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Mahejibin Khan, Amit Kumar
The understanding of the 3-dimensional enzyme structure is important for the point of protein engineering and applications. Computer-based molecular modelling is a vital tool for theoretical predication of enzyme activities and finding their substrates and inhibitors. SMlipA lipase was cloned from forest soil metagenome and characterized as broad spectrum enzyme with high stability in various organic solvents. In the present study, to understand the mechanism of SMlipA lipase and to identify the key residues involved in enzyme-substrate interaction, three dimensional-computational model of SMlipA has been generated and validated for stereo-chemical and amino-acid environment quality using appropriate programs, and further validation of the active-site architecture was achieved by performing docking studies with different ligand...
October 14, 2016: Journal of Molecular Graphics & Modelling
R Balfour Sartor, Gary D Wu
Intestinal microbiota are involved in the pathogenesis of Crohn's disease, ulcerative colitis, and pouchitis. We review the mechanisms by which these gut bacteria, fungi, and viruses mediate mucosal homeostasis, via their composite genes (metagenome) and metabolic products (metabolome). We explain how alterations to their profiles and functions under conditions of dysbiosis contribute to inflammation and effector immune responses that mediate inflammatory bowel diseases (IBD) in humans and enterocolitis in mice...
October 18, 2016: Gastroenterology
Umberto Rosani, Marco Gerdol
Viral metagenomics (viromics) can provide a great contribution in expanding the knowledge of viruses and the relationship with their hosts. Viromic studies on marine organisms are still at a very early stage and only little efforts have been spent in the identification of viruses associated to marine invertebrates to date, leaving the complexity of marine viromes associated to bivalve hosts almost completely unexplored. However, the potential use of viromic approaches in the management of viral diseases affecting aquacultured species has been recently evidenced by the flourishing of studies on the Ostreid herpesvirus type-1, which has been associated with bivalve mortality events...
October 18, 2016: Virus Research
Ryo Nakao, Keita Matsuno, Yongjin Qiu, Junki Maruyama, Nao Eguchi, Naganori Nao, Masahiro Kajihara, Kentaro Yoshii, Hirofumi Sawa, Ayato Takada, Chihiro Sugimoto
Ticks harbour various microorganisms, some of which act as pathogens of humans and animals. The recent advancement of genome sequencing technologies revealed that a wide range of previously unrecognised microorganisms exist in ticks. Continuous cell lines established from ticks could play a key role in the isolation of such microorganisms; however, tick cells themselves have been known to harbour symbiotic microorganisms. The present study aimed to characterise putative RNA viral sequences detected in the culture supernatant of one of the most frequently used tick cell lines, ISE6, which was derived from embryos of the blacklegged tick Ixodes scapularis...
October 15, 2016: Ticks and Tick-borne Diseases
Milka Kostic
Every month the editors of Cell Chemical Biology bring you highlights of the most recent chemical biology literature. Our October 2016 selection includes systematic structural, biochemical, and cellular characterization of B-RAF inhibitors; connecting bacterial transporters with their physiologically relevant ligands; and rewiring yeast metabolism for industrial scale production of isoprenoids.
October 20, 2016: Cell Chemical Biology
Jiachao Zhang, Qisong Hu, Chuanbiao Xu, Sixin Liu, Congfa Li
Pepper pericarp microbiota plays an important role in the pepper peeling process for the production of white pepper. We collected pepper samples at different peeling time points from Hainan Province, China, and used a metagenomic approach to identify changes in the pericarp microbiota based on functional gene analysis. UniFrac distance-based principal coordinates analysis revealed significant changes in the pericarp microbiota structure during peeling, which were attributed to increases in bacteria from the genera Selenomonas and Prevotella...
2016: PloS One
Katariina Pärnänen, Antti Karkman, Manu Tamminen, Christina Lyra, Jenni Hultman, Lars Paulin, Marko Virta
Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are mobile and able to spread to pathogenic bacteria. Until now, studying the mobility of antibiotic resistance genes in environmental resistomes has been challenging due to inadequate sensitivity and difficulties in contig assembly of metagenome based methods. We developed a new cost and labor efficient method based on Inverse PCR and long read sequencing for studying mobility potential of environmental resistance genes...
October 21, 2016: Scientific Reports
Matthias Willmann, Silke Peter
The increasing threat of antimicrobial resistance poses one of the greatest challenges to modern medicine. The collection of all antimicrobial resistance genes carried by various microorganisms in the human body is called the human resistome and represents the source of resistance in pathogens that can eventually cause life-threatening and untreatable infections. A deep understanding of the human resistome and its multilateral interaction with various environments is necessary for developing proper measures that can efficiently reduce the spread of resistance...
October 20, 2016: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
Essowè Palanga, Denis Filloux, Darren P Martin, Emmanuel Fernandez, Daniel Gargani, Romain Ferdinand, Jean Zabré, Zakaria Bouda, James Bouma Neya, Mahamadou Sawadogo, Oumar Traore, Michel Peterschmitt, Philippe Roumagnac
Cowpea, (Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as "poor man's meat", cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso...
2016: PloS One
Francesco Savino, Andrea Quartieri, Angela De Marco, Maria Garro, Alberto Amaretti, Stefano Raimondi, Marta Simone, Maddalena Rossi
AIM: This study compared the faecal microbial composition of formula-fed infants who did and did not have colic. METHODS: Faecal samples from formula-fed infants under 16 weeks of age with (n=38) and without (n=39) colic were collected at Department of Pediatrics in Turin, Italy, between February 2014 and October 2015. The pH and faecal ammonia were determined and total bacteria, bifidobacteria, lactic acid bacteria (LAB) and coliforms were quantified by fluorescent in situ hybridisation (FISH)...
October 20, 2016: Acta Paediatrica
Matthew D Hladilek, Karen F Gaines, James M Novak, David A Collard, Daniel B Johnson, Thomas Canam
Despite our dependency on treatment facilities to condition wastewater for eventual release to the environment, our knowledge regarding the effects of treated water on the local watershed is extremely limited. Responses of lotic systems to the treated wastewater effluent have been traditionally investigated by examining the benthic macroinvertebrate assemblages and community structure; however, these studies do not address the microbial diversity of the water systems. In the present study, planktonic and benthic bacterial community structure were examined at 14 sites (from 60 m upstream to 12,100 m downstream) and at two time points along an aquatic system receiving treated effluent from the Charleston Wastewater Treatment Plant (Charleston, IL)...
November 2016: Environmental Monitoring and Assessment
Ana C Henriques, Rui M S Azevedo, Paolo De Marco
Methanesulfonic acid (MSA) is a relevant intermediate of the biogeochemical cycle of sulfur and environmental microorganisms assume an important role in the mineralization of this compound. Several methylotrophic bacterial strains able to grow on MSA have been isolated from soil or marine water and two conserved operons, msmABCD coding for MSA monooxygenase and msmEFGH coding for a transport system, have been repeatedly encountered in most of these strains. Homologous sequences have also been amplified directly from the environment or observed in marine metagenomic data, but these showed a base composition (G + C content) very different from their counterparts from cultivated bacteria...
2016: PeerJ
David Hibbett, Kessy Abarenkov, Urmas Koljalg, Maarja Opik, Benli Chai, James R Cole, Qiong Wang, Pedro W Crous, Vincent A R G Robert, Thorunn Helgason, Josh Herr, Paul Kirk, Shiloh Lueschow, Kerry O'Donnell, Henrik Nilsson, Ryoko Oono, Conrad L Schoch, Christopher Smyth, Donny Walker, Andrea Porras-Alfaro, John W Taylor, David M Geiser
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes...
October 19, 2016: Mycologia
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
Philippe Chouvarine, Lutz Wiehlmann, Patricia Moran Losada, David S DeLuca, Burkhard Tümmler
Ever-increasing affordability of next-generation sequencing makes whole-metagenome sequencing an attractive alternative to traditional 16S rDNA, RFLP, or culturing approaches for the analysis of microbiome samples. The advantage of whole-metagenome sequencing is that it allows direct inference of the metabolic capacity and physiological features of the studied metagenome without reliance on the knowledge of genotypes and phenotypes of the members of the bacterial community. It also makes it possible to overcome problems of 16S rDNA sequencing, such as unknown copy number of the 16S gene and lack of sufficient sequence similarity of the "universal" 16S primers to some of the target 16S genes...
2016: PloS One
Katherine A Dunn, Jessica Moore-Connors, Brad MacIntyre, Andrew Stadnyk, Nikhil A Thomas, Angela Noble, Gamal Mahdi, Mohsin Rashid, Anthony R Otley, Joseph P Bielawski, Johan Van Limbergen
BACKGROUND: Exclusive enteral nutrition (EEN) is a first-line therapy in pediatric Crohn's disease (CD) thought to induce remission through changes in the gut microbiome. With microbiome assessment largely focused on microbial taxonomy and diversity, it remains unclear to what extent EEN induces functional changes that thereby contribute to its therapeutic effect. METHODS: Fecal samples were collected from 15 pediatric CD patients prior to and after EEN treatment, as well as from 5 healthy controls...
November 2016: Inflammatory Bowel Diseases
Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
Lada E Petrovskaya, Ksenia A Novototskaya-Vlasova, Sultan Sh Gapizov, Elena V Spirina, Ekaterina V Durdenko, Elizaveta M Rivkina
Siberian permafrost is a unique environment inhabited with diverse groups of microorganisms. Among them, there are numerous producers of biotechnologically relevant enzymes including lipases and esterases. Recently, we have constructed a metagenomic library from a permafrost sample and identified in it several genes coding for potential lipolytic enzymes. In the current work, properties of the recombinant esterases obtained from this library are compared with the previously characterized lipase from Psychrobacter cryohalolentis and other representatives of the hormone-sensitive lipase family...
October 18, 2016: Bioengineered
Jianhua Yang, Anna Joëlle Ruff, Stefanie Nicole Hamer, Feng Cheng, Ulrich Schwaneberg
Escherichia coli is a common host for recombinant protein production in which production titers are highly dependent on the employed expression system. Promoters are thereby a key element to control gene expression levels. In this study, a novel PLICable promoter toolbox was developed which enables in a single cloning step and after a screening experiment to identify out of ten IPTG-inducible promoters (T7, A3, lpp, tac, pac, Sp6, lac, npr, trc and syn) the most suitable one for high level protein production...
October 18, 2016: Biotechnology Journal
Ahmed Abdelfattah, Santa O Cacciola, Saveria Mosca, Rocco Zappia, Leonardo Schena
Citrus greasy spot (CGS) is a disease of citrus with worldwide distribution and recent surveys have revealed a high level of incidence and severity of symptoms of the disease in Sicily, southern Italy. Although Mycosphaerel la citri (anamorph Zasmidium citri-griseum) and other related species are generally considered as causal agents, the etiology of CGS is still unclear. Here, we report the use of an amplicon metagenomic approach to investigate the fungal communities on citrus leaves symptomatic or asymptomatic for CGS from an orchard in Sicily showing typical CGS symptoms...
October 18, 2016: Microbial Ecology
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