Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    ReDU: a framework to find and reanalyze public mass spectrometry data
    Jarmusch, Alan K. ; Wang, Mingxun ; Aceves, Christine M. ; Advani, Rohit S. ; Aguirre, Shaden ; Aksenov, Alexander A. ; Aleti, Gajender ; Aron, Allegra T. ; Bauermeister, Anelize ; Bolleddu, Sanjana ; Bouslimani, Amina ; Caraballo Rodriguez, Andres Mauricio ; Chaar, Rama ; Coras, Roxana ; Elijah, Emmanuel O. ; Ernst, Madeleine ; Gauglitz, Julia M. ; Gentry, Emily C. ; Husband, Makhai ; Jarmusch, Scott A. ; Jones, Kenneth L. ; Kamenik, Zdenek ; Gouellec, Audrey Le; Lu, Aileen ; McCall, Laura Isobel ; McPhail, Kerry L. ; Meehan, Michael J. ; Melnik, Alexey V. ; Menezes, Riya C. ; Montoya Giraldo, Yessica Alejandra ; Nguyen, Ngoc Hung ; Nothias, Louis Felix ; Nothias-Esposito, Mélissa ; Panitchpakdi, Morgan ; Petras, Daniel ; Quinn, Robert A. ; Sikora, Nicole ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vrbanac, Alison ; Weldon, Kelly C. ; Knight, Rob ; Bandeira, Nuno ; Dorrestein, Pieter C. - \ 2020
    Nature Methods : techniques for life scientists and chemists 17 (2020)9. - ISSN 1548-7091 - p. 901 - 904.

    We present ReDU (https://redu.ucsd.edu/), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one’s own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.

    Mass spectrometry searches using MASST
    Wang, Mingxun ; Jarmusch, Alan K. ; Vargas, Fernando ; Aksenov, Alexander A. ; Gauglitz, Julia M. ; Weldon, Kelly ; Petras, Daniel ; Silva, Ricardo da; Quinn, Robert ; Melnik, Alexey V. ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Felix ; Aceves, Christine M. ; Panitchpakdi, Morgan ; Brown, Elizabeth ; Ottavio, Francesca Di; Sikora, Nicole ; Elijah, Emmanuel O. ; Labarta-Bajo, Lara ; Gentry, Emily C. ; Shalapour, Shabnam ; Kyle, Kathleen E. ; Puckett, Sara P. ; Watrous, Jeramie D. ; Carpenter, Carolina S. ; Bouslimani, Amina ; Ernst, Madeleine ; Swafford, Austin D. ; Zúñiga, Elina I. ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Loomba, Rohit ; Knight, Rob ; Bandeira, Nuno ; Dorrestein, Pieter C. - \ 2020
    Nature Biotechnology 38 (2020). - ISSN 1087-0156 - p. 23 - 26.
    Similar factors underlie tree abundance in forests in native and alien ranges
    Sande, Masha T. van der; Bruelheide, Helge ; Dawson, Wayne ; Dengler, Jürgen ; Essl, Franz ; Field, Richard ; Haider, Sylvia ; Kleunen, Mark van; Kreft, Holger ; Pagel, Joern ; Pergl, Jan ; Purschke, Oliver ; Pyšek, Petr ; Weigelt, Patrick ; Winter, Marten ; Attorre, Fabio ; Aubin, Isabelle ; Bergmeier, Erwin ; Chytrý, Milan ; Dainese, Matteo ; Sanctis, Michele De; Fagundez, Jaime ; Golub, Valentin ; Guerin, Greg R. ; Gutiérrez, Alvaro G. ; Jandt, Ute ; Jansen, Florian ; Jiménez-Alfaro, Borja ; Kattge, Jens ; Kearsley, Elizabeth ; Klotz, Stefan ; Kramer, Koen ; Moretti, Marco ; Niinemets, Ülo ; Peet, Robert K. ; Penuelas, Josep ; Petřík, Petr ; Reich, Peter B. ; Sandel, Brody ; Schmidt, Marco ; Sibikova, Maria ; Violle, Cyrille ; Whitfeld, Timothy J.S. ; Wohlgemuth, Thomas ; Knight, Tiffany M. - \ 2020
    Global Ecology and Biogeography 29 (2020)2. - ISSN 1466-822X - p. 281 - 294.
    abundance - dissimilarity - forest - functional traits - global - plant invasion - trees

    Aim: Alien plant species can cause severe ecological and economic problems, and therefore attract a lot of research interest in biogeography and related fields. To identify potential future invasive species, we need to better understand the mechanisms underlying the abundances of invasive tree species in their new ranges, and whether these mechanisms differ between their native and alien ranges. Here, we test two hypotheses: that greater relative abundance is promoted by (a) functional difference from locally co-occurring trees, and (b) higher values than locally co-occurring trees for traits linked to competitive ability. Location: Global. Time period: Recent. Major taxa studied: Trees. Methods: We combined three global plant databases: sPlot vegetation-plot database, TRY plant trait database and Global Naturalized Alien Flora (GloNAF) database. We used a hierarchical Bayesian linear regression model to assess the factors associated with variation in local abundance, and how these relationships vary between native and alien ranges and depend on species’ traits. Results: In both ranges, species reach highest abundance if they are functionally similar to co-occurring species, yet are taller and have higher seed mass and wood density than co-occurring species. Main conclusions: Our results suggest that light limitation leads to strong environmental and biotic filtering, and that it is advantageous to be taller and have denser wood. The striking similarities in abundance between native and alien ranges imply that information from tree species’ native ranges can be used to predict in which habitats introduced species may become dominant.

    Current climate, isolation and history drive global patterns of tree phylogenetic endemism
    Sandel, Brody ; Weigelt, Patrick ; Kreft, Holger ; Keppel, Gunnar ; Sande, Masha T. van der; Levin, Sam ; Smith, Stephen ; Craven, Dylan ; Knight, Tiffany M. - \ 2020
    Global Ecology and Biogeography 29 (2020)1. - ISSN 1466-822X - p. 4 - 15.
    biogeography - climate stability - historical contingency - islands - isolation - phylogenetic endemism - trees

    Aim: We mapped global patterns of tree phylogenetic endemism (PE) to identify hotspots and test hypotheses about possible drivers. Specifically, we tested hypotheses related to current climate, geographical characteristics and historical conditions and assessed their relative importance in shaping PE patterns. Location: Global. Time period: We used the present distribution of trees, and predictors covering conditions from the mid-Miocene to present. Major taxa studied: All seed-bearing trees. Methods: We compiled distributions for 58,542 tree species across 463 regions worldwide, matched these to a recent phylogeny of seed plants and calculated PE for each region. We used a suite of predictor variables describing current climate (e.g., mean annual temperature), geographical characteristics (e.g., isolation) and historical conditions (e.g., tree cover at the Last Glacial Maximum) in a spatial regression model to explain variation in PE. Results: Tree PE was highest on islands, and was higher closer to the equator. All three groups of predictor variables contributed substantially to the PE pattern. Isolation and topographic heterogeneity promoted high PE, as did high current tree cover. Among mainland regions, temperature seasonality was strongly negatively related to PE, while mean annual temperature was positively related to PE on islands. Some relationships differed among the major floristic regions. For example, tree cover at the Last Glacial Maximum was a positive predictor of PE in the Palaeotropics, while tree cover at the Miocene was a negative predictor of PE in the Neotropics. Main conclusions: Globally, PE can be explained by a combination of geographical, historical and current factors. Some geographical variables appear to be key predictors of PE. However, the impact of historic and current climate variables differs considerably among the major floristic regions, reflecting their unique histories. Hence, the current distribution of trees is the result of globally relevant geographical drivers and regional climatic histories.

    Data from: Current climate, isolation and history drive global patterns of tree phylogenetic endemism
    Sandel, Brody ; Weigelt, Patrick ; Kreft, Holger ; Keppel, Gunnar ; Sande, Masha van der; Levin, Sam ; Smith, Stephen ; Craven, Dylan ; Knight, Tiffany M. - \ 2019
    Dryad
    trees - endemism - Biogeography - historical contingency - phylogenetic endemism - isolation - islands - current - species richness - climate stability
    Aim: We mapped global patterns of tree phylogenetic endemism (PE) to identify hotspots and test hypotheses about possible drivers. Specifically, we tested hypotheses related to current climate, geographical characteristics and historical conditions, and assessed their relative importance in shaping PE patterns. Location: Global. Time period: We used the present distribution of trees, and predictors covering conditions from the mid-Miocene to present. Major taxa studied: All seed-bearing trees. Methods: We compiled distributions for 58,542 tree species across 463 regions worldwide, matched these to a recent phylogeny of seed plants, and calculated PE for each region. We used a suite of predictor variables describing current climate (e.g. mean annual temperature), geographical characteristics (e.g. isolation) and historical conditions (e.g. tree cover at the last glacial maximum) in a spatial regression model to explain variation in PE. Results: Tree PE was highest on islands, and was higher closer to the equator. All three groups of predictor variables contributed substantially to the PE pattern. Isolation and topographic heterogeneity promoted high PE, as did high current tree cover. Among mainland regions, temperature seasonality was strongly negatively related to PE, while mean annual temperature was positively related to PE on islands. Some relationships differed among the major floristic regions. For example, tree cover at the last glacial maximum was a positive predictor of PE in the Paleotropics, while tree cover at the Miocene was a negative predictor of PE in the Neotropics. Main conclusions: Globally, PE can be explained by a combination of geographic, historical, and current factors. Some geographic variables appear to be key predictors of PE. However, the impact of historic and current climate variables differs considerably among the major floristic regions, reflecting their unique histories. Hence, the current distribution of trees is the result of globally relevant geographic drivers and regional climatic histories.
    Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology (2019). - ISSN 1087-0156

    In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

    Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
    Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis
    Lees, John A. ; Ferwerda, Bart ; Kremer, Philip H.C. ; Wheeler, Nicole E. ; Valls Serón, Mercedes ; Croucher, Nicholas J. ; Gladstone, Rebecca A. ; Bootsma, Hester J. ; Rots, Nynke Y. ; Wijmega-Monsuur, Alienke J. ; Sanders, Elisabeth A.M. ; Trzciński, Krzysztof ; Wyllie, Anne L. ; Zwinderman, Aeilko H. ; Berg, Leonard H. van den; Rheenen, Wouter van; Veldink, Jan H. ; Harboe, Zitta B. ; Lundbo, Lene F. ; Groot, Lisette C.P.G.M. de; Schoor, Natasja M. van; Velde, Nathalie van der; Ängquist, Lars H. ; Sørensen, Thorkild I.A. ; Nohr, Ellen A. ; Mentzer, Alexander J. ; Mills, Tara C. ; Knight, Julian C. ; Plessis, Mignon du; Nzenze, Susan ; Weiser, Jeffrey N. ; Parkhill, Julian ; Madhi, Shabir ; Benfield, Thomas ; Gottberg, Anne von; Ende, Arie van der; Brouwer, Matthijs C. ; Barrett, Jeffrey C. ; Bentley, Stephen D. ; Beek, Diederik van de - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723 - 14 p.

    Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.

    What agricultural practices are most likely to deliver “sustainable intensification” in the UK?
    Dicks, Lynn V. ; Rose, David C. ; Ang, Frederic ; Aston, Stephen ; Birch, A.N.E. ; Boatman, Nigel ; Bowles, Elizabeth L. ; Chadwick, David ; Dinsdale, Alex ; Durham, Sam ; Elliott, John ; Firbank, Les ; Humphreys, Stephen ; Jarvis, Phil ; Jones, Dewi ; Kindred, Daniel ; Knight, Stuart M. ; Lee, Michael R.F. ; Leifert, Carlo ; Lobley, Matt ; Matthews, Kim ; Midmer, Alice ; Moore, Mark ; Morris, Carol ; Mortimer, Simon ; Murray, T.C. ; Norman, Keith ; Ramsden, Stephen ; Roberts, Dave ; Smith, Laurence G. ; Soffe, Richard ; Stoate, Chris ; Taylor, Bryony ; Tinker, David ; Topliff, Mark ; Wallace, John ; Williams, Prysor ; Wilson, Paul ; Winter, Michael ; Sutherland, William J. - \ 2019
    Food and Energy Security 8 (2019)1. - ISSN 2048-3694

    Sustainable intensification is a process by which agricultural productivity is enhanced whilst also creating environmental and social benefits. We aimed to identify practices likely to deliver sustainable intensification, currently available for UK farms but not yet widely adopted. We compiled a list of 18 farm management practices with the greatest potential to deliver sustainable intensification in the UK, following a well-developed stepwise methodology for identifying priority solutions, using a group decision-making technique with key agricultural experts. The list of priority management practices can provide the focal point of efforts to achieve sustainable intensification of agriculture, as the UK develops post-Brexit agricultural policy, and pursues the second Sustainable Development Goal, which aims to end hunger and promote sustainable agriculture. The practices largely reflect a technological, production-focused view of sustainable intensification, including for example, precision farming and animal health diagnostics, with less emphasis on the social and environmental aspects of sustainability. However, they do reflect an integrated approach to farming, covering many different aspects, from business organization and planning, to soil and crop management, to landscape and nature conservation. For a subset of 10 of the priority practices, we gathered data on the level of existing uptake in English and Welsh farms through a stratified survey in seven focal regions. We find substantial existing uptake of most of the priority practices, indicating that UK farming is an innovative sector. The data identify two specific practices for which uptake is relatively low, but which some UK farmers find appealing and would consider adopting. These practices are: prediction of pest and disease outbreaks, especially for livestock farms; staff training on environmental issues, especially on arable farms.

    Erratum to: The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
    GigaScience 7 (2018)12. - ISSN 2047-217X
    Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition
    Cochran, Alyssa T. ; Bauer, Jemma ; Metcalf, Jessica L. ; Lovecka, Petra ; Jong, Martina S. de; Warris, S. ; Mooijman, P.J.W. ; Meer, I.M. van der; Knight, Rob ; Pilon-Smits, E.A.H. - \ 2018
    Phytobiomes Journal 2 (2018)2. - ISSN 2471-2906 - p. 82 - 91.
    Little is known about the microbiomes associated with plants with unusual properties, including plants that hyperaccumulate toxic elements such as selenium (Se). Se hyperaccumulators contain up to 1.5% of their dry weight in Se, concentrations shown to affect ecological interactions with herbivores, fungal pathogens and neighboring plants. Hyperaccumulators also enrich their surrounding soil with Se, which may alter the rhizobiome. To investigate whether plant Se affects rhizobacterial diversity and composition, we used a combination of culture-independent and culture-based approaches. Sequencing of 16S rRNA gene amplicons using the Illumina platform revealed that the rhizosphere microbiomes of Se hyperaccumulators were significantly different from nonaccumulators from the same site, with a higher average relative abundance of Pedobacter and Deviosa. Additionally, hyperaccumulators harbored a higher rhizobacterial species richness when compared with nonaccumulators from the same family on the same site. Independent from Se present at the site or in the host plant, the bacterial isolates were extremely resistant to selenate and selenite (up to 200 mM) and could reduce selenite to elemental Se. In conclusion, Se hyperaccumulation does not appear to negatively affect rhizobacterial diversity, and may select for certain taxa in the rhizosphere microbiome. Additionally, Se resistance in hyperaccumulator-associated bacteria and archaea may be widespread and not under selection by the host plant.
    Publisher Correction : Enterotypes in the landscape of gut microbial community composition
    Costea, Paul I. ; Hildebrand, Falk ; Arumugam, Manimozhiyan ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O’Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2018
    Nature Microbiology 3 (2018). - ISSN 2058-5276
    In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.
    Detecting macroecological patterns in bacterial communities across independent studies of global soils
    Ramirez, Kelly S. ; Knight, Christopher G. ; Hollander, Mattias de; Brearley, Francis Q. ; Constantinides, Bede ; Cotton, Anne ; Creer, Si ; Crowther, Thomas W. ; Davison, John ; Delgado-Baquerizo, Manuel ; Dorrepaal, Ellen ; Elliott, David R. ; Fox, Graeme ; Griffiths, Robert I. ; Hale, Chris ; Hartman, Kyle ; Houlden, Ashley ; Jones, David L. ; Krab, Eveline J. ; Maestre, Fernando T. ; McGuire, Krista L. ; Monteux, Sylvain ; Orr, Caroline H. ; Putten, Wim H. van der; Roberts, Ian S. ; Robinson, David A. ; Rocca, Jennifer D. ; Rowntree, Jennifer ; Schlaeppi, Klaus ; Shepherd, Matthew ; Singh, Brajesh K. ; Straathof, Angela L. ; Bhatnagar, Jennifer M. ; Thion, Cécile ; Heijden, Marcel G.A. van der; Vries, Franciska T. de - \ 2018
    Nature Microbiology 3 (2018). - ISSN 2058-5276 - p. 189 - 196.
    The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
    Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
    Bowers, Robert M. ; Kyrpides, Nikos C. ; Stepanauskas, Ramunas ; Harmon-Smith, Miranda ; Doud, Devin ; Reddy, T.B.K. ; Schulz, Frederik ; Jarett, Jessica ; Rivers, Adam R. ; Eloe-Fadrosh, Emiley A. ; Tringe, Susannah G. ; Ivanova, Natalia N. ; Copeland, Alex ; Clum, Alicia ; Becraft, Eric D. ; Malmstrom, Rex R. ; Birren, Bruce ; Podar, Mircea ; Bork, Peer ; Weinstock, George M. ; Garrity, George M. ; Dodsworth, Jeremy A. ; Yooseph, Shibu ; Sutton, Granger ; Glöckner, Frank O. ; Gilbert, Jack A. ; Nelson, William C. ; Hallam, Steven J. ; Jungbluth, Sean P. ; Ettema, Thijs J.G. ; Tighe, Scott ; Konstantinidis, Konstantinos T. ; Liu, Wen Tso ; Baker, Brett J. ; Rattei, Thomas ; Eisen, Jonathan A. ; Hedlund, Brian ; McMahon, Katherine D. ; Fierer, Noah ; Knight, Rob ; Finn, Rob ; Cochrane, Guy ; Karsch-Mizrachi, Ilene ; Tyson, Gene W. ; Rinke, Christian ; Lapidus, Alla ; Meyer, Folker ; Yilmaz, Pelin ; Parks, Donovan H. ; Eren, A.M. - \ 2017
    Nature Biotechnology 35 (2017)8. - ISSN 1087-0156 - p. 725 - 731.

    We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

    Softly, softly, mosquitoes outwit human victims
    Muijres, F.T. - \ 2017
    Enterotypes in the landscape of gut microbial community composition
    Costea, Paul I. ; Hildebrand, Falk ; Manimozhiyan, Arumugam ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O'Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2017
    Nature Microbiology 3 (2017)1. - ISSN 2058-5276 - p. 8 - 16.
    Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
    The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
    GigaScience 6 (2017)10. - ISSN 2047-217X
    16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
    Lactational oestrus and reproductive performance following a delayed limited nursing schedule in primiparous sows
    Chen, T.Y. ; Turpin, D.L. ; Knight, A.L. ; Bouwman, E.G. ; Soede, N.M. ; Kirkwood, R.N. ; Langendijk, P. - \ 2017
    Theriogenology 96 (2017). - ISSN 0093-691X - p. 42 - 48.
    Follicle - Lactation - Ovulation - Primiparous sow - Progesterone

    With conventional lactation management, sows only conceive after weaning. However, intermittent suckling (IS) enables follicle growth and ovulation during lactation by reducing the suckling-induced inhibition of gonadotrophins. The current study evaluated IS regimes initiated at Day 21 or Day 28 post farrowing compared to conventional weaning on Day 28, in primiparous sows. Sows (Large White and Large White x Landrace) were randomly allocated to Control (C28; n = 44), IS21 (n = 29) and IS28 (n = 34) treatments at Day 20. Sows in IS21 and IS28 were subjected to intermittent suckling from Day 21 or Day 28 post farrowing. During IS, sows were separated from their piglets for 8 h daily, then weaned 7 d later at Day 28 and Day 35 respectively, whereas piglets in the C28 treatment had continuous access to sows until weaning at Day 28. Percentage of IS sows that showed oestrus during lactation was 59% (16/27) in IS21 and 72% (21/29) in IS28 (P > 0.05). Cumulatively over the lactation and 7 d post-weaning period, 93% of IS21, 85% of IS28 and 93% (31/33) of C28 sows showed oestrus (P > 0.05). Pregnancy rate at Day 30 post mating, for sows that were mated during lactation was 93% (15/16) in IS21 and 95% (20/21) in IS28, whereas C28 sows had a 96% (30/31) pregnancy rate (P > 0.05). No difference was found in the time of oestrus relative to weaning (C28) or onset of IS (IS21 and IS28) (P > 0.05). The IS sows that did not ovulate before weaning all showed oestrus within 7 days from weaning, and the weaning to oestrus interval was similar to control sows (P > 0.05). However, for all IS sows (across IS treatments) that showed lactational ovulation, LH secretion pattern at onset of IS was different (P < 0.05) from the sows that did not ovulate in lactation. Plasma progesterone concentration tended to be lower in the IS21 treatment (P < 0.10) compared to the C28 sows at 4 d after ovulation. The subsequent litter size was not affected by treatments although numerically lower for IS21 (P > 0.05). The present study showed that in modern primiparous sows, lactational oestrus can be induced and pregnancy can be maintained at a similar rate and producing comparable subsequent litter sizes to conventionally weaned sows when IS commenced at four weeks post farrowing. However, when IS commences at three weeks post farrowing, this may affect the percentage of sows showing oestrus in lactation and may potentially influence subsequent litter size.

    Predicting bee community responses to land-use changes : Effects of geographic and taxonomic biases
    Palma, Adriana De; Abrahamczyk, Stefan ; Aizen, Marcelo A. ; Albrecht, Matthias ; Basset, Yves ; Bates, Adam ; Blake, Robin J. ; Boutin, Céline ; Bugter, Rob ; Connop, Stuart ; Cruz-López, Leopoldo ; Cunningham, Saul A. ; Darvill, Ben ; Diekötter, Tim ; Dorn, Silvia ; Downing, Nicola ; Entling, Martin H. ; Farwig, Nina ; Felicioli, Antonio ; Fonte, Steven J. ; Fowler, Robert ; Franzén, Markus ; Goulson, Dave ; Grass, Ingo ; Hanley, Mick E. ; Hendrix, Stephen D. ; Herrmann, Farina ; Herzog, Felix ; Holzschuh, Andrea ; Jauker, Birgit ; Kessler, Michael ; Knight, M.E. ; Kruess, Andreas ; Lavelle, Patrick ; Féon, Violette Le; Lentini, Pia ; Malone, Louise A. ; Marshall, Jon ; Pachón, Eliana Martínez ; McFrederick, Quinn S. ; Morales, Carolina L. ; Mudri-Stojnic, Sonja ; Nates-Parra, Guiomar ; Nilsson, Sven G. ; Öckinger, Erik ; Osgathorpe, Lynne ; Parra-H, Alejandro ; Peres, Carlos A. ; Persson, Anna S. ; Petanidou, Theodora ; Poveda, Katja ; Power, Eileen F. ; Quaranta, Marino ; Quintero, Carolina ; Rader, Romina ; Richards, Miriam H. ; Roulston, Tai ; Rousseau, Laurent ; Sadler, Jonathan P. ; Samnegård, Ulrika ; Schellhorn, Nancy A. ; Schüepp, Christof ; Schweiger, Oliver ; Smith-Pardo, Allan H. ; Steffan-Dewenter, Ingolf ; Stout, Jane C. ; Tonietto, Rebecca K. ; Tscharntke, Teja ; Tylianakis, Jason M. ; Verboven, Hans A.F. ; Vergara, Carlos H. ; Verhulst, Jort ; Westphal, Catrin ; Yoon, Hyung Joo ; Purvis, Andy - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322 - 14 p.

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

    Assessing resilience of dairy cattle by studying impact of heat stress on predicted feed intake
    Vanrobays, M.L. ; Hammami, Hedi ; laine, Aurelie ; Soyeurt, Hélène ; Vandenplas, J. ; Froidmont, E. ; Gengler, Nicolas - \ 2015
    In: Feeding behaviour as an indicator of health and welfare. - DairyCare COST Action FA1308 - ISBN 9780993017629 - p. 49 - 49.
    Milk production and feed intake of dairy cows are both affected by heat stress (HS) which is also a potentially important cause of discomfort for animals. Therefore, strategies allowing mitigation of HS effects are required. Genetic selection appears to be a good solution because this tool permits to improve cumulatively and continuously traits of interest. In this context, the goal of this study was to estimate genetic variation of milk yield and predicted feed intake over the whole trajectory of temperature humidity index (THI) using a reaction norm approach. A total of 30,161 fat and protein corrected milk (FPCM) yield records from 4,577 Holstein cows were used. These data were collected between June 2009 and December 2010 in 453 herds in the Walloon Region of Belgium. Daily dry matter intake (DMI; g/d) of dairy cows were estimated at the day of FPCM records from the prediction equation of NRC (2001), which is based on predicted body weight, FPCM, and week of lactation. Body weight of cows was estimated using a two-step approach allowing to predict body weight throughout the lactation from body weight calculated using linear conformation traits. Daily values of THI were computed from meteorological data using the mean of daily values of dry bulb temperature and relative humidity. Bivariate random regression test-day models with random linear regressions on THI values were developed for FPCM and DMI. Estimated average daily heritability for FCPM was 0.08 and decreased slightly at extreme THI values (from 0.10 (THI = 17) to 0.06 (THI =75)). Heritabilities of DMI also decreased with increasing THI values: from 0.11 (THI=17) to 0.05 (THI=75). Genetic correlations between FPCM and DMI were positive and ranged from 0.85 (THI=17) to 0.55 (THI=75). This decrease could be explained by the decrease of DMI under HS which could be balanced by the buffering effect of body tissue mobilization. Combining these novel results with known effects of HS on body fat mobilization might help to disentangle complex relationships between mobilization and intake under HS; this being also an important issue in assessing well-being of dairy cattle and their resilience potential to HS.
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