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
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.
Phylogeny and systematics of Demospongiae in light of new small-subunit ribosomal DNA (18S) sequences
Redmond, N.E. ; Morrow, C. ; Thacker, R.W. ; Diaz, M.C. ; Boury-Esnaul, N. ; Cardenas, P.D. ; Hajdu, E. ; Lobo-Hajdu, G. ; Picton, B.E. ; Pomponi, S.A. ; Kayal, E. ; Collins, A.G. - \ 2013
Integrative and Comparative Biology 53 (2013)3. - ISSN 1540-7063 - p. 388 - 415.
glass sponges porifera - phylum porifera - molecular phylogeny - animal phylogeny - gene-sequences - fossil record - evolution - hexactinellida - classification - verongida
The most diverse and species-rich class of the phylum Porifera is Demospongiae. In recent years, the systematics of this clade, which contains more than 7000 species, has developed rapidly in light of new studies combining molecular and morphological observations. We add more than 500 new, nearly complete 18S sequences (an increase of more than 200%) in an attempt to further enhance understanding of the phylogeny of Demospongiae. Our study specifically targets representation of type species and genera that have never been sampled for any molecular data in an effort to accelerate progress in classifying this diverse lineage. Our analyses recover four highly supported subclasses of Demospongiae: Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha. Within Keratosa, neither Dendroceratida, nor its two families, Darwinellidae and Dictyodendrillidae, are monophyletic and Dictyoceratida is divided into two lineages, one predominantly composed of Dysideidae and the second containing the remaining families (Irciniidae, Spongiidae, Thorectidae, and Verticillitidae). Within Myxospongiae, we find Chondrosida to be paraphyletic with respect to the Verongida. We amend the latter to include species of the genus Chondrosia and erect a new order Chondrillida to contain remaining taxa from Chondrosida, which we now discard. Even with increased taxon sampling of Haploscleromorpha, our analyses are consistent with previous studies; however, Haliclona species are interspersed in even more clades. Haploscleromorpha contains five highly supported clades, each more diverse than previously recognized, and current families are mostly polyphyletic. In addition, we reassign Janulum spinispiculum to Haploscleromorpha and resurrect Reniera filholi as Janulum filholi comb. nov. Within the large clade Heteroscleromorpha, we confirmed 12 recently identified clades based on alternative data, as well as a sister-group relationship between the freshwater Spongillida and the family Vetulinidae. We transfer Stylissa flabelliformis to the genus Scopalina within the family Scopalinidae, which is of uncertain position. Our analyses uncover a large, strongly supported clade containing all heteroscleromorphs other than Spongillida, Vetulinidae, and Scopalinidae. Within this clade, there is a major division separating Axinellidae, Biemnida, Tetractinellida, Bubaridae, Stelligeridae, Raspailiidae, and some species of Petromica, Topsentia, and Axinyssa from Agelasida, Polymastiidae, Placospongiidae, Clionaidae, Spirastrellidae, Tethyidae, Poecilosclerida, Halichondriidae, Suberitidae, and Trachycladus. Among numerous results: (1) Spirophorina and its family Tetillidae are paraphyletic with respect to a strongly supported Astrophorina within Tetractinellida; (2) Agelasida is the earliest diverging lineage within the second clade listed above; and (3) Merlia and Desmacella appear to be the earliest diverging lineages of Poecilosclerida.
Summary of the first round analyses of the Third International Workshop on Swine Leukocyte Differentiation Antigens
Haverson, K. ; Saalmuller, A. ; Chen, Z. ; Huang, C.A. ; Simon, A. ; Seebach, J. ; Boersma, W.J.A. ; Zwart, R. ; Niewold, T.A. ; Thacker, E. ; Llanes, D. ; Lastra, J.M.P. de la; Engelhardt, H. ; Ezquerra, A. ; Alonso, F. ; Dominguez, J. ; Ledbetter, J.A. ; Grosmaire, L. ; Lee, R. ; Nielsen, J. ; Salmon, H. ; Valpotic, I. ; Sver, L. ; Lackovic, G. ; Summerfield, A. ; Khanna, K.V. - \ 2001
Veterinary Immunology and Immunopathology 80 (2001)1-2. - ISSN 0165-2427 - p. 25 - 34.
The reactivity of 155 monoclonal antibodies submitted to the Third International Workshop on Swine Leukocyte Differentiation Antigens, together with 41 internal standards, was analysed by flow cytometry on 29 different pig cell targets as well as two human cell targets as a means of establishing suitable panels of monoclonal antibodies for more detailed clustering analyses by the various subsections of the workshop. Results were collected either without further gating, with gating based on FS/SS characteristics or with gating based on the co-expression of a reference antibody in two-colour flow cytometry. The CD or SWC reactivity of the internal standards had been established in previous workshops. Data sets were subsequently analysed by statistical clustering using the Leucocyte Typing Database IV software. The resulting 18 cluster groups were allocated to the appropriate second round sections of the workshop, after reviewing the overall cellular reactivity of each cluster as well as the specificity of known standards which clustered in a group. Copyright
|Reproductive Management of Pigs
Hughes, P. ; Flowers, B. ; Kemp, B. ; Kirkwood, R. ; Levis, D. ; Soede, N.M. ; Thacker, P. ; Tilton, J. - \ 2000
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The effect of immunoneutralization of PMSG at a gonadotropin-induced oestrus on the duration of ovulation and reproductive performance of sows.
Kirkwood, R.N. ; Soede, N.M. ; Dyck, G.W. ; Thacker, P.A. - \ 1995
Animal Science 61 (1995)2. - ISSN 1357-7298 - p. 321 - 324.
|Foraging behaviour programs in ruminants.
Tolkamp, B.J. ; Ketelaars, J.J.M.H. - \ 1994
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