A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Effects of gamma radiation on suitability of stored cereal pest eggs and the reproductive capability of the egg parasitoid Trichogramma evanescens (Trichogrammatidae: Hymenoptera)

A study was conducted to determine parasitization suitability and preference of irradiated and untreated eggs of the Mediterranean flour moth (MFM), Ephestia kuehniella Zeller, and the Angoumois grain moth (AGM), Sitotroga cerealella (Olivier) for mass-production and augmentative releases of T. evanescens Westwood in cereal storage and processing facilities. Eggs of both species irradiated with 200 Gy could be effectively used for propagation of T. evanescens in the sterilized host eggs. The irradiated host eggs of E. kuehniella were markedly preferred over eggs of S. cerealella. A dose of 200 and 150 Gy prevented adult emergence of E. kuehniella and S. cerealella, respectively. Treatment of immature stages of the parasitoid inside the host eggs or treatment of adults of T. evanescens with low-level doses (ranging between 0 and 140 Gy) resulted in significant reduction in the number of parasitized eggs, adult emergence and progeny production (F-1) as radiation dose increased. Our study showed that MFM and AGM eggs killed by gamma radiation could be used for the rearing and release of T. evanescens into commodity storages without any risk of increasing the pest population

The protective role of melatonin in experimental hypoxic brain damage

Background: It is known that oxygen-derived free radicals play an important role in the pathogenesis of brain injury. Melatonin is a powerful scavenger of the oxygen free radicals. In this study, the protective effect of melatonin against the damage inflicted by reactive oxygen species during brain hypoxia was investigated in newborn rats using biochemical parameters

The potential of near and mid-infrared spectroscopy for rapid quantification of oleuropein, total phenolics, total flavonoids and antioxidant activity in olive tree (Olea europaea) leaves

Natural foods and food-related antioxidants such as phenolic phytochemicals are of great interest due to their preventive properties against oxidative damage. Olive tree leaves contain high quality and amount of phenolic compounds including oleuropein and therefore considered as nutraceutically valuable materials. The composition of olive leaves, its phenolics and antioxidant power are influenced by numerous factors causing great variation among samples. Additionally, traditionalanalytical methods performed to quantify these parameters in each product entail long and complicated sample preparation procedures, the use of toxic chemicals, skilled labors, instrumentation and sophisticated laboratory conditions. One appealing alternative is the use of infrared spectroscopy since it gives information about the food composition quickly and it is amulti-parametric and environmentally friendly choice. Therefore, we investigated the oleuropein, total phenolic content, total flavonoid content and antioxidant activity levels of 23 common cultivars of olive leaves harvested from Turkey and Italy using traditional reference methods and also developed near and mid-infrared based partial least squares regression (PLSR) models to predict these parameters without the need of sample preparation. Internal validations of the PLSR calibration models were done using full cross-validation and yielded very high correlation coefficients (≥ 0.95) and low errors in predictions (% standard error of cross-validation for parameters were lower than 7.54%). The levels of all the parameters of interest could be successfully predicted using both NIR and MIR instrumentation within seconds. Overall, infrared spectroscopy along with chemometrics exhibited great potential for future olive leave studies

Determination of rainfall-runoff relationship in Yenicegoruce Basin with

The goal of this study is to model rainfall-runoff process using HEC-HMS developed by U.S. Army Corps of Engineers for the 10,508 km(2) catchment that has E01A012-Yenicegoruce stream gage at its outlet which is located just at the upstream of the point where Meric and Ergene Rivers meet. This study is conducted as a part of 115Y064 numbered "Development of a geographical information systems based decision-making tool for water quality management of Ergene watershed using pollutant fingerprints" project funded by TUBITAK. First, meteorological parameters such as daily precipitation and temperature, and daily streamflow data that are observed in and around the study catchment are collected. Then land use, hydrologic soil groups and digital elevation data of the catchment are collected and integrated into Geographic Information System (GIS) environment. Digital maps compiled in GIS environment were transferred into WMS for the calculation of basin parameters, and then the hydrological model for the basin is developed in HEC-HMS using these data. The model is calibrated using daily streamflow values of 1997-2002 and validated for 2003-2005 data. The model results obtained at the Yenicegoruce stream gage has Nash-Sutcliffe Efficiency (NSE) values of 0.8 and 0.75 for calibration and validation, respectively. Hydrological models for Hayrabolu, Luleburgaz and Inanli sub-catchments represented by stream gages D01A008, E01A006 and E01A012, respectively are developed and calibrated as well. Model performances are evaluated using statistical measures such as NSE values and correlations.C1 [Mesta, Buket] Orta Dogu Tekn Univ, Fen Bilimleri Enstitusu, Yer Sistem Bilimleri, Ankara, Turkey.[Kargi, Pinar Gokce; Ayvaz, M. Tamer] Pamukkale Univ, Muhendislik Fak, Insaat Muhendisligi Bolumu, Denizli, Turkey.[Tezyapar, Ipek; Goktas, Recep Kaya] Kocaeli Univ, Muhendislik Fak, Cevre Muhendisligi Bolumu, Kocaeli, Turkey.[Kentel, Elcin] Orta Dogu Tekn Univ Univ, Muhendislik Fak, Insaat Muhendisligi Bolumu, Ankara, Turkey.[Tezel, Ulas] Bogazici Univ, Cevre Muhendisligi Bolumu, Cevre Bilimleri Enstitusu, Istanbul, Turkey

Antidiabetic potential and multi-biological activities of Trachystemon orientalis extracts

yalcin, emine/0000-0002-5280-5375WOS: 000493661900039Due to the increase in exposure to chemical substances, the investigation of natural compounds with protective effects has become popular. So in this study the antimicrobial, antioxidant, antimutagenic activities and enzyme inhibitory effects of Trachystemon orientalis leaf and stem extracts were investigated. Antimicrobial effect was determined by disc diffusion method and the antimutagenic effect was investigated by Ames/Salmonella/microsomal test. Antioxidant properties of T. orientalis extracts were determined by investigating the phytochemical contents and 2,2-diphenyl-1-picrylhydrazyl (DPPH) removal activity. The antidiabetic activity of the extracts was investigated by alpha-amylase and alpha-glucosidase enzyme inhibition. It has been determined that all extracts exhibit antimicrobial activity at different ratios and the highest antimicrobial activity was obtained with a 21 +/- 0.4 mm inhibition zone against Escherichia coli. The highest DPPH removal activity of leaf and stem extracts was determined to be 65.1 +/- 2.4% and 59.4 +/- 2.7%, respectively. In enzyme inhibitory analysis, it was determined that the alpha-glucosidase inhibitory effect of extracts was higher than the alpha-amylase inhibition effect. In antimutagenity test, the highest antimutagenic effects of leaf and stem extract were determined as 78.2 +/- 1.1% and 67.2 +/- 1.5%, respectively. As a result, T. orientalis leaf and stem extracts were determined as a potential natural antimicrobial, antimutagenic and antioxidant source with a moderately high antidiabetic activity