulmonary disease (COPD) and from nine control cases without known pulmonary disease...
September 2018: MSystems
Yoshikazu Furuta, Hayato Harima, Emiko Ito, Fumito Maruyama, Naomi Ohnishi, Ken Osaki, Hirohito Ogawa, David Squarre, Bernard Mudenda Hang'ombe, Hideaki Higashi
Bacillus anthracis is a Gram-positive endospore-forming bacterial species that causes anthrax in both humans and animals. In Zambia, anthrax cases are frequently reported in both livestock and wildlife, with occasional transmission to humans, causing serious public health problems in the country. To understand the genetic diversity of B. anthracis strains in Zambia, we sequenced and compared the genomic DNA of B. anthracis strains isolated across the country. Single nucleotide polymorphisms clustered these strains into three groups...
September 2018: MSystems
Demetrius DiMucci, Mark Kon, Daniel Segrè
Microbes affect each other's growth in multiple, often elusive, ways. The ensuing interdependencies form complex networks, believed to reflect taxonomic composition as well as community-level functional properties and dynamics. The elucidation of these networks is often pursued by measuring pairwise interactions in coculture experiments. However, the combinatorial complexity precludes an exhaustive experimental analysis of pairwise interactions, even for moderately sized microbial communities. Here, we used a machine learning random forest approach to address this challenge...
September 2018: MSystems
Matthew D Servinsky, Rebecca L Renberg, Matthew A Perisin, Elliot S Gerlach, Sanchao Liu, Christian J Sund
Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fermented in the presence of arabinose, revealing a hierarchy of pentose utilization in this organism (L. Aristilde, I. A. Lewis, J. O. Park, and J. D. Rabinowitz, Appl Environ Microbiol 81:1452-1462, 2015,
September 2018: MSystems
Joshua Ladau, Yu Shi, Xin Jing, Jin-Sheng He, Litong Chen, Xiangui Lin, Noah Fierer, Jack A Gilbert, Katherine S Pollard, Haiyan Chu
Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (∼75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ∼50 years ago than with current climate...
September 2018: MSystems
Whitney E England, Ted Kim, Rachel J Whitaker
Viruses that infect the widespread opportunistic pathogen Pseudomonas aeruginosa have been shown to influence physiology and critical clinical outcomes in cystic fibrosis (CF) patients. To understand how CRISPR-Cas immune interactions may contribute to the distribution and coevolution of P. aeruginosa and its viruses, we reconstructed CRISPR arrays from a highly sampled longitudinal data set from CF patients attending the Copenhagen Cystic Fibrosis Clinic in Copenhagen, Denmark (R. L. Marvig, L. M. Sommer, S...
September 2018: MSystems
Saisai Cheng, Xin Ma, Shijie Geng, Xuemei Jiang, Yuan Li, Luansha Hu, Jianrong Li, Yizhen Wang, Xinyan Han
Fecal microbiota transplantation (FMT) is one of the most effective ways to regulate the gut microbiota. Here, we investigated the effect of exogenous fecal microbiota on gut function from the perspective of analysis of the mucosal proteomes in a piglet model. A total of 289 differentially expressed proteins were annotated with 4,068 gene ontology (GO) function entries in the intestinal mucosa, and the levels of autophagy-related proteins in the forkhead box O (FoxO) signaling pathway were increased whereas the levels of proteins related to inflammation response were decreased in the recipient...
September 2018: MSystems
James C Stegen, Amy E Goldman
The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) aims to galvanize a global community to provide the scientific basis for improved management of dynamic river corridors. WHONDRS is a global research consortium working to understand connections among dynamic hydrology, biogeochemistry, and microbiology in river corridors from local to global scales. WHONDRS ascribes to the perspective that resources, knowledge, and data belong to the community as a whole and that science advances more rapidly and more robustly through community ownership...
September 2018: MSystems
Yue O O Hu, Luisa W Hugerth, Carina Bengtsson, Arlisa Alisjahbana, Maike Seifert, Anaga Kamal, Åsa Sjöling, Tore Midtvedt, Elisabeth Norin, Juan Du, Lars Engstrand
Salmonella infection is one of the main causes of food-borne diarrheal diseases worldwide. Although most Salmonella infections can be cleared without treatment, some cause serious illnesses that require antibiotic treatment. In view of the growing emergence of antibiotic-resistant Salmonella strains, novel treatments are increasingly required. Furthermore, there is a striking paucity of data on how a balanced human gut microbiota responds to Salmonella infection. This study aimed to evaluate whether a balanced gut microbiota protects against Salmonella growth and to compare two antimicrobial approaches for managing Salmonella infection: bacteriophage (phage) treatment and antibiotic treatment...
September 2018: MSystems
Johannes Cairns, Katariina Koskinen, Reetta Penttinen, Tommi Patinen, Anna Hartikainen, Roosa Jokela, Liisa Ruusulehto, Sirja Viitamäki, Sari Mattila, Teppo Hiltunen, Matti Jalasvuori
Mobile genetic elements such as conjugative plasmids are responsible for antibiotic resistance phenotypes in many bacterial pathogens. The ability to conjugate, the presence of antibiotics, and ecological interactions all have a notable role in the persistence of plasmids in bacterial populations. Here, we set out to investigate the contribution of these factors when the conjugation network was disturbed by a plasmid-dependent bacteriophage. Phage alone effectively caused the population to lose plasmids, thus rendering them susceptible to antibiotics...
September 2018: MSystems
Sarah J Quillin, Adam J Hockenberry, Michael C Jewett, H Steven Seifert
Neisseria gonorrhoeae mounts a substantial transcriptional program in response to hydrogen peroxide (HP), a prominent reactive oxygen species (ROS) encountered during infection. We tested which strain FA1090 genes show differential transcript abundance in response to sublethal amounts of HP to differentiate HP-responsive signaling from widespread cellular death and dysregulation. RNA sequencing (RNA-Seq) revealed that 150 genes were significantly upregulated and 143 genes downregulated following HP exposure...
September 2018: MSystems
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