Time is a stronger predictor of microbiome community composition than tissue in external mucosal surfaces of Atlantic salmon (Salmo salar) reared in a semi-natural freshwater environment

Open Access via the Elsevier Agreement This work was supported by the UKRI project ROBUSTSMOLT [grant numbers BBSRC BB/S004270/1 and BB/S004432/1]. There was also co-funding from the Scottish Aquaculture Innovation Centre.Peer reviewedPublisher PD

A Temporally Dynamic Gut Microbiome in Atlantic Salmon During Freshwater Recirculating Aquaculture System (RAS) Production and Post-seawater Transfer

This study was funded by the UKRI project ROBUSTSMOLT (BBSRC BB/S004270/1 and BB/S004432/1). There was also cofunding from the Scottish Aquaculture Innovation Centre. ACKNOWLEDGMENTS The authors would like to thank John Richmond and staff at MOWI and the Centre for Genome Enabled Biology and Medicine (CGEBM) at the University of Aberdeen, particularly Dr. Ewan Campbell, for help with amplification protocols, conducting 16S library preparation and sequencing. The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA729215.Peer reviewedPublisher PD

Microbiomes in the context of developing sustainable intensified aquaculture

With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in “closed” aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture

Imprinting methylation predicts hippocampal volumes and hyperintensities and the change with age in later life.

Funder: Rural and Environment Science and Analytical Services Division; doi: http://dx.doi.org/10.13039/100011310Epigenetic imprinting is important for neurogenesis and brain function. Hippocampal volumes and brain hyperintensities in late life have been associated with early life circumstances. Epigenetic imprinting may underpin these associations. Methylation was measured at 982 sites in 13 imprinted locations in blood samples from a longitudinal cohort by bisulphite amplicon sequencing. Hippocampal volumes and hyperintensities were determined at age 64y and 72y using MRI. Hyperintensities were determined in white matter, grey matter and infratentorial regions. Permutation methods were used to adjust for multiple testing. At 64y, H19/IGF2 and NESPAS methylation predicted hippocampal volumes. PEG3 predicted hyperintensities in hippocampal grey matter, and white matter. GNASXL predicted grey matter hyperintensities. Changes with age were predicted for hippocampal volume (MEST1, KvDMR, L3MBTL, GNASXL), white matter (MEST1, PEG3) and hippocampal grey matter hyperintensities (MCTS2, GNASXL, NESPAS, L3MBTL, MCTS2, SNRPN, MEST1). Including childhood cognitive ability, years in education, or socioeconomic status as additional explanatory variables in regression analyses did not change the overall findings. Imprinting methylation in multiple genes predicts brain structures, and their change over time. These findings are potentially relevant to the development of novel tests of brain structure and function across the life-course, strategies to improve cognitive outcomes, and our understanding of early influences on brain development and function

Imprinting methylation in SNRPN and MEST1 in adult blood predicts cognitive ability.

Genomic imprinting is important for normal brain development and aberrant imprinting has been associated with impaired cognition. We studied the imprinting status in selected imprints (H19, IGF2, SNRPN, PEG3, MEST1, NESPAS, KvDMR, IG-DMR and ZAC1) by pyrosequencing in blood samples from longitudinal cohorts born in 1936 (n = 485) and 1921 (n = 223), and anterior hippocampus, posterior hippocampus, periventricular white matter, and thalamus from brains donated to the Aberdeen Brain Bank (n = 4). MEST1 imprint methylation was related to childhood cognitive ability score (-0.416 95% CI -0.792,-0.041; p = 0.030), with the strongest effect evident in males (-0.929 95% CI -1.531,-0.326; p = 0.003). SNRPN imprint methylation was also related to childhood cognitive ability (+0.335 95%CI 0.008,0.663; p = 0.045). A significant association was also observed for SNRPN methylation and adult crystallised cognitive ability (+0.262 95%CI 0.007,0.517; p = 0.044). Further testing of significant findings in a second cohort from the same region, but born in 1921, resulted in similar effect sizes and greater significance when the cohorts were combined (MEST1; -0.371 95% CI -0.677,-0.065; p = 0.017; SNRPN; +0.361 95% CI 0.079,0.643; p = 0.012). For SNRPN and MEST1 and four other imprints the methylation levels in blood and in the five brain regions were similar. Methylation of the paternally expressed, maternally methylated genes SNRPN and MEST1 in adult blood was associated with cognitive ability in childhood. This is consistent with the known importance of the SNRPN containing 15q11-q13 and the MEST1 containing 7q31-34 regions in cognitive function. These findings, and their sex specific nature in MEST1, point to new mechanisms through which complex phenotypes such as cognitive ability may be inherited. These mechanisms are potentially relevant to both the heritable and non-heritable components of cognitive ability. The process of epigenetic imprinting-within SNRPN and MEST1 in particular-and the factors that influence it, are worthy of further study in relation to the determinants of cognitive ability

Temporal changes in skin and gill microbiomes of Atlantic salmon in a recirculating aquaculture system – Why do they matter?

Mucosal surfaces are key components of teleost health, providing defence against opportunistic pathogens and other insults. Maintaining the integrity of mucosal surfaces and their associated microbial communities, especially the gill and skin that have large surface areas exposed to the environment is essential. Production of Atlantic salmon in land-based recirculating aquaculture systems (RAS) has increased significantly in recent years as it allows greater control over stability of the environment in which fish are reared, reduces water demand and minimises environmental impacts. However, little is known about the impact of the RAS environment upon the temporal dynamics of skin and gill mucosal microbiomes. In this study we examined microbial communities in gill mucus, skin mucus and rearing water throughout freshwater (FW) RAS production, and at 1-week and 4-weeks following transfer to seawater (SW) in open cage production using 16S rRNA sequencing. Microbial diversity and richness in skin and gill mucus of fish reared in a RAS system were temporally dynamic. Dynamics in richness and diversity were similar in the two mucosal tissues, and to some extent also mirrored that of the surrounding water. Dysbiosis indicated by an abrupt decline in diversity during FW production coincided with an increase in the relative abundance of two taxa belonging to the RAS-biofilter-associated nitrogen-cycling genus Hydrogenophaga in RAS tank water and this was also observed in gill and skin mucus. Extensive overlap in core taxa was observed between gill and skin mucus, but host-specific cores were non-existent during the dysbiotic event with all cores present in the rearing water. Diversity remained stable during the transition from FW to SW, but distinct community composition and core taxa were observed in the two environments. Although RAS are closely controlled, significant temporal variation could be observed in temperature as well as levels of CO2 and nitrogen compounds, reflecting the increasing biological load within the system over time. The results presented here suggest that, in terms of microbiomes, dysbiosis may occur in both the RAS environment and fish mucosal surfaces over time, but microbial communities have the capability to recover