Miocene waterfowl and other birds from central Otago, New Zealand

Copyright © The Natural History Museum 2007Abundant fossil bird bones from the lower Bannockburn Formation, Manuherikia Group, an Early-Middle Miocene lacustrine deposit, 16–19 Ma, from Otago in New Zealand, reveal the “St Bathans Fauna” (new name), a first Tertiary avifauna of land and freshwater birds from New Zealand. At least 23 species of birds are represented by bones, and probable moa, Aves: Dinornithiformes, by eggshell. Anatids dominate the fauna with four genera and five species described as new: a sixth and largest anatid species is represented by just one bone. This is the most diverse Early-Middle Miocene duck fauna known worldwide. Among ducks, two species of dendrochenines are most numerous in the fauna, but a tadornine is common as well. A diving petrel (Pelecanoididae: Pelecanoides) is described, so extending the geological range of this genus worldwide from the Pliocene to the Middle Miocene, at least. The remaining 16 taxa are left undescribed but include: a large species of gull (Laridae); two small waders (Charadriiformes, genus indet.), the size of Charadrius bicinctus and Calidris ruficollis, respectively; a gruiform represented by one specimen similar to Aptornis; abundant rail (Rallidae) bones, including a common flightless rail and a rarer slightly larger taxon, about the size of Gallirallus philippensis; an ?eagle (Accipitridae); a pigeon (Columbidae); three parrots (Psittacidae); an owlet nightjar (Aegothelidae: Aegotheles sp.); a swiftlet (Apodidae: Collocalia sp.); and three passerine taxa, of which the largest is a member of the Cracticidae. The absence of some waterbirds, such as anserines (including swans), grebes (Podicipedidae) and shags (Phalacrocoracidae), among the abundant bones, indicates their probable absence from New Zealand in the Early-Middle Miocene.T. H. Worthy, A. J. D. Tennyson, C. Jones, J. A. McNamara and B. J. Dougla

An analysis of the intestinal immune response of pigs divergent in feed efficiency following an ex-vivo lipopolysaccharide challenge

This data is additional data that is not appropriate to publish in the main manuscript which is described below. While feed efficiency is influenced by multiple physiological processes, it is not known how efficient and inefficient pigs differ in relation to their basal immune response, and particularly their innate immune response to a microbial challenge. Hence, the objective was to examine the expression of genes relating to the innate immune response in basal colonic tissue and colonic tissue following an ex-vivo lipopolysaccharide (LPS) challenge from pigs divergent in residual feed intake (RFI). Pigs that differed in RFI were selected from two different farms of origin. Colonic tissue was harvested, and two experimental conditions were explored: the first was basal unchallenged tissue and the second was colonic tissue following an ex-vivo LPS challenge. RNA was extracted and tested on a Nanostring panel of 72 genes coding for barrier defence proteins, transmembrane receptors, kinases, transcription regulators, cytokines and cytokine regulators. In the basal unchallenged tissue, the LRFI pigs had increased expression of AOAH, AP1, TRAM and the cytokines TNF, IL10 and CXCL8, compared to the HRFI pigs (P<0.05), with a significant effect of farm of origin on 31 genes (P<0.05). In the LPS challenged tissues, the LRFI group had higher expression of TLR1, TLR7, TLR8, GPR43/FFAR2, JAK2 and NFAM1 compared to the HRFI group (P<0.05). In conclusion, these data suggest that LRFI pigs have an upregulated basal colonic inflammatory state and a disparate response to an LPS challenge compared to the inefficient HRFI pigs. This immune profile potentially enhances their capacity to respond to an infectious challenge

The impact of vitamin D3 supplementation on the faecal and oral microbiome of dairy calves indoors or at pasture

Abstract Vitamin D (VitD) is emerging as an immune regulator in addition to its established role in metabolism and mineral homeostasis. This study sought to determine if in vivo VitD modulated the oral and faecal microbiome in Holstein–Friesian dairy calves. The experimental model consisted of two control groups (Ctl-In, Ctl-Out) which were fed with a diet containing 6000 IU/Kg of VitD3 in milk replacer and 2000 IU/Kg in feed, and two treatment groups (VitD-In, VitD-Out) with 10,000 IU/Kg of VitD3 in milk replacer and 4000 IU/Kg in feed. One control and one treatment group were moved outdoors post-weaning at approximately 10 weeks of age. Saliva and faecal samples were collected after 7 months of supplementation and analysis of the microbiome was performed using 16S rRNA sequencing. Bray–Curtis dissimilarity analysis identified that both sampling site (oral vs. faecal) and housing (indoor vs. outdoor) had significant influences on the composition of the microbiome. The calves housed outdoors had greater microbial diversity in the faecal samples based on Observed, Chao1, Shannon, Simpson and Fisher measures in comparison to calves housed indoors (P < 0.05). A significant interaction between housing and treatment was observed for the genera Oscillospira, Ruminococcus, CF231 and Paludibacter in faecal samples. The genera Oscillospira and Dorea were increased while Clostridium and Blautia were decreased following VitD supplementation in the faecal samples (P < 0.05). An interaction between VitD supplementation and housing was detected in the abundance of the genera Actinobacillus and Streptococcus in the oral samples. VitD supplementation increased the genera Oscillospira, Helcococcus and reduced the genera Actinobacillus, Ruminococcus, Moraxella, Clostridium, Prevotella, Succinivibrio and Parvimonas. These preliminary data suggest that VitD supplementation alters both the oral and faecal microbiome. Further research will now be conducted to establish the significance of microbial alterations for animal health and performance

The Effects of the Marine-Derived Polysaccharides Laminarin and Chitosan on Aspects of Colonic Health in Pigs Challenged with Dextran Sodium Sulphate

This study examined the effects of dietary supplementation with laminarin or chitosan on colonic health in pigs challenged with dextran sodium sulphate (DSS). Weaned pigs were assigned to: (1) a basal diet (n = 22); (2) a basal diet + laminarin (n = 10); and (3) a basal diet + chitosan (n = 10). On d35, the basal group was split, creating four groups: (1) the basal diet (control); (2) the basal diet + DSS; (3) the basal diet + laminarin + DSS; and (4) the basal diet + chitosan + DSS. From d39&ndash;42, the pigs were orally challenged with DSS. On d44, colonic tissue/digesta samples were collected. The basal DSS group had reduced growth, higher pathology score and an increased expression of MMP1, IL13 and IL23 compared with the controls (p &lt; 0.05); these parameters were similar between the DSS-challenged groups (p &gt; 0.05). In the basal DSS group, the relative abundance of beneficial taxa including Prevotella and Roseburia were reduced while Escherichia/Shigella were increased, compared with the controls (p &lt; 0.05). The relative abundance of Escherichia/Shigella was reduced and the molar proportions of acetate were increased in the laminarin DSS group compared with the basal DSS group (p &lt; 0.01), suggesting that laminarin has potential to prevent pathogen proliferation and enhance the volatile fatty acid profile in the colon in a porcine model of colitis

Improve animal health to reduce livestock emissions: quantifying an open goal

Greenhouse gas (GHG) emissions from livestock production must be urgently tackled to substantially reduce their contribution to global warming. Simply reducing livestock numbers to this end risks impacting negatively on food security, rural livelihoods and climate change adaptation. We argue that significant mitigation of livestock emissions can be delivered immediately by improving animal health and hence production efficiency, but this route is not prioritized because its benefits, although intuitive, are poorly quantified. Rigorous methodology must be developed to estimate emissions from animal disease and hence achievable benefits from improved health through interventions. If, as expected, climate change is to affect the distribution and severity of health conditions, such quantification becomes of even greater importance. We have therefore developed a framework and identified data sources for robust quantification of the relationship between animal health and greenhouse gas emissions, which could be applied to drive and account for positive action. This will not only help mitigate climate change but at the same time promote cost-effective food production and enhanced animal welfare, a rare win-win in the search for a sustainable planetary future

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs

This study aims identifying candidate genes and pathways associated with feed efficiency (FE) in pigs. Liver and duodenum transcriptomes of 37 gilts showing high and low residual feed intake (RFI) were analysed by RNA-Seq. Gene expression data was explored through differential expression (DE) and weighted gene co-expression network analyses. DE analysis revealed 55 and 112 differentially regulated genes in liver and duodenum tissues, respectively. Clustering genes according to their connectivity resulted in 23 (liver) and 25 (duodenum) modules of genes with a co-expression pattern. Four modules, one in liver (with 444 co-expressed genes) and three in duodenum (gathering 37, 126 and 41 co-expressed genes), were significantly associated with FE indicators. Intra-module analyses revealed tissue-specific candidate genes; 12 of these genes were also identified as DE between individuals with high and low RFI. Pathways enriched by the list of genes showing DE and/or belonging to FE co-expressed modules included response to oxidative stress, inflammation, immune response, lipid metabolism and thermoregulation. Low overlapping between genes identified in duodenum and liver tissues was observed but heat shock proteins were associated to FE in both tissues. Our results suggest tissue-specific rather than common transcriptome regulatory processes associated with FE in pigs