Read by QxMD icon Read

Gene expression microbiome

Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H Janssen, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts...
October 19, 2016: Microbiome
John Chu, Xavier Vila-Farres, Daigo Inoyama, Melinda Ternei, Louis J Cohen, Emma A Gordon, Boojala Vijay B Reddy, Zachary Charlop-Powers, Henry A Zebroski, Ricardo Gallardo-Macias, Mark Jaskowski, Shruthi Satish, Steven Park, David S Perlin, Joel S Freundlich, Sean F Brady
Here we present a natural product discovery approach, whereby structures are bioinformatically predicted from primary sequence and produced by chemical synthesis (synthetic-bioinformatic natural products, syn-BNPs), circumventing the need for bacterial culture and gene expression. When we applied the approach to nonribosomal peptide synthetase gene clusters from human-associated bacteria, we identified the humimycins. These antibiotics inhibit lipid II flippase and potentiate β-lactam activity against methicillin-resistant Staphylococcus aureus in mice, potentially providing a new treatment regimen...
October 17, 2016: Nature Chemical Biology
Joshua M A Stough, Stephen P Dearth, Joshua E Denny, Gary R LeCleir, Nathan W Schmidt, Shawn R Campagna, Steven W Wilhelm
C57BL/6 mice are widely used for in vivo studies of immune function and metabolism in mammals. In a previous study, it was observed that when C57BL/6 mice purchased from different vendors were infected with Plasmodium yoelii, a causative agent of murine malaria, they exhibited both differential immune responses and significantly different parasite burdens: these patterns were reproducible when gut contents were transplanted into gnotobiotic mice. To gain insight into the mechanism of resistance, we removed whole ceca from mice purchased from two vendors, Taconic Biosciences (low parasitemia) and Charles River Laboratories (high parasitemia), to determine the combined host and microflora metabolome and metatranscriptome...
2016: Frontiers in Microbiology
Marie Chantal Lemfack, Srinivasa Rao Ravella, Nicola Lorenz, Marco Kai, Kirsten Jung, Stefan Schulz, Birgit Piechulla
The skin microbiota is import for body protection. Here we present the first comprehensive analysis of the volatile organic compound (VOC) profiles of typical skin-resident corynebacterial and staphylococcal species. The VOC profile of Staphylococcus schleiferi DSMZ 4807 was of particular interest as it is dominated by two compounds, 3-(phenylamino)butan-2-one and 3-(phenylimino)butan-2-one (schleiferon A and B, respectively). Neither of these has previously been reported from natural sources. Schleiferon A and B inhibited the growth of various Gram-positive species and affected two quorum-sensing-dependent phenotypes - prodigiosin accumulation and bioluminescence - of Gram-negative bacteria...
September 27, 2016: Systematic and Applied Microbiology
Allison L Richards, Michael B Burns, Adnan Alazizi, Luis B Barreiro, Roger Pique-Regi, Ran Blekhman, Francesca Luca
Many studies have demonstrated the importance of the gut microbiota in healthy and disease states. However, establishing the causality of host-microbiota interactions in humans is still challenging. Here, we describe a novel experimental system to define the transcriptional response induced by the microbiota in human cells and to shed light on the molecular mechanisms underlying host-gut microbiota interactions. In primary human colonic epithelial cells, we identified over 6,000 genes that change expression at various time points following co-culturing with the gut microbiota of a healthy individual...
July 2016: MSystems
Ta-Chiang Liu, Bhaskar Gurram, Megan T Baldridge, Richard Head, Vy Lam, Chengwei Luo, Yumei Cao, Pippa Simpson, Michael Hayward, Mary L Holtz, Pavlos Bousounis, Joshua Noe, Diana Lerner, Jose Cabrera, Vincent Biank, Michael Stephens, Curtis Huttenhower, Dermot P B McGovern, Ramnik J Xavier, Thaddeus S Stappenbeck, Nita H Salzman
BACKGROUND: Paneth cell dysfunction has been implicated in a subset of Crohn's disease (CD) patients. We previously stratified clinical outcomes of CD patients by using Paneth cell phenotypes, which we defined by the intracellular distribution of antimicrobial proteins. Animal studies suggest that Paneth cells shape the intestinal microbiome. However, it is unclear whether Paneth cell phenotypes alter the microbiome complexity in CD subjects. Therefore, we analyzed the correlation of Paneth cell phenotypes with mucosal microbiome composition and ileal RNA expression in pediatric CD and noninflammatory bowel disease (non-IBD) patients...
June 2, 2016: JCI Insight
Wei Liu, Jimmy W Crott, Lin Lyu, Anna C Pfalzer, Jinchao Li, Sang-Woon Choi, Yingke Yang, Joel B Mason, Zhenhua Liu
Obesity is an established risk factor for colorectal cancer (CRC). Our previous study indicated that obesity increases activity of the pro-tumorigenic Wnt-signaling. Presently, we sought to further advance our understanding of the mechanisms by which obesity promotes CRC by examining associations between microbiome, inflammation and Wnt-signaling in Apc(+/1638N) mice whose obesity was induced by one of two modalities, diet- or genetically-induced obesity. Three groups were employed: Apc(+/1638N)Lepr(+/+) fed a low fat diet (10% fat), Apc(+/1638N)Lepr(+/+) fed a high fat diet (60% fat, diet-induced obesity), and Apc(+/1638N)Lepr(db/db) fed a low fat diet (genetically-induced obesity)...
2016: Journal of Cancer
Muthukrishnan Eaaswarkhanth, Duo Xu, Colin Flanagan, Margarita Rzhetskaya, M Geoffrey Hayes, Ran Blekhman, Nina Jablonski, Omer Gokcumen
Human skin has evolved rapidly, leaving evolutionary signatures in the genome. The filaggrin (FLG) gene is widely studied for its skin-barrier function in humans. The extensive genetic variation in this gene, especially common loss-of-function (LoF) mutations, has been established as primary risk factors for atopic dermatitis. To investigate the evolution of this gene, we analyzed 2,504 human genomes and genotyped the copy number variation of filaggrin repeats within FLG in 126 individuals from diverse ancestral backgrounds...
September 27, 2016: Genome Biology and Evolution
Alexandre Smirnov, Konrad U Förstner, Erik Holmqvist, Andreas Otto, Regina Günster, Dörte Becher, Richard Reinhardt, Jörg Vogel
The functional annotation of transcriptomes and identification of noncoding RNA (ncRNA) classes has been greatly facilitated by the advent of next-generation RNA sequencing which, by reading the nucleotide order of transcripts, theoretically allows the rapid profiling of all transcripts in a cell. However, primary sequence per se is a poor predictor of function, as ncRNAs dramatically vary in length and structure and often lack identifiable motifs. Therefore, to visualize an informative RNA landscape of organisms with potentially new RNA biology that are emerging from microbiome and environmental studies requires the use of more functionally relevant criteria...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Xie Jianping, Han Yubo, Liu Gang, Bai Linquan
In 2015, there are significant progresses in many aspects of the microbial genetics in China. To showcase the contribution of Chinese scientists in microbial genetics, this review surveys several notable progresses in microbial genetics made largely by Chinese scientists, and some key findings are highlighted. For the basic microbial genetics, the components, structures and functions of many macromolecule complexes involved in gene expression regulation have been elucidated. Moreover, the molecular basis underlying the recognition of foreign nucleic acids by microbial immune systems was unveiled...
September 20, 2016: Yi Chuan, Hereditas
Richard D Beger, Warwick Dunn, Michael A Schmidt, Steven S Gross, Jennifer A Kirwan, Marta Cascante, Lorraine Brennan, David S Wishart, Matej Oresic, Thomas Hankemeier, David I Broadhurst, Andrew N Lane, Karsten Suhre, Gabi Kastenmüller, Susan J Sumner, Ines Thiele, Oliver Fiehn, Rima Kaddurah-Daouk
INTRODUCTION BACKGROUND TO METABOLOMICS: Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or "-omics" level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person's metabolic state provides a close representation of that individual's overall health status...
2016: Metabolomics: Official Journal of the Metabolomic Society
Yuko Tsuruta, Laura Q Rogers, Helen Krontiras, William E Grizzle, Andrew D Frugé, Robert A Oster, Heidi R Umphrey, Lee W Jones, Maria Azrad, Wendy Demark-Wahnefried
INTRODUCTION: Obesity is a known risk factor for postmenopausal breast cancer and is associated with poorer prognosis for premenopausal and postmenopausal patients; however, the aetiological mechanisms are unknown. Preclinical studies support weight loss via caloric restriction and increased physical activity as a possible cancer control strategy, though few clinical studies have been conducted. We undertook a feasibility trial among women recently diagnosed with stage 0-II breast cancer hypothesising that presurgical weight loss would be feasible, safe and result in favourable changes in tumour markers and circulating biomarkers...
September 15, 2016: BMJ Open
Marjorie M Walker
Chronic and complex gut syndromes are complex to diagnose and manage, but good clinicopathologic correlation, recognition of new entities, understanding (and understanding the limits) of genetic susceptibility and the importance of the microbiome, dysbiosis and influence of the environmental allows development of new models for diagnosis. An awareness of overlap in chronic gut syndromes has been clarified by the realization that inflammatory pathways involved in chronic gut disease can arise through variable gene expression that is influenced by the environment in susceptible individuals...
October 2016: Journal of Clinical Gastroenterology
Ruben Props, Frederiek-Maarten Kerckhof, Peter Rubbens, Jo De Vrieze, Emma Hernandez Sanabria, Willem Waegeman, Pieter Monsieurs, Frederik Hammes, Nico Boon
High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances...
September 9, 2016: ISME Journal
Sabrina Duranti, Federica Gaiani, Leonardo Mancabelli, Christian Milani, Andrea Grandi, Angelo Bolchi, Andrea Santoni, Gabriele Andrea Lugli, Chiara Ferrario, Marta Mangifesta, Alice Viappiani, Simona Bertoni, Valentina Vivo, Fausta Serafini, Maria Raffaella Barbaro, Alessandro Fugazza, Giovanni Barbara, Laura Gioiosa, Paola Palanza, Anna Maria Cantoni, Gian Luigi de'Angelis, Elisabetta Barocelli, Nicola de'Angelis, Douwe van Sinderen, Marco Ventura, Francesca Turroni
Ulcerative colitis (UC) is associated with a substantial alteration of specific gut commensals, some of which may be involved in microbiota-mediated protection. In this study, microbiota cataloging of UC patients by 16S rRNA microbial profiling revealed a marked reduction of bifidobacteria, in particular the Bifidobacterium bifidum species, thus suggesting that this taxon plays a biological role in the aetiology of UC. We investigated this further through an in vivo trial by testing the effects of oral treatment with B...
December 2016: FEMS Microbiology Ecology
Emily K Cope, Andrew N Goldberg, Steven D Pletcher, Susan V Lynch
BACKGROUND: Diverse microbial communities colonize healthy sinus mucosa and specific species within these communities are capable of protecting the host from pathogenic infection. However, little is known of the dynamics of upper airway infection and the role of the sinus mucosal microbiome in short- and longer-term outcomes using clinical isolates from patients with chronic rhinosinusitis. METHODS: We examine microbiome and immune dynamics after murine sinus infection with Pseudomonas aeruginosa EC1, isolated previously from a chronic rhinosinusitis patient...
September 6, 2016: International Forum of Allergy & Rhinology
Adi Millman, Daniel Dar, Maya Shamir, Rotem Sorek
A common strategy for regulation of gene expression in bacteria is conditional transcription termination. This strategy is frequently employed by 5'UTR cis-acting RNA elements (riboregulators), including riboswitches and attenuators. Such riboregulators can assume two mutually exclusive RNA structures, one of which forms a transcriptional terminator and results in premature termination, and the other forms an antiterminator that allows read-through into the coding sequence to produce a full-length mRNA. We developed a machine-learning based approach, which, given a 5'UTR of a gene, predicts whether it can form the two alternative structures typical to riboregulators employing conditional termination...
August 29, 2016: Nucleic Acids Research
Molly K Gibson, Bin Wang, Sara Ahmadi, Carey-Ann D Burnham, Phillip I Tarr, Barbara B Warner, Gautam Dantas
Development of the preterm infant gut microbiota is emerging as a critical research priority(1). Since preterm infants almost universally receive early and often extended antibiotic therapy(2), it is important to understand how these interventions alter gut microbiota development(3-6). Analysis of 401 stools from 84 longitudinally sampled preterm infants demonstrates that meropenem, cefotaxime and ticarcillin-clavulanate are associated with significantly reduced species richness. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness, but these can be predicted with 85% accuracy based on the relative abundance of only two bacterial species and two antibiotic resistance (AR) genes at treatment initiation...
2016: Nature Microbiology
Ki-Wook Kim, Jesse W Williams, Ya-Ting Wang, Stoyan Ivanov, Susan Gilfillan, Marco Colonna, Herbert W Virgin, Emmanuel L Gautier, Gwendalyn J Randolph
Peritoneal and pleural resident macrophages in the mouse share common features and in each compartment exist as two distinct subpopulations: F4/80(+) macrophages and MHC II(+) CD11c(+) macrophages. F4/80(+) macrophages derive from embryonic precursors, and their maintenance is controlled by Gata6. However, the origin and regulatory factors that maintain MHC II(+) macrophages remain unknown. Here, we show that the MHC II(+) macrophages arise postnatally from CCR2-dependent precursors that resemble monocytes...
September 19, 2016: Journal of Experimental Medicine
Meital Gury-BenAri, Christoph A Thaiss, Nicolas Serafini, Deborah R Winter, Amir Giladi, David Lara-Astiaso, Maayan Levy, Tomer Meir Salame, Assaf Weiner, Eyal David, Hagit Shapiro, Mally Dori-Bachash, Meirav Pevsner-Fischer, Erika Lorenzo-Vivas, Hadas Keren-Shaul, Franziska Paul, Alon Harmelin, Gérard Eberl, Shalev Itzkovitz, Amos Tanay, James P Di Santo, Eran Elinav, Ido Amit
Innate lymphoid cells (ILCs) are critical modulators of mucosal immunity, inflammation, and tissue homeostasis, but their full spectrum of cellular states and regulatory landscapes remains elusive. Here, we combine genome-wide RNA-seq, ChIP-seq, and ATAC-seq to compare the transcriptional and epigenetic identity of small intestinal ILCs, identifying thousands of distinct gene profiles and regulatory elements. Single-cell RNA-seq and flow and mass cytometry analyses reveal compartmentalization of cytokine expression and metabolic activity within the three classical ILC subtypes and highlight transcriptional states beyond the current canonical classification...
August 25, 2016: Cell
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"