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Feedomics: Promises for food security with sustainable food animal

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 Trends in Analytical Chemistry 107 (2018) 130e141

Contents lists available at ScienceDirect

Trends in Analytical Chemistry

journal homepage: www.elsevier.com/locate/trac

Feedomics: Promises for food security with sustainable food animal

production
Hui-Zeng Sun, Le Luo Guan*
Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, T6G 2P5, AB, Canada

a r t i c l e i n f o a b s t r a c t

Article history: The production of adequate and nutritious animal proteins for the increasing human population is an
Available online 7 August 2018 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
Keywords: research, an emerging field using omics technologies, to understand and uncover the mechanisms
Animal production and health involved in many biological processes that determine animal productivity, product quality, and health as
Feed science
a result of the interactions among feed, environment, animal genetics, physiology, and its symbiotic
Genomics
microbiota. In this review, we summarize the findings to date based on the omics approaches including
Epigenomics
Proteomics
(meta)genomics, epigenomics, (meta)transcriptomics, proteomics, and metabolomics in food animal
Metabolomics species and consider how these can be used to understand the processes from the “gate” to “plate”. We
(Meta)genomics also highlight future directions for applying feedomics in fundamental and practical studies to improve
(Meta)transcriptomics the quantity, quality, safety and functional properties of food animal products.
microRNAs © 2018 Elsevier B.V. All rights reserved.
Feedomics

1. Introduction which directly affect the animal's performance and welfare. In

By 2050, the world human population is projected to reach 9.4
billion [1]. Animal protein (milk, egg, fish, and meat) is an integral
component of the human diet globally, and it has contributed to the
development and elimination of poverty in human society. To meet
the demand of the increasing human population, the global food
animal production is expected to increase 2.3% annually to 2050 [2].
Currently, food animal production consumes more than 32% of
global human edible cereal grains (e.g., corns, barley) and occupies
approximately 40% of all arable land [3]. Over the past several de-
cades, many technologies have been applied to improve food ani-
mal production efficiency. First, the modern commercial food
animal sector has adapted to a highly intensive management sys-
tem with using the high proportion of cereal grains in the diets.
Second, since the 1960s, as one such “innovation”, antimicrobial
growth promotants have been widely applied to improve the pro-
duction efficiency of food animals. Third, recent advanced research
in molecular genetics has shown some promise for breeding more
efficient animals [4]. However, the high grain-fed animals are more
susceptible to metabolic dysfunction, disorders, and diseases [5],
* Corresponding author.
E-mail address: lguan@ualberta.ca (L.L. Guan).
addition, food animal production has been considered to have a
negative environmental impact due to the emission of greenhouse
gases (methane, CO2) and the release of nitrous compounds (NO2,
ammonia) and phosphate [6]. Moreover, the recent attention on
reducing the antimicrobial growth promotants in food animal
production has driven the need to seek alternative feeding strate-
gies to maintain sustainable production [7]. Therefore, improving
the sustainability of food animal production is urgent and vital to
promote animals' welfare, to prevent further expansion of occupied
arable land, and to reduce the negative environmental impact.
Even with the rapid development of feed science, vast hard-to-
decipher biological mechanisms still limit the regulatory strategies
of sustainable food animal production. The “Foodomics” was first
proposed as a discipline for studying the food and nutrition do-
mains through the application and integration of advanced omics
technologies to improve human well-being, health, and confidence
by Cifuentes in 2009 [8]. Although the word feedomics can be
found in the titles of a PhD thesis [9] and a project (https://cphpig.
ku.dk/english/news/2015/haja/), a systematic definition and
detailed introduction are still lacking. Similar to “foodomics”, we
propose the term “feedomics” for food animal research, which
devises a systematic omics approach to understand the process
from “gate” to “plate” for animal productivity and health as well as
the product nutritional value for the human. In this review, we

https://doi.org/10.1016/j.trac.2018.07.025
0165-9936/© 2018 Elsevier B.V. All rights reserved.
 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141 131

integrate the knowledge of feed science, animal nutrition, animal

Abbreviations genetics and genomics, animal physiology and microbiology, plant
science and biochemistry, analytical chemistry, bioinformatics,
DE differential expressed engineering, and so on, which push forward the development and
ESI electrospray ionization inter-application of related disciplines.
GC-TOF/MS gas chromatography-time of flight/mass
spectrometry 2.2. The omics technologies applied in feedomics
GC-Q-MS gas chromatography-quadrupole-mass
spectrometry In feedomics, genomics is the study of all genetic information
GIT gastrointestinal tract (the genome) about a food animal organism mainly through gen-
GWAS genome-wide association study otyping and/or whole genome sequencing [10]. In transcriptomics,
HPLC high-performance liquid chromatography the expression patterns of all genes in the specific cell and/or tissue
ICAT isotope-coded affinity tag type under certain nutritional, physiological and environmental
LC-MS liquid chromatographyemass spectrometry conditions are studied [11]. Although genomics and tran-
MALDI-TOF/MS matrix-assisted laser desorption ionization- scriptomics provide the functional potential and the activity of the
time of flight/mass spectrometry functional coding genes, only ~3% of the genome encodes proteins,
MeDIP-Seq methylated DNA immunoprecipitation- with the rest of the genome being non-coding regions, and up to
sequencing 80% of the genome including non-coding regions is transcribed
MiRNA microRNA [12]. The non-coding RNAs are likely to contribute more in func-
NGS next-generation sequencing tional transcriptomes, which has led to an increasing emphasis on
NMR nuclear magnetic resonance studying the food animal non-coding small RNAs (especially
RFI residual feed intake microRNAomes) [13]. Chemical changes on the genome including
RNA-Seq RNA-Sequencing chromatin remodeling, histone protein modification and DNA
SILAC stable isotope labeling with amino acids in cell methylation have been considered to alter the phenotypic out-
culture comes in food animals, which may be passed on to the offspring
SNP single nucleotide polymorphisms and can be investigated by epigenomics [14]. Proteomics refers to
UHPLC-QQQ-MS ultra-high-performance liquid all of the proteins derived from coding-gene expression and
chromatography-triple quadrupole-mass translation and post-translational modifications, which serve as the
spectrometry main components of the proteome of food animal [15]. The large set
UPLC-Q-TOF-MS/MS ultra-performance liquid of downstream metabolites represents the final products of the
chromatography-quadrupole-time of genome, transcriptome, and proteome and reflects the external
flight-mass spectrometry/mass phenotype most directly, which can be qualitatively and quantita-
spectrometry tively analyzed using untargeted and targeted metabolomics in
feedomics [16]. The study of microbiomics provides information on
all the microbes of a given microbiota community (referring mainly
to epithelia and digesta of the gastrointestinal tract (GIT) in food
review the main omics approaches recently used in different food animals) in response to feeding intake [17]. Metagenomics and
animal species and their potential roles in helping achieve sus- metatranscriptomics are the main feedomics approaches that are
tainable developed food animal production. currently used to explore the genes and transcripts of the micro-
biome, and they provide a comprehensive understanding of the
2. The definition and analytical technologies of feedomics microorganisms’ composition, function, and undergoing activities
[18].
2.1. Definition and concept of feedomics The powerful force and holistic perspectives of feedomics are
mainly attributed to the advanced omics analytical systems, which
The recent advanced analytical technologies, especially with can potentially capture all molecules at different biological levels
high-throughput characteristics, unbiased, and untargeted “omics”, and generate their corresponding big datasets (which can be
have created the new era of feed science and animal nutrition/ defined as the feedome). The high-throughput next-generation
health and made it possible to identify complex findings at a system sequencing (NGS) techniques are widely applied to generate fee-
biological level. Here, we define feedomics as an emerging research dome datasets. To be specific, the untargeted whole genome, epi-
field that studies feed science, animal nutrition and animal pro- genome, transcriptome, microbial metagenome and
duction/health in a global molecular and systematic scale by using metatranscriptome datasets can be generated using NGS platforms
high sensitivity and resolution omics technologies. These omics such as Illumina NextSeq, MiSeq, HiSeq 2000, HiSeq 3000, HiSeq
methodologies include genomics, epigenomics, transcriptomics, 4000 with different depths [19], and even third-generation
proteomics, metabolomics, metagenomics, and metatran- sequencing methods such as 3-D genomic Hi-C [20]. Further, pro-
scriptomics. Recent efforts have been made to apply omics in food teomes and metabolomes can be identified by spectrometry- and
animal field (focused mainly on cattle, sheep, swine, poultry, and chromatography-based technologies, including liquid
fish) to address research questions and industrial problems, but chromatography-mass spectrometry (LC-MS) and gas
most published studies focus on only a single “omic” approach and chromatography-time of flight/MS (GC-TOF/MS) [21].
lack a linkage between the feed input and the end products. Proteomics and metabolomics are more relied-upon analytical
Therefore, we propose a general workflow of feedomics that in- techniques compared with other omics methods [22]. Proteomics is
cludes defining scientific questions, determining experimental of great importance to assess food animal productivity (especially
design, sampling collection, molecular (DNA, RNA, proteins, or for meat and milk safety and quality), health, and welfare [23]. MS-
metabolites) extraction, identification using high-throughput based proteomic techniques usually consist of an ion source
platforms, data analysis, mechanism interpretation, and valida- (nebulize the peptides into ionized droplets), a mass analyzer
tion. These steps contribute to a series of systematic processes and (measures the mass-to-charge ratio (m/z) of the ionized analyte)
132 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141

and a detector (records the ion numbers of each m/z value) [24].
Electrospray ionization (ESI) and matrix-assisted laser desorption/
ionization (MALDI) are widely used in MS-based proteomics to
produce ions; the former is normally combined with advanced
separation tools such as GC and high-performance liquid chroma-
tography (HPLC) to analyze complex peptides, and the latter is
commonly harnessed to analyze relatively simple samples [25].
With the rapid advances in analytical chemistry techniques and
data analysis methods, metabolomics has become more accessible
to broad research areas in food animal-related disciplines, such as
animal health and disease, animal nutrition, human health and
nutrition, and feed analysis [26]. MS-based analytical technologies
are most commonly applied in metabolite identification because of
the high selectivity, sensitivity and structural information of the
detected metabolites [27]. TOF or quadrupole (Q) is usually com-
bined with MS as a mass analyzer to strengthen the accuracy and
resolution of mass measurement [28]. Prior to MS detection, a GC or
LC separation tool is required based on the chemical properties of
the metabolites in the sample. Typically, LC is more suitable for
detecting non-volatile metabolites such as hydroxy-carboxylic
acids, and GC is easier to capture volatile metabolites such as
xylene [29]. Meanwhile, derivatization can be utilized to make the
polar compounds volatile enough for GC detection. Untargeted
metabolomics usually use one or several of various high-
throughput technologies, especially mass spectrometry-based
platforms (GC-MS, GC-TOF/MS, GC
GC-TOF/MS, GC-Q-MS, LC-
MS, ultra-performance liquid chromatography (UPLC)-Q-TOF-MS/
MS) to get a full scan of all metabolites (what metabolites are
present and the relative abundance of these metabolites) that play
an important role in capturing unknown or novel metabolites,
subtle pathways and key mechanisms. Furthermore, the metabo-
lites of interest can be examined using targeted metabolomics (the
real concentration), with the commonly used techniques including
GC-TOF/MS, GC-Q-MS, UPLC-Q-TOF-MS/MS, and UHPLC-QQQ-MS.
For metabolomics studies, it is important to determine which
samples should be used for analysis due to the different charac-
teristic of samples, various compound extraction methods, high
costs and lack of databases.
These approaches vary in their resolution, sensitivity, accuracy,
coverage, stability, run time, sample loading amount, cost per
sample and so on, so it is important to choose suitable techniques
based on different research objectives and comparable information
including the applications, advantages, and limitations of major
analytical technologies applied in feedomics (Table 1).

Table 1
The applications, advantages, and limitations of major analytical technologies applied in feedomics.

Analytical technologies Applications in feedomics Advantages Limitations

NextSeq Whole (meta)genomics and (meta) High output range; High coverage Costly
transcriptomics;
Epigenomics
Ion Torrent PGM Targeted DNA, RNA and microbial sequencing Short run time; High output per hour Low sequencing quality; High error rate
Hi-C Genomes conformation [20] Can detect chromatin interactions Low resolution; High noise
BeadChip DNA methylation; Genotyping [38e43] Cost-effective for large samples; Not suitable for low frequency sites
Microarray Genotyping; DNA methylation; Gene Simple workflow Low dynamic range; Need probe design
expression [58,60], sequences
microRNA [66,68]
HiSeq Metagenomics [116,119,120]; High-throughput; Broader dynamic range Short reads; High cost; High computation
Transcriptomics [35,52e55,61]; needs
Metatranscriptomics
[18,117,119]; MicroRNAome [67,70,71];
MeDIP-Seq based epigenomics [78,79];
Bisulfite-Seq based epigenomics [83]
MiSeq 16S metagenomics [116,121] Long reads Low output
Methylated DNA DNA methylation rates [75] Easy and quick to perform; High accuracy Lack specific sites information
qualification kit
Pyrosequencing Methylation and genomic variation, microbial Long reads Low accuracy; Costly
diversity
[101,115,118]
ChIP-on-chip Histone modifications in epigenomics Aim at broad binding Lack whole genome scan; Require
highly specific antibodies
ChIP-Seq Histone modifications in epigenomics High resolution; High coverage; Low Costly; Relative slow
sample loading
LC-MS/MS Separation and qualitative analysis in Less sample loading; High coverage; Easy to be affected by the MS stability
HPLC-TOF/MS proteomics High accuracy
[86,88,90]and metabolomics [96,104]
MALDI-TOF/MS Identification and quantitative analysis of High throughput; High sensitivity Low accuracy
HPLC/ESI-MS proteomics Long analysis time
[85,114]
i-TRAQ Proteome quantitative analysis [86,87,92,114] High throughput; Time saving Costly
SILAC High label efficiency Only used for live cell
ICAT Broad compatibility Only label peptides containing cysteine,
and can only mark two samples
NMR Untargeted metabolomics [95,105] High reproducibility; Simple sample Low sensitivity; Less feature metabolites
preparation observation; Poor database
GC-MS Identification and relative quantitative analysis High throughput and sensitivity Complex extraction and derivatization
of process
GC-TOF/MS untargeted and targeted metabolomics Wide m/z range; High sensitivity Relatively low qualitative ability
GC
GC-TOF/MS [94,97e102,105,108,110,113] Four dimensions of analytical resolution Low robustness of instruments
GC-Q-TOF/MS Untargeted and targeted metabolome High quantitative stability; High selection; Costly
quantitative High scan speed
UPLC-Q-TOF-MS/MS analysis [109] Good quantitative reproducibility; Low resolution; Costly
High accuracy; High sensitivity
 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141 133

3. The applications of different feedomics technologies for
sustainable food animal production
3.1. Genomics and nutrigenetics in food animal production
efficiency and quality
Genotyping aims to identify trait-associated genetic variations
(such as a single nucleotide polymorphism (SNP), a variation in a
single nucleotide that occurs at a specific position on the genome)
that can be potentially be used for genomic breeding and/or targeted
section [30]. High coverage SNP datasets through the whole genome
not only help detect low abundance SNPs but also enable the efficient
screening and tracking of genetic markers that could transfer from
parents to offspring [31]. Released whole genome sequences of major
food animal species such as cattle [32], chicken [33], sheep [34], pig
[35] and a number of aquatic animals [36] have promoted the
application of high-throughput genetic SNP markers and accelerated
genetic improvement for food animal production and efficiency. For
example, a genome-wide association study (GWAS) was successfully
used to identify genetic variants, regions, and candidate genes
associated with feed efficiency. In total, 25, 66, and 12 SNPs have
been found to be associated with residual feed intake (RFI, one of the
measures for feed efficiency) in hybrid bulls [37], Angus steers [38]
and Yorkshire pigs [39] using the BeadChip measurement. The ge-
netic variation identified by BeadChips is further identified which
candidate genes are associated with animal feed efficiency for Nelore
cattle [40], hybrid bulls [37], pig [41], and chicken [42] (all genes and
their functions are summarized in Table 2). Similarly, Sanchez

Table 2
The information of different phenotypes related genes in feedomics.

Name Full name or location Tissues Traits Animals

HRH4 Histamine Receptor H4 Blood Feed efficiency Nelore cattle [40]

ALDH7A1 Aldehyde Dehydrogenase 7 Family Member A1
APOA2 Apolipoprotein A2
LIN7C Lin-7 Homolog C, Crumbs Cell Polarity Complex
Component
CXADR CXADR, Ig-Like Cell Adhesion Molecule
ADAM12 ADAM Metallopeptidase Domain 12
MAP7 Microtubule Associated Protein 7
GHR Growth Hormone Receptor Liver Hybrid bulls [37]
CAST Calpastatin
ACAD11 Acyl-CoA Dehydrogenase Family Member 11
UGT3A1 UDP Glycosyltransferase Family 3 Member A1
XIRP2 Xin Actin Binding Repeat Containing 2 Backfat Pig [41]
TTC29 Tetratricopeptide Repeat Domain 29
SOGA1 Suppressor Of Glucose, Autophagy Associated 1
MAS1 MAS1 Proto-Oncogene
GPCR G Protein-Coupled Receptor
GPK5 G Protein-Coupled Receptor Kinase 5
GPR155 G Protein-Coupled Receptor 155
ZFYVE26 Zinc Finger FYVE-Type Containing 26
HTR1B 5-Hydroxytryptamine Receptor 1B Blood Chicken [42]
RGS3 Regulator Of G Protein Signaling 3
ABCG2 ATP-binding cassette sub-family G member 2 Milk Milk protein Dairy cow [43]
AGPAT6 1-acylglycerol-3-phosphate O-acyltransferase 6
DGAT1 diacylglycerol O-acyltransferase 1
DHX15 DEAH-box helicase 15
MROH1 maestro heat like repeat family member 1
SLC37A1 solute carrier family 37 member 1
CSN3 casein kappa
PKD2 polycystin 2, transient receptor potential cation
channel
HERC3 HECT and RLD domain containing E3 ubiquitin
protein ligase 3
ALPL alkaline phosphatase, liver/bone/kidney
AHKH ANKH inorganic pyrophosphate transport regulator
SEL1L3 SEL1L family member 3
MGST1 microsomal glutathione S-transferase 1
CSN1S2 casein alpha-S2
MEPE matrix extracellular phosphoglycoprotein
PICALM phosphatidylinositol binding clathrin assembly protein
SEPSECS Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA
synthase
BOP1 block of proliferation 1
CSN1S1 casein alpha s1
CSN2 casein beta
RECQL4 RecQ like helicase 4
PAEP progestagen-associated endometrial protein
GPR120 G protein-coupled receptors Adipose, skeletal muscle, ileum, Fat deposition Pig [48] [49],
jejunum, duodenum, kidney, lung,
spleen, liver, and heart; blood,
muscle and ear
CYP19A1A cytochrome P450, family 19, subfamily A, polypeptide 1 Ovary Ovarian development Japanese flounder [75]
FOXL2 forkhead box L2
SMAD1 SMAD Family Member 1 Blood and muscle Body size Sheep [78]
TSC1 Tuberous Sclerosis 1
AKT1 AKT Serine/Threonine Kinase 1
134 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141
reported the 22 most plausible candidate genes associated with milk
protein composition in dairy cattle using GWAS [43] (Table 2). Thus,
whole genome- and genotyping-based GWAS studies will allow re-
searchers to discover gene markers that can be exploited in future
breeding programs to achieve high feed efficiency and high-quality
products farm animals.
Although genetic information can indicate the performance
potential of the animals, nutrients act as an important intermediate
to affect the biological and metabolic processes that determine the
overall performance [44]. It is known that diet can alter the
expression of genes, signaling, and metabolic pathways in the cells,
which subsequently changes the physiological status and finally
leads to different phenotypes [45]. Additionally, different genetics
may drive cellular responses and host metabolism to the nutrients,
which has been defined as “nutrigenetics” in human-related
studies. Nutrigenetics is used to reveal the relationship between
diet and the animal genome and aims to understand whether and
how the individual genetic components drive the responses to di-
etary variation [46]. The concept of identifying the genetic markers
related to dietary responses has been applied in swine production.
Using the widely studied G protein-coupled receptor (GPR120) gene
as an example, this gene encodes the omega-3 fatty acid receptor
which is involved in various physiological homeostasis processes
such as fat deposition, regulation of appetite and food preference
[47]. The variants in GPR120 have been significantly associated with
fat deposition and growth in pigs [48], and a recent study has
identified 3 SNPs (g.114743623G>C; g.114764865G>A; and
g.114765469C>T) among different breeds, including Italian Large
White, Italian Duroc, Italian Landrace, Casertana, Pietrain, Meishan,
and wild boars, which are associated with average daily gain [49].
Ichimura et al. demonstrated and verified that GPR120 had a key
role in sensing dietary fat and controlling energy balance in both
humans and rodents [50], suggesting that different breeds of pigs
may have different ways to exact energy from diet for growth.
However, no study has been performed on how the varied GPR120
genotypes could lead to altered dietary responses within the same
breed and whether it relates to performance. To date, the linkage of
“genetics” and “nutrition” is scarce in food animal production.
Genome-wide nutrigenetics could be a powerful tool for defining
appropriate feeding practices to raise more sustainable food ani-
mals based on an animal's genetic potentials. The variability of
marker genes (such as GPR120 gene) should be considered by using
nutrigenetics approaches to define the appropriate feeding prac-
tices, to obtain more efficient feed in heavy pigs, and to evaluate
host gene-feeding interactions.
3.2. Transcriptomics and nutrigenomics in food animal production
and health
3.2.1. Transcriptomics
As mentioned above, having the greatest genetic potential does
not guarantee the best performance of the animals since the
function of genes can be affected by many factors, with the tran-
scription process from DNA to mRNA being one of the first deter-
minant factors. The emerging studies of RNA molecules (also
defined as transcriptomics) can therefore provide valuable infor-
mation on whether “important/key genes” are being “transcribed
or not”. As one of the outcomes of transcriptomic studies, differ-
ential expressed (DE) gene analysis is used to elucidate the changes
in biological functions and metabolic pathways that are related to
production trait variation. Using feed efficiency in cattle as an
example, this trait is complex, and its biology has been proposed
but remains largely unidentified [51]. A recent study identified 70
and 19 total genes that were differentially expressed in the liver of
Holstein and Jersey dairy cows with different feed efficiency,
respectively, using RNA-Sequencing (RNA-Seq)-based tran-
scriptomics with the HiSeq 2500 machine. These genes were
involved in steroid hormone biosynthesis, lipid metabolism, and
drug metabolism cytochrome P450 [52]. A similar approach
sequenced by the HiSeq 2000 system was used to study rumen
epithelial tissues of cattle with varied feed efficiency and found 122
DE genes involved in the function of acetylation, remodeling of
adherens junctions, cytoskeletal dynamics, cell migration, and cell
turnover [53]. Based on these findings, transcriptomics can deter-
mine the underlying regulating functions of these two digestive
organs and can help identify the biological mechanism underlying
feed efficiency. In addition, RNA-Seq based transcriptomic studies
provide a fundamental understanding of functional aspects of tis-
sues. A recent study revealed transcriptomes of digestive tissues in
sheep, showing the GIT transcriptomes are mainly driven by
epidermal differentiation complex genes [54]. Such work can pro-
vide novel insights into fundamental issues concerning mammalian
digestive and gastrointestinal systems, which can directly impact
animal growth and performance through feed digestion and
nutrient absorption.
In addition to the understanding of altered molecular mecha-
nisms related to animal production, the transcriptomic-based
approach can be applied to study the molecular mechanisms of
animal health. For example, the whole blood transcriptome has
been proven to be a potential molecular phenotype diagnostic tool
for food animal health. A recent study using the RNA-Seq based
whole blood transcriptomics with the HiSeq 2000 instrument
identified 246 DE genes in sick pigs involved in a variety of systemic
immune and inflammatory responses to many physiological pro-
cesses, thus suggesting their gene marker functions are associated
with health status in commercial pigs [55]. Similarly, blood tran-
scripts can be applied as biomarkers for selecting pigs with reduced
susceptibility to Salmonella shedding [56]. Increasing dietary DHA
levels were associated with the upregulation of hepatic immune
pathways, especially chemokine signaling, FC epsilon RI signaling
and natural killer cell-mediated cytotoxicity pathways in Atlantic
salmon, which expanded our understanding of how functional di-
etary nutrients elicit signaling molecules and a physiological
impact [57]. Moreover, transcriptomic analysis of circulating leu-
kocytes in blood using a microarray identified novel aspects of the
host systemic inflammatory response to sheep scab mites, which
provided new insights into the mechanisms of local allergen-
induced inflammatory responses [58]. However, transcriptomics
research in animal health is still in its infancy due to the high cost,
lack of large phenotype data collection, and challenges in sample
collection as well as the complex causal relationship. Broader ap-
plications of animal health transcriptomics may be expected in the
near future with the dropping cost of NGS technologies and suc-
cessful experience from human studies.
3.2.2. Nutrigenomics
As mentioned in section 3.1, diet can influence the physiological
status of the host, which could be caused by the altered gene
expression at the cellular, tissue and organ levels. To study such
changes in response to diet, nutrigenomics has been widely
accepted as a concept for investigating the effects of feed or nu-
trients on gene expression, which provides understanding on how
nutrition affects metabolic pathways and diet-gene interactions
[59]. Research on nutrigenomics provide the promise to uncover
key biological responses to nutrients in food animal species,
especially when considering the dietary supplementations. Recent
research based on a microarray revealed how Zn supplementation
altered the expression of genes in jugular venous blood of lactating
sheep, which is related to immunity and cardiac contraction pat-
terns [60]. Similarly, the dietary nutritional level can alter the genes
 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141 135

involved in spermatogenesis or apoptosis in testis of sheep, thus
providing a cellular and molecular understanding of the testis
response to nutrition and potential nutrition strategies to improve
reproduction [61]. Using nutrigenomics, the impact of dietary
manipulations on the immune system in fish is becoming clearer
[62]. Nutrigenomics make it possible to formulate individualized
diet from alternative feed resources, to further develop precision
feeding strategies in terms of productivity enhancement and/or to
prevent diet-induced diseases. In summary, the transcriptomics
and nutrigenomics studies can help develop the targeted diet
modifications for highly efficient food animal production and low
diet-related disease risk in the defined farm population. The food
animal-based nutrigenomics has just started and focused on only
limited number of animals, so it lacks specific, convincing evidence
about diet-gene interactions. There is still a long way to make real
personalized nutrition using food animal nutrigenomics even with
high hope.
3.3. MicroRNAomes in food animal production and health
MicroRNAs (miRNAs) have been identified as important post-
transcriptional regulators of gene expression and have been
proven to affect stress, tissue development, and reproduction in
food animal species [63]. To date, most of the studies on miRNA
discovery are based on RNA-Seq, although miRNA microarrays can
also be effective for screening the known miRNAs. The currently
known miRNA genes in animals including human, orangutan,
cattle, horse, pig, sheep, dog, mouse, rat, chicken, platypus,
zebrafish, tetraodon, zebra finch and fruit fly were 1881, 642, 808,
715, 383, 106, 502, 1193, 495, 740, 396, 346, 132, 247 and 256,
respectively [64]. Similar to coding genes, the genetic variability of
miRNA genes were identified, and the cattle had the most poly-
morphic miRNA genes, followed by human, fruit fly, mouse,
chicken, pig, horse, and sheep (ranged from 3.8% in tetraodon to
91.7% in cattle) [65].
We summarized the miRNAs reported to be associated with
nitrogen efficiency, heat stress, early pregnancy, lipid metabolism
immune response, fat depot and so on in food animals, and this
summary also showed the predicted targets of certain miRNAs and
their specificity to different tissues and species in Table 3. Such
findings highlight the potential regulatory correlations between
miRNAs and different phenotypes. Our lab is among one of the first
to study bovine miRNAs and has established methods for studying
bovine tissue [66] and circulating miRNAs [67] using the micro-
array and HiSeq 2000 system, respectively. We have identified
miRNAs from many tissues and body fluids (whole blood, serum,
and milk) and have discovered bovine miRNAs that are associated
with dairy cow nitrogen utilization efficiency, gut tissue develop-
ment, fat adipogenesis and foodborne pathogen shedding in pigs
[68e70]. One of our recent efforts revealed the features of miRNAs
in bovine sera and exosomes and found that miRNAs from sera may
be preferable for detecting inflammation while miRNAs from exo-
somes should be better for monitoring muscle development and
lipid metabolism status in cattle [67]. In addition, other studies
have shown that the circulating miRNAs from plasma and serum
can be used as informative biomarkers for food animal health and
well-being (also summarized in Table 3), such as miR-26a for cattle
early pregnancy [71] and miR-19a and miR-19b for cattle heat stress
[72]. The miR-3570 could target and inhibit the expression of the
mitochondrial antiviral signaling protein, thereby inhibiting NF-kB
and IRF3 signaling-mediated immunity in teleost fish [73], which
was identified as a novel mechanism for virus evasion in fish. The

Table 3
The information of different phenotypes related microRNAs in feedomics.

Name Predicted targetsa Tissues Traits Animals

miR-99b ST6GALNAC4, HS3ST2, KBTBD8 Rumen Nitrogen efficiency Holstein cows [70]
miR-2336 C6ORF50, COLCA2, CD28, DOK4, LIN52, EVA1B, MATR3 Duodenum
miR-652 ISL1 Jejunum
miR-1 GJA1, POGK, ARCN1, SH3BGRL3, PGRMC1, TAGLN2, Liver
TMSB4X, SLC44A1, TWF1
miR-181a ZNF781, ZNF283, ZNF788, ZNF791, ZNF136, ZNF594, Mammary gland
ZNF788, ZNF302, ZFP30, RBAK, CTD-2228K2.5, ZNF268, Serum Heat stress Holstein cows [72]
ZFP82, ZNF527, CTD-2140B24.4, ZNF140, CDON, UBN2,
ZNF470, ZNF256, ZNF23
miR-26a STRADB, CHORDC1, KLHL42, SLC25A16, HMGA2, TET2, Blood Early pregnancy Holstein-Friesian heifers [71]
MAB21L1, TAF13, PIH1D3, CKS2, OSBPL11, THAP2, CREBZF, UBN2
miR-19a KBTBD8, ZMYND11, EXOC6B, C11orf96, FOXD4L2, UBL3, ENPP5, Serum Heat stress Holstein cows [72]
miR-19b FGF6, CNOT6, CHIC1, PMEPA1, SGK1, SLC26A7, MDM4, LONRF1,
ADRB1, RAP2C, PIK3CB, MPPED2, PTEN, HBP1, PFN2
miR-27b GORASP1, KIAA1109, AKIRIN1, NOVA1, ONECUT2, FAM65B, EBI3,
PLK2, NGFRAP1, HOXA5, CCNC
miR-30a-5p TNXB, AC002451.1, MKRN3, EED, DLGAP1, B3GNT5, LHX8, INO80D,
RP11-160N1.10, ANKRA2, KLHL20, STX2, PIP4K2A, SRSF7, DESI2
miR-181b Same as miR-181a
miR-345-3p DAZ4, C4orf6, ZNF616, ZNF189, PRR26, ATF7IP2, LINC00998, HMGCS1
miR-1246 CDR1as, TMPRSS11A, GSG1L, FUT9, ZNF23, ORC6, AL355390.1, LCE2D
miR-196 HOXC8, HOXA7, HOXB8, RP1-170O19.20, NR6A1, HOXA9, HMGA2, Adipose tissue Fat depot Hereford
Aberdeen Angus [66]
HOXB7, HAND1
miR-2454 e
miR-33a e Lipid metabolism Beef cattle [122]
miR-1281 HIST2H3A, AL592284.1, C22orf46, SLC11A1, GAB2, LTB, MSANTD1, LIF,
TEX22, CTD-3214H19.16, FAM98A, ADAMTS13
miR-214 ANKRD65 Blood Immune responses to Pig [69]
miR-331-3p TSPAN18, ZNF513 Salmonella infection
miR-3570 MAVS Cell line Immune Response to Teleost fish [73]
Rhabdovirus
miR-378 e Cell line Osteoblast differentiation [122]
a
Predicted targets, only selected the target gene with cumulative weighted contextþþ score less than 0.7. The target genes of selected miRNAs were commonly predicted
by TargetScan Relase 6.0 (http://www.targetscan.org/) [123] and miRanda (http://www.microrna.org/microrna/home.do).
136 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141
current progress in the miRNAome area has provided influential
evidence of miRNAs associated with various diseases and the po-
tential biomarkers applied for disease prevention and diagnosis.
These miRNAs offer potential roles in assisting industry with
management strategies to improve cattle production, health, and
welfare.
In addition, many miRNAs have been identified from crops and
observed in some public animal miRNA datasets; for example, one
study verified that miR-168a in rice can bind to the low-density
lipoprotein receptor adapter protein 1 mRNA of human/mouse,
with the inhibited expression of this mRNA in liver and a decrease
in low-density lipoprotein removal from mouse plasma based on
in vitro and in vivo experiments [74]. Such findings significantly
extend our understanding of the role of miRNAs from food/feed on
animals. For food animals, the feed miRNAs may serve as “bioac-
tive” components that can pass through the food animal GIT, enter
the circulatory system, and regulate the expression of target genes
in different various organs. This suggests that developing miRNA-
based feed additives may be a lighting direction for the future
biotechnology and food animal commodity to alter animal gene
expression for improving productivity and health. In ruminants, the
feed miRNAs may be degraded in the rumen, but they may be able
to escape the destructive conditions in monogastric animals. To
date, no research has been done to see whether feed-derived
miRNAs can enter and regulate the physiological functions in
food animal conditions, which has a great potential for developing
miRNAs into a novel nutrient component.
3.4. Epigenomics in food animal phenotypic variations
Epigenetic regulation is another factor that can affect gene
expression that may alter the genetic potential. As part of the
epigenetic machinery, DNA methylation-driven epigenetic changes
in response to dietary variation have been largely observed in
different food animal species. For example, the variation trend of
the DNA methylation level in promoter and exon 1 of CYP19A1A and
coding region of FOXL2 was negatively associated with their
expression levels during ovarian development in Japanese flounder
using the methylated DNA kit [75], which clarified the functions of
these 2 genes in ovary development from an epigenetic perspec-
tive. The changed gene expression and methylation of non-
structural maintenance of chromosomes subunits of condensin I
in the liver and skeletal muscle of offspring was observed using
Bisulfite sequencing (Bisulfite-Seq) with QIAGEN sequencing ser-
vices when high and low feed protein level applied in the pregnant
pig diet, which indicated an involvement of DNA methylation by
maternal protein supply [76]. It has also been reported that DNA
methylation differences had a highly significant effect on muscle
fiber density and drip loss in a Chinese native chicken breed [77]. In
addition, the DNA methylation of SMAD1, TSC1, and AKT1 genes
showed significant differences across different sheep breeds, and 6
CpG islands were significantly correlated with RNA expression and
body size using the methylated DNA immunoprecipitation-
sequencing (MeDIP-Seq) with the HiSeq 2000 system [78]. More-
over, Genome-wide DNA methylation profiles have been reported
in bovine muscle tissue [79] and placentas [80] using the MeDIP-
Seq with the HiSeq 2000 system; pig neocortex, spleen, liver,
femoral muscle, olfactory epithelium and pulmonary alveolar
macrophages cell lines [81]; sheep muscle [82] using the reduced
representation Bisulfite-Seq with the HiSeq 2000 analyzer; and
chicken pectoral muscle tissues [77], retina, cornea and brain using
the Bisulfite-Seq with the HiSeq 2500 platform [83]. Moreover, it
has been suggested that DNA methylation may play a regulatory
role in silencing of gene expression related to milk protein in the
dairy cow [84]. Although such relationships have not been studied
during dietary changes, it is speculated that different feeds could
lead to shifts in the methylation pattern, which could be related to
phenotypic changes. Studies are increasingly starting to reveal the
evidence of epigenetic-regulated gene expression under various
environmental conditions, but most of them have focused only on
DNA methylation. Studies on other epigenetic mechanisms such as
histone modification and how to determine the heritability of
epigenetic-driven traits are also needed. Specifically, how the feed
composition could alter the epigenomes and whether the altered
epigenetic variations can be passed to the next generation are
largely unknown. For meat animals, the epigenetics should more
contribute to the unexplained phenotypic variation in food animal
production traits, but for milk production animals, the epigenetic
variations that persist throughout life and be transmitted to the
next generation are worth being studied well. Therefore, feed se-
lection or management strategies should take the epigenetic marks
into consideration, which is needed to achieve the targeted out-
comes for growth, physiology and performance.
3.5. Proteomics in food animal production, product quality, and
health
The number of proteomics and metabolomics research in food
animal species has rapidly increased, indicating another advanced
research era for furthering our understanding of animal biology.
Based on the HPLC/ESI-MS proteomics method, cow milk adulter-
ation in goat milk was quantified [85], and LC-MS/MS-based whey
proteomics revealed that the milk quality was genetically and
biologically diverse among ruminants. The milk could be grouped
into three clusters: (1) cow, buffalo, and yak milk; (2) goat, cow,
buffalo, and yak milk; and (3) camel milk [86]. It is known that
different feeding strategies are applied for milk-producing rumi-
nants, which contribute many of the components in the milk. This
study provided information on nutritional values for human intake
could also help to develop better strategies in the non-cow rumi-
nants for productivity and milk quality. In addition, the proteomes
have been reported to be associated with meat quality in beef, pork,
and chicken, such as beef muscle color, meat tenderness, fresh,
lean-to-fat ratio, intramuscular fat content and quality in different
breeds using the iTRAQ labeling-based proteomics [87]. The dietary
yeast cell wall extracts caused a change in the proteomic profile of
Atlantic salmon skin mucus, and the calreticulin-like protein was
identified as a putative biomarker for yeast-derived functional
feeds using LC-MS/MS-based proteomics [88]. Meanwhile, the
targeted feeding and management proteomics have shown positive
outcomes to improve the water-holding capacity in pork loin meat
(using feed additive) and meat quality in swine production [89],
lamb meat tenderness studied by the HPLC-Q-TOF/MS [90], meat
quality and yield, color, and oxidative stability, and woody broiler
breast in poultry production identified by the ESI-Q-TOF/MS [91].
These results suggest that proteomics is a powerful tool that can
guide the production of more customer-traits products. Although
many studies have accelerated proteomics research in food animal
product traits, their linkage to feed biochemistry, genomics, and
microbiomics should be investigate urgently, especially the mech-
anism of certain nutrients on production-related biology and
nutrient pathways from feed to product at the molecular level.
Proteomics can also be a valuable tool for evaluating food animal
welfare and coping with unavoidable stress challenges. It is re-
ported that the proteome changed in normal milk exosomes, milk
fat globule membranes and whey proteomes from cows infected
with mastitis using iTRAQ labeling-based proteomics [92]. Further,
a combined omics study with proteomics, transcriptomics, and
metabolomics showed that the carbohydrate metabolism and
cytoskeleton stabilization cellular mechanisms in muscle tissue
 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141
were affected by the restraint and transport stress in chickens [93],
suggesting that omics can be applied for the potential diagnosis of
animal health. Based on these findings, food animal proteomics has
revealed the physiological, pathological, and putative diagnostic
information through hundreds or even thousands of proteins under
different diets and environmental and nutritional statuses. This
information can therefore help optimize feed at both the quanti-
tative and qualitative levels to improve an animal's metabolic ac-
tivity to produce high quantity and desirable quality meat and milk
and to balance animal production and animal health and welfare.
3.6. Metabolomics to drive sustainable food animal production
We summarized the study level, type, and topic in the applica-
tion of metabolomics on food animals in Fig. 1 to help select the
suitable platform when performing food animal metabolomics
studies. The food animal untargeted and targeted metabolomics are
typically classified into overall and partial levels based on the
sample characteristics, which represent the comprehensive meta-
bolism profiles of the whole organism and unique metabolism
patterns of a certain tissue or organ, respectively (Fig. 1). Blood (as
well as plasma and serum) and urine metabolomics in food animals
are widely assessed to address well-being (beef cattle welfare,
hormone abuse in cattle, dairy cow insulin resistance with cinna-
mon using GC-MS and UPLC-MS/MS [94], asphyxia, resuscitation
and weaning stress in pig using NMR [95]), health (dairy cows
hepatic lipidosis, ketosis, milk fever, displaced abomasum, lame-
ness using LC-MS/MS [96], cold stress response in the discus fish
using GC-TOF/MS [97]), comprehensive metabolism with GC-TOF/
MS [98], and biomarker (infeed antibiotics in piglets using GC-MS
[99], forage type induced different milk protein productions using
GC-TOF/MS [100]) related problems. Digesta, fecal and saliva
metabolomics have also been studied, which are assigned to the
partial level (Fig. 1) and provide information about feed utilization,
nutrient digest and interface with the microbiome (rumen micro-
biome in goat using GC-TOF/MS [101] and hindgut microbiome in
pig using GC-MS [102]). The tissue (major about liver, muscle, ad-
ipose, mammary gland, rumen, and gut), milk and single cell
metabolomics also belong to a partial level, with the research topic
Fig. 1. Study level, type, and topic in the application of metabolomics in food animal.
137
of nutrients partition, specific function, output analyzed by
Electrophoresis-TOF/MS [103], and metabolism evaluation (insulin
neutralization and fasting in chicken [104] and potential metabolic
disorder of cattle using NMR, GC-MS and direct flow injection-MS/
MS [105]).
Since the metabolites are located at the end of biological path-
ways, transfer the information of DNA, RNA, and protein and reflect
the real metabolic profiling under internal and external stimulates,
metabolomics generates lots of internal phenotypes (also called
“metabotype”), which can link well to external phenotypes [106].
Accumulating evidence identified by NMR suggests that metab-
otypes can benefit the sustainable food animal industry in many
aspects. For instance, plasma metabolites are associated with var-
iations in production traits in beef cattle and varied abundance of
creatine, hippurate and carnitine accounted for 32% of the pheno-
typic variation in RFI [107]. The accuracy of prediction using these
metabolites associated with feed efficiency was 95%, which
strongly indicated plasma metabolites could be used as markers for
selection for these traits [107]. In addition, Melzer et al. proposed
that metabolites can be used to predict milk traits based on their
research on the 190 milk metabolites identified from 1305 Holstein
cows over 18 commercial farms using GC-MS [108]. In addition, the
rumen fluid metabolomics showed a high association between
rumen metabolites and feed efficiency on crossbreed steers using
UPLC-Q-TOF-MS/MS [109]. Moreover, Sharifi et al. detected signif-
icant associations between egg yolk metabolites and hatchability
traits in laying hens using GC-TOF/MS [110]. Using direct analysis in
real time-TOF/MS-based metabolomics, the differentiation of
common carp muscle in response to dietary supplementation was
feasible [111]. These findings suggest that metabolomics is a
powerful tool for evaluating diet on food animal health and product
quality, which would promote sustainable food animal production
and reduce animal welfare concerns. However, the metabolites for
food animal species lack a known coverage database. Dr. Wishart's
lab at the University of Alberta has built an open-access and
comprehensive livestock metabolome database (LMDB, http://
www.lmdb.ca) with 1070 metabolites from different tissues and
biofluids of 5 major livestock species (bovine, ovine, caprine,
equine, and porcine) in 149 peer-reviewed papers, which could
138 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141
serve as a hub for food animal researchers and the food animal
industry to further advance the field of food animal metabolomics
[106]. This is currently the only database for the food animal
metabolome, but it only compiles data from published papers
without validation or in-depth investigation.
3.7. Proteomics and metabolomics to understand the utilization of
alternative feed source
Proteomics and metabolomics were also successfully applied
in the mechanical characterization of alternative feed source. Crop
by-products is one type of alternative feed sources, especially for
ruminants. Enhancing the utilization of crop by-products to pro-
duce high-quality food animal product is a promising direction to
achieve sustainable food animal production. Corn stover (CS) and
rice straw (RS), as the most abundant crop by-products, can
significantly lower both the milk production and milk protein
content when replacing 23% of alfalfa hay (AH, current practice in
the modern dairy farm) in dairy cow diets [112]. The rumen fluid,
serum, milk and urine metabolomics showed that the gluconeo-
genesis, pyruvate metabolism, tricarboxylic acid cycle, glycer-
olipid metabolism, and aspartate metabolism pathways were the
most enriched in AH [98]; CS-fed cows had significantly down-
regulated glycine, serine, and threonine metabolism, tyrosine
metabolism, and phenylalanine metabolism compared with AH-
fed cows [113]; and hippuric acid and N-methyl-glutamic in the
urine were further identified as potential biomarkers for
discriminating CS and AH diets [100]. The proteome results
showed 231 up-regulated and 286 down-regulated proteins and
inhibited energy and fatty acid metabolism in the mammary
gland tissue in the RS group [114]. The above information pro-
vided a new understanding of and applicable candidates for the
mechanisms of crop by-product utilization. However, the lack of
interactions with feed metabolomics and proteomics is the com-
mon limitation of these studies.
Fig. 2. Future directions of feedomics. The four compositions of feedomics (feed, food animal, products, and human) were illustrated with grey color. The grey arrow represents the
currently studied contents in feedomics. The blue arrow represents the future research directions in feedomics. The corresponding targets and omics tools are also described in the
figure.
3.8. Microbiomics with metagenomics and metatranscriptomics in
food animal production
Tremendous research has shown that symbiotic and commensal
microbiota play vital roles in feed digestion and in shaping host
functions. Food animal microbes play important roles in extracting
nutrients and energy harvesting from the feed, regulating methane
emissions, relating inflammatory responses, affecting fat storage,
and promoting gut epithelium renewal, as revealed by the pyro-
sequencing using the HiSeq 2500 system [115]. For this review, we
use the rumen microbiome as an example to highlight the recent
research on its role in cattle feed efficiency and methane emission.
Ruminants harbor a complex rumen microbiome that can convert
human indigestible feed materials into volatile fatty acids and other
nutrients so the host can produce high-quality protein meat and
milk. The recent metagenomics research on rumen microbiome of
dairy cows revealed that microbial diversity, microbial taxa, and
genes are associated with different feed efficiency using HiSeq
2500 and MiSeq systems [116]. Similarly, the rumen metatran-
scriptomic profiling of beef cattle rumen showed active microbial
taxa and functions associated with feed efficiency beef cattle using
the HiSeq 2000 system [117]. Based on rumen metagenomics and
metatranscriptomics, methanogenesis pathway transcription pro-
files were identified to be correlated with methane yields in sheep
[118], and Kamke et al. further revealed that low-methane-yield
sheep had a Sharpea-enriched microbiome with a more lactic acid
formation and utilization using rumen identified with meta-
genomics and metatranscriptomics using the HiSeq 2000 system
[119]. These findings provide a foundation for developing new
nutritional and management strategies to mitigate methane
emission and improve feed efficiency by manipulating the micro-
biota composition and functions. In other food animal species,
metagenomics analysis showed that microbiota and functional
capacities in the cecum have also been reported to be associated
with feed efficiency in finishing pigs identified by HiSeq 2500
 H.-Z. Sun, L.L. Guan / Trends in Analytical Chemistry 107 (2018) 130e141
platform [120] and in chickens using the MiSeq system [121],
suggesting that the regulation of microorganism composition could
be applied to the pig production industry. The above ecological and
mechanistic understanding of the GIT microbiome could lead to an
increase in productivity and an environmentally friendly food an-
imal industry. The limitations of these studies are that they do not
consider the potential roles and interactions with feed and envi-
ronment microbiomes.
4. Conclusions and future outlooks
In this paper, we proposed the concept of “feedomics” in feed
science and animal nutrition area and provided a detailed review
of the recent studies applying genomics, epigenomics, tran-
scriptomics, proteomics, metabolomics, metagenomics and met-
atranscriptomics strategies to study the production and health
issues of food animals. Feedomics provides a new understanding
of the complex biochemical mechanisms involved in the inter-
action of diet, environment, host physiology, microbial functions
and phenotypes and has the promise to be well developed into a
targeted method for improving the quantity, quality, safety and
functional properties of food animal products while reducing the
use of antimicrobial growth promotants and mitigating green-
house gas emissions from the food animal sectors using regular
or alternative feed resource or novel feed additives (e.g., miRNAs)
to meet the increasing human consumption demand in the
future. These omics-based strategies provide important insights
into animal biological information and omics-based nutrition,
which are far beyond but also tightly associated with the mea-
surement results from traditional techniques. The crucial power
of these omics methods is revealing true causal internal pheno-
types (gene, transcripts, protein, and metabolites), metabolic
functions, regulatory pathways leading to improved feed effi-
ciency, well animal welfare, and sustainable development in the
food animal industry. The outcomes of omics should be applied
in nutritional regulation, the breeding program (especially for
the local breeds in extremely regions) and management
improvement practice, which would be great benefit to animals
in the future.
Except for the currently studied contents of improving food
animal sectors’ efficiency and sustainability from input (feed) to
output (product) in feedomics, several other directions such as
feed quality assessment, interactions with plant omics and
biochemistry, food animal impact on human health and future
customer-traits evaluation, should be paid attention to in future
work (Fig. 2). Using plant genomics, proteomics, metabolomics
and miRNAs to develop a species-specific flavor feed, contami-
nation reduction feed, and less-emission (methane, CO2) feed
source will be novel investigations in the feed quality assessment
of feedomics (Fig. 2). Feedomics could also be a powerful tool to
reveal the underlying mechanism of food animal on human
health, such as antimicrobial resistance and zoonosis. Mean-
while, evaluating future customer traits such as being rich in
natural healthy molecules and live ingredients will require
tremendous efforts of feedomics, especially by proteomics,
metabolomics, and microbiomics. The action of different levels of
biomolecules (e.g., DNA, mRNA, miRNA, protein, lipid, metabo-
lite) will play a vital role and provide clues for feed, food animal,
product and human in future feedomics studies. The integrated
application of multi-omics, especially for the entire pool of
different levels of biomolecules, to understand the information
flow will be a new trend in feedomics. Feedomics is still in its
infancy period, so further enhancing its analytical sensitivity,
accuracy, coverage depth and matched databases is still a big
challenge for future work.
139
Acknowledgments
This work was supported by China Opportunity Fund (spon-
sored by University of Alberta, RES0031665) and NSERC Discovery
grant.
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