Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint

Effect of DNA extraction and sample preservation method on rumen bacterial population

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Promoting mental health and well-being in schools: examining mindfulness, relaxation and strategies for safety and well-being in English primary and secondary schools—study protocol for a multi-school, cluster randomised controlled trial (INSPIRE)

There are increasing rates of internalising difficulties, particularly anxiety and depression, being reported in children and young people in England. School-based universal prevention programmes are thought to be one way of helping tackle such difficulties. This paper describes an update to a four-arm cluster randomised controlled trial (http://www.isrctn.com/ISRCTN16386254), investigating the effectiveness of three different interventions when compared to usual provision, in English primary and secondary pupils. Due to the COVID-19 pandemic, the trial was put on hold and subsequently prolonged. Data collection will now run until 2024. The key changes to the trial outlined here include clarification of the inclusion and exclusion criteria, an amended timeline reflecting changes to the recruitment period of the trial due to the COVID-19 pandemic and clarification of the data that will be included in the statistical analysis, since the second wave of the trial was disrupted due to COVID-19. Trial registration ISRCTN Registry ISRCTN16386254. Registered on 30 August 2018

Host genetic effects on the rumen microbiome as revealed by rumen content exchange in lactating cows

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Promising potential of high-throughput molecular phenotyping of freshwater fishes for environmental assessment

The recent democratisation of high-throughput molecular phenotyping allows the rapid expansion of promising untargeted multi-dimensional approaches (e.g. epigenomics, transcriptomics, proteomics, metabolomics, as well as microbiome metabarcoding), that now represent innovative perspectives for environmental assessments. Indeed, when developed for ecologically relevant species, these emerging omics analyses may present valuable alternatives for the development of novel generations of ecological indicators, that in turn could provide early warnings of eco(toxico)logical impairments. This pilot study investigates the bio-indicative potential of different multi-metric tools based on different high-throughput molecular phenotyping approaches (i.e. metabarcoding of the intestine microbiome, and liver metabolomics by nuclear magnetic resonance (NMR) and liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) on two sentinel fish species (Perca fluviatilis and Lepomis gibbosus) from a set of eight water bodies of the peri-urban area of Paris (France). We show that the LC-MS metabolome dataset allows remarkably clear separation of individuals according to the species but also according to their respective sampling lakes. Interestingly, the similar variations of Perca and Lepomis metabolomes occur locally indicating that local environmental constraints drive the observed metabolome variations beyond their obvious genetic differences. Thus, the development of such reliable molecular phenotyping for environmental monitoring constitutes a promising and innovative bio-indicative tool for environmental assessment

Species-, genus- and family- level taxonomic resolution of the 15 primer pairs tested <i>in silico</i> on the 18S-NemaBase.

Species-, genus- and family- level taxonomic resolution of the 15 primer pairs tested in silico on the 18S-NemaBase.</p

Weblogos built on primer sequences from nematodes.

The height of stacks corresponds to the nucleotide conservation at that position; the height of symbols within stacks indicates the relative frequency of each nucleotide at that position.</p

Results of <i>in silico</i> PCRs testing the taxonomic coverage and the resolution of 15 primer pairs proposed for nematode metabarcoding.

Metabarcode length refers to the length of the amplified fragment.</p

Specificity of the 15 primer pairs tested <i>in silico</i> on the whole Genbank database.

a) Specificity was measured as the N of nematode sequences / total N of amplified sequences. b) N of nematode species amplified by the different primer pairs, when the in silico PCR is run on the whole GenBank.</p

Taxonomic coverage (proportion of amplified sequences) of the 15 primer pairs tested <i>in silico</i> on the 18S-NemaBase.

Taxonomic coverage (proportion of amplified sequences) of the 15 primer pairs tested in silico on the 18S-NemaBase.</p