Recent highlights
Li et al., Microbiome,(2019)7: 6
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle
Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.
Sun et al., Bioinformatics,(2018)bty883
Landscape of multi-tissue global gene expression reveals the regulatory signatures of feed efficiency in beef cattle
The transcriptome of 189 samples across four tissues from 48 beef steers with varied feed efficiency were generated using Illumina HiSeq4000. The analysis of global gene expression profiles of four tissues, functional analysis of tissue-shared and -unique genes, co-expressed network construction of tissue-shared genes, weighted correlations analysis between gene modules and feed efficiency-related traits in each tissue were performed. Among four tissues, the transcriptome of muscle tissue was distinctive from others, while those of rumen and backfat tissues were similar. The associations between co-expressed genes and feed efficiency related traits at single or all tissues level exhibited that the gene expression in the rumen, liver, muscle and backfat were the most correlated with feed conversion ratio, dry matter intake, average daily gain and residual feed intake, respectively. The 19 overlapped genes identified from the strongest module–trait relationships in four tissues are potential generic gene markers for feed efficiency.
Zhou et al., Microbiome,(2018)6:62
Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle
Background: Understanding the host impact on its symbiotic microbiota is important in redirecting the
rumen microbiota and thus improving animal performance. The current study aimed to understand how
rumen microbiota were altered and re-established after being emptied and receiving content from donor,
thus to understand the impact of such process on rumen microbial fermentation and to explore the
microbial phylotypes with higher manipulation potentials.
Results: Individual animal had strong effect on the re-establishment of the bacterial community according to
the observed profiles detected by both fingerprinting and pyrosequencing. Most of the bacterial profile recovery patterns
and extents at genus level varied among steers; and each identified bacterial genus responded to transfaunation
differently within each host. Coriobacteriaceae, Coprococcus, and Lactobacillus were found to be the most responsive and
tunable genera by exchanging rumen content. Besides, the association of 18 bacterial phylotypes with host fermentation
parameters suggest that these phylotypes should also be considered as the regulating targets in improving host feed
efficiency. In addition, the archaeal community had different re-establishment patterns for each host as determined by
fingerprint profiling: it was altered after receiving non-native microbiome in some animals, while it resumed its original
status after the adaptation period in the other ones.
Conclusions: The highly individualized microbial re-establishment process suggested the importance of considering host
genetics, microbial functional genomics, and host fermentation/performance assessment when developing effective and
selective microbial manipulation methods for improving animal feed efficiency.
Keywords: Adaptation, Beef cattle, Transfaunation, Rumen microbiota
Sun and Guan, Trends in Analytical Chemistry, (2018)107:130-141
Feedomics: Promises for food security with sustainable food animal production
The production of adequate and nutritious animal proteins for the increasing human population is an urgent global task. Therefore, enhancing the efficiency and sustainability of food animal production requires advanced analytical techniques. We propose the concept of “feedomics” for food animal research, an emerging field using omics technologies, to understand and uncover the mechanisms involved in many biological processes that determine animal productivity, product quality, and health as a result of the interactions among feed, environment, animal genetics, physiology, and its symbiotic microbiota. In this review, we summarize the
findings to date based on the omics approaches including (meta)genomics, epigenomics, (meta)transcriptomics, proteomics, and metabolomics in food animal species and consider how these can be used to understand the processes from the “gate” to “plate”. We also highlight future directions for applying feedomics in fundamental and practical studies to improve the quantity, quality, safety and functional properties of food animal products