This study aimed to investigate the potential regulatory role of miRNAs in the development of gastrointestinal tract (GIT) during the early life of dairy calves. Rumen and small intestinal (mid-jejunum and ileum) tissue samples were collected from newborn (30 min after birth; n = 3), 7-day-old (n = 6), 21-day-old (n = 6), and 42-day-old (n = 6) dairy calves. The miRNA profiling was performed using Illumina RNA-sequencing and the temporal and regional differentially expressed miRNAs were further validated using qRT-PCR. Analysis of 16S rRNA gene copy numbers was used to quantify total bacteria, Bifidobacterium and Lactobacillus species. The expression of miR-143 was abundant in all three gut regions, at all time points and it targets genes involved primarily in the proliferation of connective tissue cells and muscle cells, suggesting a role in regulating rapid tissue development during the early life of calves. The expression of miR-146, miR-191, miR-33, miR-7, miR-99/100, miR-486, miR-145, miR-196 and miR-211 displayed significant temporal differences (FDR <0.05), while miR-192/215, miR-194, miR-196, miR-205 and miR-31 revealed significant regional differences (FDR <0.05). The expression levels of miR-15/16, miR-29 and miR-196 were positively correlated with the copy numbers of 16S rRNA gene of Bifidobacterium or Lactobacillus species or both (P<0.05). Functional analysis using Ingenuity Pathway Analysis identified the above mentioned differentially expressed miRNAs as potential regulators of gut tissue cell proliferation and differentiation. The bacterial density-associated miRNAs were identified as modulators of the development of lymphoid tissues (miR-196), maturation of dendritic cells (miR-29) and development of immune cells (miR-15/16). The present study revealed temporal and regional changes in miRNA expression and a correlation between miRNA expression and microbial population in the GIT during the early life, which provides further evidence for another mechanism by which host-microbial interactions play a role in regulating gut development.
References
[1]
Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124: 837–848. doi: 10.1016/j.cell.2006.02.017
[2]
Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336: 1268–1273. doi: 10.1126/science.1223490
[3]
Ayabe T, Satchell DP, Wilson CL, Parks WC, Selsted ME, et al. (2000) Secretion of microbicidal alpha-defensins by intestinal Paneth cells in response to bacteria. Nat Immunol 1: 113–118. doi: 10.1038/77783
[4]
Kobayashi KS, Chamaillard M, Ogura Y, Henegariu O, Inohara N, et al. (2005) Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract. Science 307: 731–734. doi: 10.1126/science.1104911
[5]
Akira S, Uematsu S, Takeuchi O (2006) Pathogen recognition and innate immunity. Cell 124: 783–801. doi: 10.1016/j.cell.2006.02.015
[6]
Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, et al. (2011) The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334: 255–258. doi: 10.1126/science.1209791
[7]
Rakoff-Nahoum S, Medzhitov R (2007) Regulation of spontaneous intestinal tumorigenesis through the adaptor protein MyD88. Science 317: 124–127. doi: 10.1126/science.1140488
[8]
Ivanov, II, Atarashi K, Manel N, Brodie EL, Shima T, et al. (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139: 485–498. doi: 10.1016/j.cell.2009.09.033
[9]
Olszak T, An D, Zeissig S, Vera MP, Richter J, et al. (2012) Microbial exposure during early life has persistent effects on natural killer T cell function. Science 336: 489–493. doi: 10.1126/science.1219328
[10]
Krutzfeldt J, Stoffel M (2006) MicroRNAs: a new class of regulatory genes affecting metabolism. Cell Metab 4: 9–12. doi: 10.1016/j.cmet.2006.05.009
[11]
Hausser J, Syed AP, Bilen B, Zavolan M (2013) Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res.
[12]
Song L, Tuan RS (2006) MicroRNAs and cell differentiation in mammalian development. Birth Defects Res C Embryo Today 78: 140–149. doi: 10.1002/bdrc.20070
[13]
Liang Y, Ridzon D, Wong L, Chen C (2007) Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8: 166. doi: 10.1186/1471-2164-8-166
[14]
Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, et al. (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12: 735–739. doi: 10.1016/s0960-9822(02)00809-6
[15]
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401–1414. doi: 10.1016/j.cell.2007.04.040
[16]
O'Connell RM, Rao DS, Chaudhuri AA, Baltimore D (2010) Physiological and pathological roles for microRNAs in the immune system. Nat Rev Immunol 10: 111–122. doi: 10.1038/nri2708
Popovic R, Riesbeck LE, Velu CS, Chaubey A, Zhang J, et al. (2009) Regulation of mir-196b by MLL and its overexpression by MLL fusions contributes to immortalization. Blood 113: 3314–3322. doi: 10.1182/blood-2008-04-154310
[19]
Biton M, Levin A, Slyper M, Alkalay I, Horwitz E, et al. (2011) Epithelial microRNAs regulate gut mucosal immunity via epithelium-T cell crosstalk. Nat Immunol 12: 239–246. doi: 10.1038/ni.1994
[20]
O'Neill LA, Sheedy FJ, McCoy CE (2011) MicroRNAs: the fine-tuners of Toll-like receptor signalling. Nat Rev Immunol 11: 163–175. doi: 10.1038/nri2957
[21]
Zhou R, Gong AY, Eischeid AN, Chen XM (2012) miR-27b targets KSRP to coordinate TLR4-mediated epithelial defense against Cryptosporidium parvum infection. PLOS Pathog 8: e1002702. doi: 10.1371/journal.ppat.1002702
[22]
Dalmasso G, Nguyen HT, Yan Y, Laroui H, Charania MA, et al. (2011) Microbiota modulate host gene expression via microRNAs. PLOS One 6: e19293. doi: 10.1371/journal.pone.0019293
[23]
Li M, Penner GB, Hernandez-Sanabria E, Oba M, Guan LL (2009) Effects of sampling location and time, and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen. J Appl Microbiol 107: 1924–1934. doi: 10.1111/j.1365-2672.2009.04376.x
[24]
Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40: 37–52. doi: 10.1093/nar/gkr688
[25]
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26: 407–415. doi: 10.1038/nbt1394
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140. doi: 10.1093/bioinformatics/btp616
[28]
Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society 57.
[29]
Stevenson DM, Weimer PJ (2007) Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Appl Microbiol Biotechnol 75: 165–174. doi: 10.1007/s00253-006-0802-y
[30]
Walter J, Hertel C, W.Tannock G, Lis CM, Munro K, et al. (2001) Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella Species in Human Feces by Using Group-Specific PCR Primers and Denaturing Gradient Gel Electrophoresis. Appl Environ Microbiol 67: 7. doi: 10.1128/aem.67.6.2578-2585.2001
[31]
Malmuthuge N, Li M, Chen Y, Fries P, Griebel PJ, et al. (2012) Distinct commensal bacteria associated with ingesta and mucosal epithelium in the gastrointestinal tracts of calves and chickens. FEMS Microbiol Ecol 79: 337–347. doi: 10.1111/j.1574-6941.2011.01220.x
[32]
Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1. doi: 10.1186/gb-2003-5-1-r1
[33]
Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152–157. doi: 10.1093/nar/gkq1027
[34]
Pritchard CC, Cheng HH, Tewari M (2012) MicroRNA profiling: approaches and considerations. Nat Rev Genet 13: 358–369. doi: 10.1038/nrg3198
[35]
Huang J, Ju Z, Li Q, Hou Q, Wang C, et al. (2011) Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle. Int J Biol Sci 7: 1016–1026. doi: 10.7150/ijbs.7.1016
[36]
Bao H, Kommadath A, Sun X, Meng Y, Arantes AS, et al. (2013) Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species. BMC Genomics 14: 609. doi: 10.1186/1471-2164-14-609
[37]
Jin W, Grant JR, Stothard P, Moore SS, Guan LL (2009) Characterization of bovine miRNAs by sequencing and bioinformatics analysis. BMC Mol Biol 10: 90. doi: 10.1186/1471-2199-10-90
[38]
Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, et al. (2009) miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460: 705–710. doi: 10.1038/nature08195
[39]
Wang X, Hu G, Zhou J (2010) Repression of versican expression by microRNA-143. J Biol Chem 285: 23241–23250. doi: 10.1074/jbc.m109.084673
[40]
Chew R, Long MS (2008) Gastrointestinal System.
[41]
Cristino AS, Tanaka ED, Rubio M, Piulachs MD, Belles X (2011) Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae). PLoS One 6: e19350. doi: 10.1371/journal.pone.0019350
[42]
McLeod KR, Baldwin RLt, Solomon MB, Baumann RG (2007) Influence of ruminal and postruminal carbohydrate infusion on visceral organ mass and adipose tissue accretion in growing beef steers. J Anim Sci 85: 2256–2270. doi: 10.2527/jas.2006-359
[43]
Playford RJ, Macdonald CE, Johnson WS (2000) Colostrum and milk-derived peptide growth factors for the treatment of gastrointestinal disorders. Am J Clin Nutr 72: 5–14.
[44]
Korn T, Mitsdoerffer M, Croxford AL, Awasthi A, Dardalhon VA, et al. (2008) IL-6 controls Th17 immunity in vivo by inhibiting the conversion of conventional T cells into Foxp3+ regulatory T cells. Proc Natl Acad Sci U S A 105: 18460–18465. doi: 10.1073/pnas.0809850105
[45]
Gaboriau-Routhiau V, Rakotobe S, Lecuyer E, Mulder I, Lan A, et al. (2009) The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 31: 677–689. doi: 10.1016/j.immuni.2009.08.020
[46]
Kamada N, Seo SU, Chen GY, Nunez G (2013) Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol 13: 321–335. doi: 10.1038/nri3430
[47]
Nagaraja AK, Creighton CJ, Yu Z, Zhu H, Gunaratne PH, et al. (2010) A link between mir-100 and FRAP1/mTOR in clear cell ovarian cancer. Mol Endocrinol 24: 447–463. doi: 10.1210/me.2009-0295
[48]
Liu G, Burns S, Huang G, Boyd K, Proia RL, et al. (2009) The receptor S1P1 overrides regulatory T cell-mediated immune suppression through Akt-mTOR. Nat Immunol 10: 769–777. doi: 10.1038/ni.1743
[49]
Growney JD, Shigematsu H, Li Z, Lee BH, Adelsperger J, et al. (2005) Loss of Runx1 perturbs adult hematopoiesis and is associated with a myeloproliferative phenotype. Blood 106: 494–504. doi: 10.1182/blood-2004-08-3280
[50]
North TE, Stacy T, Matheny CJ, Speck NA, de Bruijn MF (2004) Runx1 is expressed in adult mouse hematopoietic stem cells and differentiating myeloid and lymphoid cells, but not in maturing erythroid cells. Stem Cells 22: 158–168. doi: 10.1634/stemcells.22-2-158
[51]
Sheldrake RF, Husband AJ (1985) Immune defences at mucosal surfaces in ruminants. J Dairy Res 52: 599–613. doi: 10.1017/s0022029900024560
[52]
Groschwitz KR, Ahrens R, Osterfeld H, Gurish MF, Han X, et al. (2009) Mast cells regulate homeostatic intestinal epithelial migration and barrier function by a chymase/Mcpt4-dependent mechanism. Proc Natl Acad Sci U S A 106: 22381–22386. doi: 10.1073/pnas.0906372106
[53]
De Winter BY, van den Wijngaard RM, de Jonge WJ (2012) Intestinal mast cells in gut inflammation and motility disturbances. Biochim Biophys Acta 1822: 66–73. doi: 10.1016/j.bbadis.2011.03.016
[54]
Mebius RE (2003) Organogenesis of lymphoid tissues. Nat Rev Immunol 3: 292–303. doi: 10.1038/nri1054
[55]
Jost T, Lacroix C, Braegger CP, Chassard C (2012) New insights in gut microbiota establishment in healthy breast fed neonates. PLOS One 7: e44595. doi: 10.1371/journal.pone.0044595
[56]
Masotti A (2012) Interplays between gut microbiota and gene expression regulation by miRNAs. Front Cell Infect Microbiol 2: 137. doi: 10.3389/fcimb.2012.00137
[57]
Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, et al. (2009) High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137: 1716–1724 e1711-1712.
[58]
Macfarlane S, Dillon JF (2007) Microbial biofilms in the human gastrointestinal tract. J Appl Microbiol 102: 1187–1196. doi: 10.1111/j.1365-2672.2007.03287.x
[59]
van Baarlen P, Wells JM, Kleerebezem M (2013) Regulation of intestinal homeostasis and immunity with probiotic lactobacilli. Trends Immunol 34: 208–215. doi: 10.1016/j.it.2013.01.005
[60]
Hart AL, Lammers K, Brigidi P, Vitali B, Rizzello F, et al. (2004) Modulation of human dendritic cell phenotype and function by probiotic bacteria. Gut 53: 1602–1609. doi: 10.1136/gut.2003.037325
