Avianomics: The Beginning at the End
DOI:
https://doi.org/10.17140/aftnsoj-6-171Abstract
The research-teaching nexus is the pinnacle of academic activity. As a scientist and educator, my overall objective is to give students access to cutting-edge research and help them develop high order inquiry skills. In addition, as research and thesis writing frequently involves the development of new complex reading skills associated with comprehension and synthesis of a tremendous volume of information, along with in-depth critical analysis, evaluation, and elegant academic writing style, I decided to assign this editorial to my 2020-Biochemical Nutrition graduate students. As my students have diverse educational and cultural backgrounds and have been exposed to a variety of tech-based learning, we decided to summarize here recent advances in omics research in avian species to facilitate the discussion by asking new questions, which may help open new vistas for future investigations. By following the “scaffolded” approach, my students highlighted progress in Transcriptomics (Komp M and Bowie R), Proteomics (Tabler T and Lee T), Kinom-ics (Hernandez RM and Zuo B), Epigenomics (Ferver A), Metabolomics (Maynard C and Mullenix G), and Microbiomics (Teyssier JR and Bodle B). I would like to thank my students for their motivation, dedication, determination, perseverance, connection, consistency, and support. I would also like to thank AFTNS-OJ for inviting me to write this editorial and I hope by getting my students involved would promote their curi-osity, help them understand complex questions, explore more sources, stimulate their independent thinking, and create research- and question-mindsets.
References
Chambers DC, Lukowski SW, Powell JE. Transcriptomics and single-cell RNA-sequencing. Respirology. 2019; 24(1): 29-36. doi: 10.1111/resp.13412
Jax E, Wink M, Kraus RHS. Avian transcriptomics: Opportunities and challenges. J Ornithol. 2018; 159: 599-629. doi: 10.1007/ s10336-018-1532-5
Wolf JB. Principles of transcriptome analysis and gene expression quantification: An RNA-seq tutorial. Mol Ecol Resour. 2013; 13: 559-572. doi: 10.1111/1755-0998.12109
Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T. Transcriptomics technologies. PLoS Comput Biol. 2017; 13: e1005457. doi: 10.1371/journal.pcbi.1005457
Li P, He F, Wu C, Zhao G, Hardwidge PR, Li N, et al. Transcriptomic analysis of chicken lungs infected with avian and bovine pasteurella multocida serotype A. Front Vet Sci. 2020; 7: 452. doi: 10.3389/fvets.2020.00452
Deist MS, Gallardo RA, Dekkers JCM, Zhou H, Lamont SJ. Novel combined tissue transcriptome analysis after lentogenic newcastle disease virus challenge in inbred chicken lines of differential resistance. Front Genet. 2020; 11: 11. doi: 10.3389/ fgene.2020.00011
Mutryn MF, Brannick EM, Fu W, Lee WR, Abasht B. Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing. BMC Genomics. 2015; 16: 399. doi: 10.1186/s12864-015-1623-0
Marchesi JAP, Ibelli AMG, Peixoto JO, Cantão ME, Pandolfi JRC, Marciano CMM, et al. Whole transcriptome analysis of the pectoralis major muscle reveals molecular mechanisms involved with white striping in broiler chickens. Poult Sci. 2019; 98: 590- 601. doi: 10.3382/ps/pey429
Beauclercq S, Hennequet-Antier C, Praud C, Godet E, Collin A, Tesseraud S, et al. Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken. Sci Rep. 2017; 7: 6447. doi: 10.1038/s41598-017-06511-6 de Oliveira HC, Ibellim AMG, Guimarães SEF, Cantão ME, de Oliveira Peixoto J, Coutinho LL, et al. RNA-seq reveals downregulated osteochondral genes potentially related to tibia bacterial chondronecrosis with osteomyelitis in broilers. BMC Genet. 2020; 21: 58. doi: 10.1186/s12863-020-00862-2
Wu Y, Wang Y, Yin D, Mahmood T, Yuan J. Transcriptome analysis reveals a molecular understanding of nicotinamide and butyrate sodium on meat quality of broilers under high stocking density. BMC Genomics21, 412 (2020). doi: 10.21203/ rs.2.16378/v2
Coble DJ, Fleming D, Persia ME, Ashwell CM, Rothschild MF, Schmidt CJ, et al. RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature. BMC Genomics. 2014; 15: 1084. doi: 10.1186/1471-2164-15-1084
Monson MS, Van Goor AG, Persia ME, Rothschild MF, Schmidt CJ, Lamont SJ. Genetic lines respond uniquely within the chicken thymic transcriptome to acute heat stress and low dose lipopolysaccharide. Sci Rep. 2019; 9: 13649. doi: 10.1038/ s41598-019-50051-0
Monson MS, Van Goor AG, Ashwell CM, Persia ME, Rothschild MF, Schmidt CJ, et al. Immunomodulatory effects of heat stress and lipopolysaccharide on the bursal transcriptome in two distinct chicken lines. BMC Genomics. 2018; 19: 643. doi: 10.1186/ s12864-018-5033-y
Yi G, Yuan J, Bi H, Yan W, Yang N, Qu L. In-depth duodenal transcriptome survey in chickens with divergent feed efficiency using RNA-Seq. PLoS One. 2015; 10: e0136765. doi: 10.1371/ journal.pone.0136765
Yang L, He T, Xiong F, Chen X, Fan X, Jin S, et al. Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis. BMC Genomics. 2020; 21: 292. doi: 10.1186/s12864-020- 6713-y
Kong BW, Song JJ, Lee JY, Hargis BM, Wing T, Lassiter K, Bottje W. Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K oligo microarray. I. Top differentially expressed genes. Poult Sci. 2011; 90: 2535-2547. doi: 10.3382/ps.2011-01435
Xu X, Zhao X, Lu L, Duan X, Qin H, Du X, et al. Transcriptomic analysis of different stages of pigeon ovaries by RNA-sequencing. Mol Reprod Dev. 2016; 83: 640-648. doi: 10.1002/ mrd.22670
Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE. Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution. Mol Ecol. 2015; 24: 1218- 1235. doi: 10.1111/mec.13113
Lu M, Bai J, Xu B, Sun QY, Wei FX, Tang XF, et al. Effect Adv Food Technol Nutr Sci Open J. 2020; 6(2): 70-78. doi: 10.17140/AFTNSOJ-6-171 of alpha-lipoic acid on relieving ammonia stress and hepatic proteomic analyses of broilers. Poult Sci. 2017; 96: 88-97. doi: 10.3382/ps/pew285
Wang Y, Guo Y, Ning D, Peng Y, Cai H, Tan J, et al. Changes of hepatic biochemical parameters and proteomics in broilers with cold-induced ascites. J Anim Sci Biotechnol. 2012; 3: 41. doi: 10.1186/2049-1891-3-41
Cumberbatch JA, Brewer D, Vidavsky I, Sharif S. Chicken major histocompatibility complex class II molecules of the B haplotype present self and foreign peptides. Anim Genet. 2006; 37: 393-396. doi: 10.1111/j.1365-2052.2006.01459.x
Polansky O, Seidlerova Z, Faldynova M, Sisak F, Rychlik I. Protein expression in the liver and blood serum in chickens in response to Salmonella Enteritidis infection. Vet Immunol Immunopathol. 2018; 205: 10-16. doi: 10.1016/j.vetimm.2018.10.006
Zhao Z, Zhao Q, Zhu S, Huang B, Lv L, Chen T, et al. iTRAQ-based comparative proteomic analysis of cells infected with Eimeria tenella sporozoites. Parasite. 2019; 26: 7. doi: 10.1051/parasite/2019009
Packialakshmi B, Liyanage R, Lay JO, Okimoto R, Rath NC. Proteomic changes in the plasma of broiler chickens with femoral head necrosis. Biomark Insights. 2016; 11: 55-62. doi: 10.4137/ BMI.S38291
Cai K, Shao W, Chen X, Campbell YL, Nair MN, Suman SP, et al. Meat quality traits and proteome profile of woody broiler breast (pectoralis major) meat. Poult Sci. 2018; 97: 337-346. doi: 10.3382/ps/pex284
Ning H, Cui Y, Song X, Chen L, Yin Z, Hua L, et al. iTRAQbased proteomic analysis reveals key proteins affecting cardiac function in broilers that died of sudden death syndrome. Poult Sci. 2019; 98: 6472-6482. doi: 10.3382/ps/pez532
Kuttappan VA, Bottje W, Ramnathan R, Hartson SD, Coon CN, Kong B-W, et al. Proteomic analysis reveals changes in carbohydrate and protein metabolism associated with broiler breast myopathy. Poult Sci. 2017; 96: 2992-2999. doi: 10.3382/ps/pex069
Xing T, Wang C, Zhao X, Dai C, Zhou G, Xu X. Proteome analysis using isobaric tags for relative and absolute analysis quantitation (iTRAQ) reveals alterations in stress-induced dysfunctional chicken muscle. J Agric Food Chem. 2017; 65: 2913-2922. doi: 10.1021/acs.jafc.6b05835
Mekchay S, Teltathum T, Nakasathien S, Pongpaichan P. Proteomic analysis of tenderness trait in Thai native and commerical broiler chicken muscles. Japan Poult Sci Assoc. 2010; 8: 8-12
Phongpa-Ngan P, Grider A, Mulligan JH, Aggrey SE, Wicker L. Proteomic analysis and differential expression in protein extracted from chicken with a varying growth rate and water-holding capacity. J Agric Food Chem. 2011; 59: 13181-13187. doi: 10.1021/ jf202622n
Liu XD, Jayasena DD, Jung Y, Jung S, Kang BS, Heo KN,et al. Differential proteome analysis of breast and thigh muscles between Korean native chickens and commercial broilers. Asian-Australasian J Anim Sci. 2012; 25: 895-902. doi: 10.5713/ ajas.2011.11374
Zheng A, Chang W, Liu G, Yue Y, Li J, Zhang S, et al. Molecular differences in hepatic metabolism between AA broiler and big bone chickens: A proteomic study. PLoS One. 2016; 11: e0164702. doi: 10.1371/journal.pone.0164702
Luo J, Zheng A, Meng K, Chang W, Bai Y, et al. Proteome changes in the intestinal mucosa of broiler (Gallus gallus) activated by probiotic Enterococcus faecium. J Proteomics. 2013; 91: 226-241. doi: 10.1016/j.jprot.2013.07.017
O'Reilly EL, Burchmore RJ, Sparks NH, Eckersall PD. The effect of microbial challenge on the intestinal proteome of broiler chickens. Proteome Sci. 2016; 15: 10. doi: 10.1186/s12953-017- 0118-0
Tu WL, Cheng C-Y, Chen C-J, Chan H-L, Wang S-H, Tang P-C, et al. Proteomic analysis of the hypothalamus of broiler-type Taiwan country chickens in response to acute heat stress. Anim Sci J. 2018; 89: 1475-1485. doi: 10.1111/asj.13060
Kong BW, Lassiter K, Piekarski-Welsher A, Dridi S, Reverter-Gomez A, Hudson NJ, et al. Proteomics of breast muscle tissue associated with the phenotypic expression of feed efficiency within a pedigree male broiler line: I. Highlight on mitochondria. PLoS One. 2016; 11: e0155679. doi: 10.1371/journal. pone.0155679
Wang L, Cheng B, Li H, Wang Y. Proteomics analysis of preadipocytes between fat and lean broilers. Br Poult Sci. 2019; 60: 522-529. doi: 10.1080/00071668.2019.1621989
Ubersax JA, Ferrell JE. Mechanisms of specificity in protein phosphorylation. Nat Rev Mol Cell Biol. 2007; 8: 530-541. doi: 10.1038/nrm2203
Cohen P. The regulation of protein function by multisite phosphorylation--a 25 year update. Trends Biochem Sci. 2000; 25: 596-601. doi: 10.1016/s0968-0004(00)01712-6
Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science. 2002; 298: 1912-1934. doi: 10.1126/science.1075762
Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, et al. Global analysis of protein activities using proteome chips. Science. 2001; 293: 2101-2105. doi: 10.1126/science.1062191
Reimer U, Reineke U, Schneider-Mergener J. Peptide arrays: Adv Food Technol Nutr Sci Open J. 2020; 6(2): 70-78. doi: 10.17140/AFTNSOJ-6-171 From macro to micro. Curr Opin Biotechnol. 2002; 13: 315-320. doi: 10.1016/s0958-1669(02)00339-7
Kogut MH, Swaggerty CL, Byrd JA, Selvaraj R, Arsenault RJ. Chicken-specific kinome array reveals that salmonella enterica serovar enteritidis modulates host immune signaling pathways in the cecum to establish a persistence infection. Int J Mol Sci. 2016; 17: 1207. doi: 10.3390/ijms17081207
Kogut MH. Genovese KJ, He H, Arsenault RJ. AMPK and mTOR: Sensors and regulators of immunometabolic changes during Salmonella infection in the chicken. Poult Sci. 2016; 95: 345-353. doi: 10.3382/ps/pev349
Napper S, Dadgar S, Arsenault RJ, Trost B, Scruten E, Kusalik A, et al. Induction of tissue- and stressor-specific kinomic responses in chickens exposed to hot and cold stresses. Poult Sci. 2015; 94: 1333-1345. doi: 10.3382/ps/pev046
Alabert C, Groth A. Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol. 2012; 13: 153-167. doi: 10.1038/nrm3288
Li J, Li R, Wang Y, Hu X, Zhao Y, Li L, et al. Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq. BMC Genomics. 2015; 16: 851. doi: 10.1186/ s12864-015-2098-8
Luo J, Mitra A, Tian F, Chang S, Zhang H, Cui K, et al. Histone methylation analysis and pathway predictions in chickens after MDV infection. PLoS One 2012; 7: e41849. doi: 10.1371/ journal.pone.0041849
Mitra A, Luo J, Zhang H, Cui K, Zhao K, Song J. Marek’s disease virus infection induces widespread differential chromatin marks in inbred chicken lines. BMC Genomics. 2012; 13: 557. doi: 10.1186/1471-2164-13-557
Mitra A, Luo J, He Y, Gu Y, Zhang H, Zhao K, et al. Histone modifications induced by MDV infection at early cytolytic and latency phases. BMC Genomics. 2015; 16: 311. doi: 10.1186/ s12864-015-1492-6
Gou Z, Liu R, Zhao G, Zheng M, Lim P, Wang H, et al. Epigenetic modification of TLRs in leukocytes is associated with increased susceptibility to Salmonella enteritidis in chickens. PLoS One. 2012; 7: e33627. doi: 10.1371/journal.pone.0033627
Kisliouk T, Yosefi S, Meiri N. MiR-138 inhibits EZH2 methyltransferase expression and methylation of histone H3 at lysine 27, and affects thermotolerance acquisition. Eur J Neurosci. 2011; 33: 224-235. doi: 10.1111/j.1460-9568.2010.07493.x
Jensen P. Behaviour epigenetics-The connection between environment, stress and welfare. Applied Animal Behaviour Science. 2014; 157: 1-7. doi: 10.1016/j.applanim.2014.02.009
Tzschentke B, Basta D. Early development of neuronal hy- 77 Dridi pothalamic thermosensitivity in birds: influence of epigenetic temperature adaptation. Comp Biochem Physiol A Mol Integr Physiol. 2002; 131: 825-832. doi: 10.1016/s1095-6433(02)00020-x
Rao K, Xiem J, Yang X, Chen L, Grossmann R. Zhao R. Maternal low-protein diet programmes offspring growth in association with alterations in yolk leptin deposition and gene expression in yolk-sac membrane, hypothalamus and muscle of developing Langshan chicken embryos. Br J Nutr. 2009; 102: 848-857. doi: 10.1017/S0007114509276434
Le Roy CI, Mappley LJ, La Ragione RM, Woodward MJ, Claus SP. NMR-based metabolic characterization of chicken tissues and biofluids: a model for avian research. Metabolomics. 2016; 12: 157. doi: 10.1007/s11306-016-1105-7
Aggrey SE, Milfort MC, Fuller AL, Yuan J, Rekaya R. Effect of host genotype and Eimeria acervulina infection on the metabolome of meat-type chickens. PLoS One. 2019; 14: e0223417. doi: 10.1371/journal.pone.0223417
Ma B, Mei X, Lei C, Li C, Gao Y-F, Kong LH, et al. Enrofloxacin shifts intestinal microbiota and metabolic profiling and hinders recovery from salmonella enterica subsp. enterica Serovar Typhimurium Infection in Neonatal Chickens. mSphere. 2020; 5: 1-16. doi: 10.1128/mSphere.00725-20
Greene E, Cauble R, Dhamad AE, Kidd MT, Kong B, Howard SM, et al. Muscle Metabolome profiles in woody breast-(un) affected broilers: Effects of quantum blue phytase-enriched diet. Front Vet Sci. 2020; 7: 458. doi: 10.3389/fvets.2020.00458
Beauclercq S, Nadal-Desbarats L, Hennequet-Antier C, Gabriel I, Tesseraud S, Calenge F, et al. Relationships between digestive efficiency and metabolomic profiles of serum and intestinal contents in chickens. Sci Rep. 2018; 8: 6678. doi: 10.1038/s41598- 018-24978-9
Metzler-Zebeli BU, Siegerstetter S-C, Magowan E, Lawlor PG, O’Connell NE, Zebeli Q. Feed restriction reveals distinct serum metabolome profiles in chickens divergent in feed efficiency traits. Metabolites. 2019; 9: 38. doi: 10.3390/metabo9020038
Park I, Oh S, Lillehoj EP, Lillehoj HS. Dietary supplementation with magnolia bark extract alters chicken intestinal metabolite levels. Front Vet Sci. 2020; 7: 157. doi: 10.3389/fvets.2020.00157
Peng ML, He QQ, Zhao JL, Li LL, Ma HT. Based serum metabolomics analysis reveals simultaneous interconnecting changes during chicken embryonic development. J Anim Physiol Anim Nutr (Berl). 2018; 102: 1210-1219. doi: 10.1111/jpn.12925
Wu S, Liu Y, Zhu L, Han D, Bello M, Yang X, et al. Hepatic metabolomic profiling changes along with postnatal liver maturation in breeder roosters. Biol Open. 2018; 7: bio.028944. doi: 10.1242/doi: 10.1242/bio.028944
Berg G, Rybakova D, Fischer D, Cernava T, M-C C Vergès, et S et al Mini Review | Volume 6 | Number 2 | Adv Food Technol Nutr Sci Open J. 2020; 6(2): 70-78. doi: 10.17140/AFTNSOJ-6-171 al. Microbiome definition re-visited: Old concepts and new challenges. Microbiome. 2020; 8: 103. doi: 10.1186/s40168-020-00875- 0
Choi JH, Kim GB, Cha CJ. Spatial heterogeneity and stability of bacterial community in the gastrointestinal tracts of broiler chickens. Poult Sci. 2014; 93: 1942-1950. doi: 10.3382/ps.2014- 03974
Wilkinson TJ, Cowan AA, Vallin HE, Onime LA, Oyama LB, Cameron SJ, et al. Characterization of the microbiome along the gastrointestinal tract of growing turkeys. Front Microbiol. 2017; 8: 1089. doi: 10.3389/fmicb.2017.01089
Best AA, Porter AL, Fraley SM, Fraley GS. Characterization of gut microbiome dynamics in developing pekin ducks and impact of management system. Front Microbiol. 2016; 7: 2125. doi: 10.3389/fmicb.2016.02125
Yitbarek A, Weese JS, Alkie TN, Parkinson J, Sharif S. Influenza a virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens. FEMS Microbiol Ecol. 2018; 94. doi: 10.1093/femsec/fix165
Li H, Liu X, Chen F, Zuo K, Wu C, Yan Y, et al. Avian influenza virus subtype H9N2 affects intestinal microbiota, barrier structure injury, and inflammatory intestinal disease in the chicken ileum. Viruses. 2018; 10: 270. doi: 10.3390/v10050270
Hird SM, Ganz H, Eisen JA, Boyce WM. The cloacal microbiome of five wild duck species varies by species and influenza A virus infection status. mSphere. 2018; 3: doi: 10.1128/ mSphere.00382-18
Cui N, Huang X, Kong Z, Huang Y, Huang Q, Yang S, et Submit your article to this journal | https://openventio.org/submit-manuscript/ al. Newcastle disease virus infection interferes with the formation of intestinal microflora in newly hatched specific-pathogen-free chicks. Front Microbiol. 2018; 9: 900. doi: 10.3389/ fmicb.2018.00900
Li L, Kubasova T, Rychlik I, Hoerr FJ, Rautenschlein S. Infectious bursal disease virus infection leads to changes in the gut associated-lymphoid tissue and the microbiota composition. PLoS One. 2018; 13: e0192066. doi: 10.1371/journal.pone.0192066
Rodriguez ML, Rebolé A, Velasco S, Ortiz LT, Treviño J, Alzueta C. Wheat- and barley-based diets with or without additives influence broiler chicken performance, nutrient digestibility and intestinal microflora. J Sci Food Agric. 2012; 92: 184-190. doi: 10.1002/jsfa.4561
Ptak A, Bedford MR, Swiatkiewicz S, Zyla K, Jozefiak D. Phytase modulates ileal microbiota and enhances growth performance of the broiler chickens. PLoS One. 2015; 10: e0119770. doi: 10.1371/journal.pone.0119770
Costa MC, Bessegatto JA, Alfieri AA, Weese JS, Filho JAB, Oba A, et al. Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken. PLoS One. 2017; 12: e0171642. doi: 10.1371/journal. pone.0171642
Wang Y, Sun J, Zhong H, Li N, Xu H, Zhu Q, et al. Effect of probiotics on the meat flavour and gut microbiota of chicken. Sci Rep. 2017; 7: 6400. doi: 10.1038/s41598-017-06677-z
Jurburg SD, Brouwer MSM, Ceccarelli D, van der Goot J, Jansman AJM, Bossers A. Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession. Microbiologyopen. 2019; 8: e00821. doi: 10.1002/mbo3.821
Published
How to Cite
Issue
Section
License

This work is licensed under a Creative Commons Attribution 4.0 International License.
All content published in Advances in Food Technology and Nutrition Sciences (AFTNS) is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). This license allows anyone to copy, distribute, transmit, and adapt the work — including for commercial purposes — provided appropriate credit is given to the original author(s) and source.