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4. The Development of a Forensic Intellectual Disability Model of Care: Synergy to Achieve Equity.

Author

Duff, M., Paki, W., Butler, R., McSweeney, C., and McKenna, B.

Abstract

There is a relative lack of research focused on people with intellectual disabilities within forensic settings and limited information describing models of care. This article describes the process of enquiry and information gathering that was synthesized to develop a specific model of care for a specialist forensic intellectual disability secure care unit within a forensic mental health service in Aotearoa (New Zealand). The obligations to address the over representation of tāngata whenua (Māori; Indigenous people of Aotearoa) and to resist the dominant Western and mental health paradigms being ineffectively imposed within this specialist service, were acknowledged as central challenges. A literature review, consultation with tāngata whaikaha hinengaro (service users) and Māori cultural input provided a platform to synthesize diverse perspectives. This resulted in the weaving together of the important elements necessary in a model of care, to optimize specialist forensic intellectual disability care and rehabilitation in Aotearoa. This article has an emphasis on the research literature, but is not a research project, rather it is a description of the process leading to a negotiated model of care to achieve equity. [ABSTRACT FROM AUTHOR]

Published
2023
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7. Revisiting observed trends in the jet streams and their link to tropical warming

Author

Woollings, T., Drouard, M., O'Reilly, C., Sexton, D., and McSweeney, C.

Abstract

We revisit observed zonal wind trends using 40 years of satellite-era reanalysis products and find evidence that general poleward shifts are emerging, often with low significance but notable similarity across different seasons and hemispheres. While much recent work has focused on the jet response to amplified Arctic warming, the observed trends are more consistent with the known sensitivity of the circulation to tropical warming. The circulation trends are within the range of historical model simulations but are relatively large compared to the models when the accompanying trends in upper tropospheric temperature gradients are considered. The balance between tropical warming and jet shifts should therefore be closely monitored in the near future. We also present a new hypothesis concerning the sensitivity of the circulation response to tropical heating which may be one factor affecting this balance., The 28th IUGG General Assembly (IUGG2023) (Berlin 2023)

Published
2023
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17. A genomic catalog of Earth’s microbiomes

Author

Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T., Nielsen, T., Kirton, E., Faria, J., Edirisinghe, J., Henry, C., Jungbluth, S., Chivian, D., Dehal, P., Wood-Charlson, E., Arkin, A., Tringe, S., Visel, A., Abreu, H., Acinas, S., Allen, E., Allen, M., Alteio, L., Andersen, G., Anesio, A., Attwood, G., Avila-Magaña, V., Badis, Y., Bailey, J., Baker, B., Baldrian, P., Barton, H., Beck, D., Becraft, E., Beller, H., Beman, J., Bernier-Latmani, R., Berry, T., Bertagnolli, A., Bertilsson, S., Bhatnagar, J., Bird, J., Blanchard, J., Blumer-Schuette, S., Bohannan, B., Borton, M., Brady, A., Brawley, S., Brodie, J., Brown, S., Brum, J., Brune, A., Bryant, D., Buchan, A., Buckley, D., Buongiorno, J., Cadillo-Quiroz, H., Caffrey, S., Campbell, A., Campbell, B., Carr, S., Carroll, J., Cary, S., Cates, A., Cattolico, R., Cavicchioli, R., Chistoserdova, L., Coleman, M., Constant, P., Conway, J., Mac Cormack, W., Crowe, S., Crump, B., Currie, C., Daly, R., DeAngelis, K., Denef, V., Denman, S., Desta, A., Dionisi, H., Dodsworth, J., Dombrowski, N., Donohue, T., Dopson, M., Driscoll, T., Dunfield, P., Dupont, C., Dynarski, K., Edgcomb, V., Edwards, E., Elshahed, M., Figueroa, I., Flood, B., Fortney, N., Fortunato, C., Francis, C., Gachon, C., Garcia, S., Gazitua, M., Gentry, T., Gerwick, L., Gharechahi, J., Girguis, P., Gladden, J., Gradoville, M., Grasby, S., Gravuer, K., Grettenberger, C., Gruninger, R., Guo, J., Habteselassie, M., Hallam, S., Hatzenpichler, R., Hausmann, B., Hazen, T., Hedlund, B., Henny, C., Herfort, L., Hernandez, M., Hershey, O., Hess, M., Hollister, E., Hug, L., Hunt, D., Jansson, J., Jarett, J., Kadnikov, V., Kelly, C., Kelly, R., Kelly, W., Kerfeld, C., Kimbrel, J., Klassen, J., Konstantinidis, K., Lee, L., Li, W., Loder, A., Loy, A., Lozada, M., MacGregor, B., Magnabosco, C., Maria da Silva, A., McKay, R., McMahon, K., McSweeney, C., Medina, M., Meredith, L., Mizzi, J., Mock, T., Momper, L., Moran, M., Morgan-Lang, C., Moser, D., Muyzer, G., Myrold, D., Nash, M., Nesbø, C., Neumann, A., Neumann, R., Noguera, D., Northen, T., Norton, J., Nowinski, B., Nüsslein, K., O’Malley, M., Oliveira, R., Maia de Oliveira, V., Onstott, T., Osvatic, J., Ouyang, Y., Pachiadaki, M., Parnell, J., Partida-Martinez, L., Peay, K., Pelletier, D., Peng, X., Pester, M., Pett-Ridge, J., Peura, S., Pjevac, P., Plominsky, A., Poehlein, A., Pope, P., Ravin, N., Redmond, M., Reiss, R., Rich, V., Rinke, C., Rodrigues, J., Rodriguez-Reillo, W., Rossmassler, K., Sackett, J., Salekdeh, G., Saleska, S., Scarborough, M., Schachtman, D., Schadt, C., Schrenk, M., Sczyrba, A., Sengupta, A., Setubal, J., Shade, A., Sharp, C., Sherman, D., Shubenkova, O., Sierra-Garcia, I., Simister, R., Simon, H., Sjöling, S., Slonczewski, J., Correa de Souza, R., Spear, J., Stegen, J., Stepanauskas, R., Stewart, F., Suen, G., Sullivan, M., Sumner, D., Swan, B., Swingley, W., Tarn, J., Taylor, G., Teeling, H., Tekere, M., Teske, A., Thomas, T., Thrash, C., Tiedje, J., Ting, C., Tully, B., Tyson, G., Ulloa, O., Valentine, D., Van Goethem, M., VanderGheynst, J., Verbeke, T., Vollmers, J., Vuillemin, A., Waldo, N., Walsh, D., Weimer, B., Whitman, T., van der Wielen, P., Wilkins, M., Williams, T., Woodcroft, B., Woolet, J., Wrighton, K., Ye, J., Young, E., Youssef, N., Yu, F., Zemskaya, T., Ziels, R., Woyke, T., Mouncey, N., Ivanova, N., Kyrpides, N., Eloe-Fadrosh, E., Consortium, I., and Agencia Estatal de Investigación (España)

Subjects
Resource, Life sciences, biology, Biomedical Engineering, FILOGENIA, Bioengineering, Genomics, Biology, Microbiology, Applied Microbiology and Biotechnology, Genome, purl.org/becyt/ford/1 [https], 03 medical and health sciences, ddc:570, EARTH MICROBIOME PROJECT, Microbiome, purl.org/becyt/ford/1.6 [https], 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, Phylum, 15. Life on land, biology.organism_classification, Computational biology and bioinformatics, Phylogenetic diversity, Evolutionary biology, Earth Microbiome Project, Molecular Medicine, Evolutionary ecology, MAGS, GENOMICS, Biotechnology, Archaea, MICROBIAL DIVERSITY
Abstract

13 pages, 5 figures, supplementary information https://doi.org/10.1038/s41587-020-0718-6.-- Data availability: All available metagenomic data, bins and annotations are available through the IMG/M portal (https://img.jgi.doe.gov/). Bulk download for the 52,515 MAGs is available at https://genome.jgi.doe.gov/GEMs and https://portal.nersc.gov/GEM. Genome-scale metabolic models for the nonredundant, high-quality GEMs are summarized at https://doi.org/10.25982/53247.64/1670777 and available in KBase (https://narrative.kbase.us/#org/jgimags). IMG/M identifiers of all metagenomes binned, including detailed information for each metagenome, are available in Supplementary Table 1.-- The pipeline used to generate the metagenome bins is available at https://bitbucket.org/berkeleylab/metabat/src/master/, Publisher Correction: A genomic catalog of Earth’s microbiomes; Nature Biotechnology 39: 520 (2021); https://doi.org/10.1038/s41587-020-00769-4, The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes, This work was conducted by the US DOE Joint Genome Institute, a DOE Office of Science User Facility (contract no. DE-AC02–05CH11231), and used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US DOE (contract no. DE-AC02–05CH11231). This work was also supported as part of the Genomic Sciences Program DOE Systems Biology KBase (award nos. DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886).-- With the funding support of the ‘Severo Ochoa Centre of Excelle

Published
2020

40. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Author

Seshadri, R, Leahy, SC, Attwood, GT, Teh, KH, Lambie, SC, Cookson, AL, Eloe-Fadrosh, EA, Pavlopoulos, GA, Hadjithomas, M, Varghese, NJ, Paez-Espino, D, Perry, R, Henderson, G, Creevey, CJ, Terrapon, N, Lapebie, P, Drula, E, Lombard, V, Rubin, E, Kyrpides, NC, Henrissat, B, Woyke, T, Ivanova, NN, Kelly, WJ, Palevic, N, Janssen, PH, Ronimus, RS, Noel, S, Soni, P, Reilly, K, Atherly, T, Ziemer, C, Wright, AD, Ishaq, S, Cotta, M, Thompson, S, Crosley, K, McKain, N, Wallace, JJ, Flint, HJ, Martin, JC, Forster, RJ, Gruninger, RJ, McAllister, T, Gilbert, R, Ouwerkerk, DJ, Klieve, AJ, Jassim, RA, Denman, S, McSweeney, C, Rosewarne, C, Koike, S, Kobayashi, Y, Mitsumori, M, Shinkai, T, Cravero, S, and Cerón Cucchi, M

Subjects
animal structures, food and beverages
Abstract

© 2018 Nature Publishing Group. All rights reserved. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen.

Published
2018

46. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

Author

Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Janssen, P. H., Abecia, Leticia, Angarita, E., Aravena, P., Arenas, G. N., Ariza, C., Kelly, W. J., Guan, L. L., Miri, V. H., Hernandez-Sanabria, E., Gomez, A. X. I., Isah, O. A., Ishaq, S., Kim, S.-H., Klieve, A., Kobayashi, Y., Parra, D., Koike, S., Kopecny, J., Kristensen, T. N., O'Neill, B., Krizsan, S. J., LaChance, H., Lachman, M., Lamberson, W. R., Lambie, S., Lassen, J., Muñoz, C., Leahy, S. C., Lee, S. S., Leiber, F., Lewis, E., Ospina, S., Lin, B., Lira, R., Lund, P., Macipe, E., Mamuad, L. L., Murovec, B., Mantovani, H. C., Marcoppido, G. A., Márquez, C., Martin, C., Martínez-Fernández, Gonzalo, Ouwerkerk, D., Martínez, M. E., Mayorga, O. L., McAllister, T. A., McSweeney, C., Newbold, C. Jamie, Mestre, L., Minnee, E., Mitsumori, M., Mizrahi, I., Molina, I., Muenger, A., Nsereko, V., O'Donovan, M., Okunade, S., Pereira, L. G. R., Pinares-Patino, C., Pope, P. B., Bannink, A., Poulsen, M., Rodehutscord, M., Rodriguez, T., Attwood, G. T., Saito, K., Sales, F., Sauer, C., Shingfield, K. J., Shoji, N., Simunek, J., Zambrano, R., Stojanović -Radić, Z., Stres, B., Sun, X., Swartz, J., Ávila, J. M., Tan, Z. L., Tapio, I., Taxis, T. M., Tomkins, N., Ungerfeld, E., Zeitz, J., Valizadeh, R., Van Adrichem, P., van Hamme, J., Van Hoven, W., Waghorn, G., Avila-Stagno, J., Wallace, R. J., Wang, M., Waters, S. M., Keogh, K., Zhou, M., Witzig, M., Wright, A.-D. G., Yamano, H., Yan, T., Yáñez Ruiz, David R., Yeoman, C. J., Zhou, H. W., Zou, C. X., Zunino, P., Barahona, R., Batistotti, M., Bertelsen, M. F., Jami, E., Brown-Kav, A., Carvajal, A. M., Cersosimo, L., Chaves, A. V., Church, J., Clipson, N., Cobos-Peralta, M. A., Cookson, A. L., Cravero, S., Carballo, O. C., Jelincic, J., Crosley, K., Cruz, Gustavo, Cucchi, M. C., De La Barra, R., De Menezes, A. B., Detmann, E., Dieho, K., Dijkstra, J., Dos Reis, W. L. S., Dugan, M. E. R., Kantanen, J., Ebrahimi, S. H., Eythórsdóttir, E., Fon, F. N., Fraga, M., Franco, F., Friedeman, C., Fukuma, N., Gagić , D., Gangnat, I., Grilli, D. J., European Commission, and De Menezes, AB

Subjects
DNA, Bacterial, Rumen, animal structures, Animal Nutrition, Microorganism, Article, 03 medical and health sciences, Species Specificity, Ruminant, Butyrivibrio, Animals, DNA Barcoding, Taxonomic, Life Science, Microbiome, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Bacteria, Geography, biology, 030306 microbiology, Host (biology), Ecology, Genetic Variation, Ruminants, Sequence Analysis, DNA, DNA, Protozoan, 15. Life on land, biology.organism_classification, Archaea, Diervoeding, Diet, Gastrointestinal Microbiome, DNA, Archaeal, Microbial population biology, 13. Climate action, Host-Pathogen Interactions, WIAS, Erratum
Abstract

© 2015 Macmillan Publishers Limited. Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific., We thank Ron Ronimus, Paul Newton, and Christina Moon for reading and commenting on the manuscript. We thank all who provided assistance that allowed Global Rumen Census collaborators to supply samples and metadata (Supplemental Text 1). AgResearch was funded by the New Zealand Government as part of its support for the Global Research Alliance on Agricultural Greenhouse Gases. The following funding sources allowed Global Rumen Census collaborators to supply samples and metadata, listed with the primary contact(s) for each funding source: Agencia Nacional de Investigación e Innovación, Martín Fraga; Alberta Livestock and Meat Agency, Canada, Tim A. McAllister; Area de Ciencia y Técnica, Universidad Juan A Maza (Resolución Proy. N° 508/2012), Diego Javier Grilli; Canada British Columbia Ranching Task Force Funding Initiative, John Church; CNPq, Hilário Cuquetto Mantovani, Luiz Gustavo Ribeiro Pereira; FAPEMIG, Hilário Cuquetto Mantovani; FAPEMIG, PECUS RumenGases, Luiz Gustavo Ribeiro Pereira; Cooperative Research Program for Agriculture Science & Technology Development (project number PJ010906), Rural Development Administration, Republic of Korea, Sang-Suk Lee; Dutch Dairy Board & Product Board Animal Feed, André Bannink, Kasper Dieho, Jan Dijkstra; Ferdowsi University of Mashhad, Vahideh Heidarian Miri; Finnish Ministry of Agriculture and Forestry, Ilma Tapio; Instituto Nacional de Tecnología Agropecuaria, Argentina (Project PNBIO1431044), Silvio Cravero, María Cerón Cucchi; Irish Department of Agriculture, Fisheries and Food, Alexandre B. De Menezes; Meat & Livestock Australia; and Department of Agriculture, Fisheries & Forestry (Australian Government), Chris McSweeney; Ministerio de Agricultura y desarrollo sostenible (Colombia), Olga Lucía Mayorga; Montana Agricultural Experiment Station project (MONB00113), Carl Yeoman; Multistate project W-3177 Enhancing the competitiveness of US beef (MONB00195), Carl Yeoman; NSW Stud Merino Breeders’ Association, Alexandre Vieira Chaves; Queensland Enteric Methane Hub, Diane Ouwerkerk; RuminOmics, Jan Kopecny, Ilma Tapio; Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government and the Technology Strategy Board, UK, R. John Wallace; Science Foundation Ireland (09/RFP/GEN2447), Sinead Waters; Secretaría de Agricultura, Ganadería, Desarrollo Rural, Pesca y Alimentación, Mario A. Cobos-Peralta; Slovenian Research Agency (project number J1-6732 and P4-0097), Blaz Stres; Strategic Priority Research Program, Climate Change: Carbon Budget and Relevant Issues (Grant No.XDA05020700), ZhiLiang Tan; The European Research Commission Starting Grant Fellowship (336355—MicroDE), Phil B. Pope; The Independent Danish Research Council (project number 4002-00036), Torsten Nygaard Kristensen; and The Independent Danish Research Council (Technology and Production, project number 11-105913), Jan Lassen. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Published
2015

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