The community ecology perspective of omics data

The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract

Potential of microbiome-based solutions for agrifood systems

Host-associated microbiomes are central to food production systems and human nutrition and health. Harnessing the microbiome may help increase food and nutrient security, enhance public health, mitigate climate change and reduce land degradation. Although several microbiome solutions are currently under development or commercialized in the agrifood, animal nutrition, biotechnology, diagnostics, pharmaceutical and health sectors , fewer products than expected have been successfully commercialized beyond food processing, and fewer still have achieved wider adoption by farming, animal husbandry and other end-user communities. This creates concerns about the translatability of microbiome research to practical applications. Inconsistent efficiency and reliability of microbiome solutions are major constraints for their commercialization and further development, and demands urgent attention

Temporal dynamics of cloacal microbiota in adult laying chickens with and without access to an outdoor range

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition

A cross-sectional observational study of the fecal microbiota in adult laying hens with and without an outdoor range

Background: Laying hens with access to outdoor ranges are exposed to additional environmental micro-organisms, including potential pathogens from wild birds. Alterations in the fecal microbiota or the relative abundance of individual genera of outdoor-housed layers may serve as an indicator for risks of exposure to potential pathogens. We therefore performed a cross-sectional field study to evaluate differences in the fecal microbiota of outdoor- vs indoor-layers across farms. Eight layer flocks (four indoor and four outdoor), from five poultry farms were sampled. Indoor and outdoor flocks were selected that had the same rearing flock of origin, and breed. In each flock, cloacal swabs were taken from ten layers, and microbiota compositions were analysed with 16S rRNA gene amplicon sequencing (region V3-V4). Conclusions: Our study shows that the cloacal microbial composition of adult laying hens in field conditions is to a limited extent, affected by the access to an outdoor range (i.e. housing type), but that the poultry house, farm, and rearing flock play a greater role in determining microbial composition. Overall, our study indicates that measuring differences in the cloacal fecal microbiota of layers as an indicator for the level of exposure to potential pathogens and the level of biosecurity seems of limited practical use

A cross-sectional observational study of the fecal microbiota in adult laying hens with and without an outdoor range

Background: Laying hens with access to outdoor ranges are exposed to additional environmental micro-organisms, including potential pathogens from wild birds. Alterations in the fecal microbiota or the relative abundance of individual genera of outdoor-housed layers may serve as an indicator for risks of exposure to potential pathogens. We therefore performed a cross-sectional field study to evaluate differences in the fecal microbiota of outdoor- vs indoor-layers across farms. Eight layer flocks (four indoor and four outdoor), from five poultry farms were sampled. Indoor and outdoor flocks were selected that had the same rearing flock of origin, and breed. In each flock, cloacal swabs were taken from ten layers, and microbiota compositions were analysed with 16S rRNA gene amplicon sequencing (region V3-V4). Conclusions: Our study shows that the cloacal microbial composition of adult laying hens in field conditions is to a limited extent, affected by the access to an outdoor range (i.e. housing type), but that the poultry house, farm, and rearing flock play a greater role in determining microbial composition. Overall, our study indicates that measuring differences in the cloacal fecal microbiota of layers as an indicator for the level of exposure to potential pathogens and the level of biosecurity seems of limited practical use