Effects of early feeding on the host rumen transcriptome and bacterial diversity in lambs

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Wang, Weimin ^a   Li, Chong ^a,b,c   Li, Fadi ^a   Wang, Xiaojuan ^a,b   Zhang, Xiaoxue ^a   Liu, Ting ^a   Nian, Fang ^a   Yue, Xiangpeng ^b   Li, Fei ^b   Pan, Xiangyu ^a   La, Yongfu ^a   Mo, Futao ^a   Wang, Fangbin ^a   Li, Baosheng ^d  

^a GANSU AGRICULTURAL UNIVERSITY   (China)

^b LANZHOU UNIVERSITY   (China)

^c Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province   (China)

^d JinchangZhongtian Sheep Industry Co Ltd   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; TRANSCRIPTOME;

ANIMAL; ANIMAL FOOD; BACTERIUM; DIET; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; MILK; RUMEN; SHEEP; WEANING;

ANIMAL FEED; ANIMAL NUTRITIONAL PHYSIOLOGICAL PHENOMENA; ANIMALS; BACTERIA; DIET; MILK; RNA, RIBOSOMAL, 16S; RUMEN; SHEEP; TRANSCRIPTOME; WEANING;

EID: 84984904478     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep32479     Document Type: Article

References (73)

1. Roh, S. G. et al. Identification of differentially expressed transcripts in bovine rumen and abomasum using a differential display method. Journal of animal science 85, 395-403 (2007).
2. Bryant, M. P., Nola, S., Cecelia, B. & Isadore, R. Studies on the composition of the ruminal flora and fauna of young calves. Journal of dairy science 41, 21 (1958).
3. Tamate, H., McGilliard, A. D., Jacoson, N. L. & Getty, R. Effect of various dietaries on the anatomical development of the stomach in the calf. Journal of dairy science 45, 13 (1962).
4. van Houtert, M. F. J. The production and metabolism of volatilefatty acids by ruminants fed roughages: A review. Anim Feed Sci Tech 43, 37 (1993).
5. Flatt, W. P., Warner, R. G. & Loosli, J. K. The influence of purified materials on the development of the ruminant stomach. Journal of dairy science 41, 8 (1958).
6. Lane, M. A. & Jesse, B. W. Effect of volatile fatty acid infusion on development of the rumen epithelium in neonatal sheep. Journal of dairy science 80, 740-746 (1997).
7. Sander, E. G., Warner, R. G., Harrison, H. N. & Loosli, J. K. The stimulatory effect of sodium butyrate and sodium propionateon the development of rumen mucosa in the young calf. Journal of dairy science 42, 6 (1959).
8. Drackley, J. K. Calf nutrition from birth to breeding. The Veterinary clinics of North America. Food animal practice 24, 55-86 (2008).
9. Lane, M. A., Baldwin, R. L. t. & Jesse, B. W. Sheep rumen metabolic development in response to age and dietary treatments. Journal of animal science 78, 1990-1996 (2000).
10. Connor, E. E., Baldwin, R. L. t., Li, C. J., Li, R. W. & Chung, H. Gene expression in bovine rumen epithelium during weaning identifies molecular regulators of rumen development and growth. Functional & integrative genomics 13, 133-142 (2013).
11. Kato, D. et al. Utilization of digital differential display to identify differentially expressed genes related to rumen development. Animal science journal= Nihon chikusan Gakkaiho (2015).
12. Connor, E. E. et al. Transcriptional regulators transforming growth factor-beta1 and estrogen-related receptor-alpha identified as putative mediators of calf rumen epithelial tissue development and function during weaning. Journal of dairy science 97, 4193-4207 (2014).
13. Flaga, J., Gorka, P., Zabielski, R. & Kowalski, Z. M. Differences in monocarboxylic acid transporter type 1 expression in rumen epithelium of newborn calves due to age and milk or milk replacer feeding. Journal of animal physiology and animal nutrition 99, 521-530 (2015).
14. Kocherginskaya, S. A., Aminov, R. I. & White, B. A. Analysis of the Rumen Bacterial Diversity under two Different Diet Conditions using Denaturing Gradient Gel Electrophoresis, Random Sequencing, and Statistical Ecology Approaches. Anaerobe 7, 119-134 (2001).
15. McAllister, T. A., Cheng, K. J., Okine, E. K. & Mathison, G. W. Dietary, environmental and microbiological aspects of methane production in ruminants. Can J Anim Sci 76, 13 (1996).
16. Tajima, K. et al. Rumen Bacterial Community Transition During Adaptation to High-grain Diet. Anaerobe 6, 12 (2000).
17. Lee, C. W. et al. Temporal patterns of gene expression after acute hindlimb ischemia in mice: insights into the genomic program for collateral vessel development. J Am Coll Cardiol 43, 474-482 (2004).
18. McSweeney, C. S. & Denman, S. E. Effect of sulfur supplements on cellulolytic rumen micro-organisms and microbial protein synthesis in cattle fed a high fibre diet. Journal of applied microbiology 103, 1757-1765 (2007).
19. Edwards, J. E., R., M. N., J., T. A. & Wallace, R. J. 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie van Leeuwenhoek 86, 263-281 (2004).
20. Wright, A. D., Auckland, C. H. & Lynn, D. H. Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Applied and environmental microbiology 73, 4206-4210 (2007).
21. Ellis, J. L. et al. Aspects of rumen microbiology central to mechanistic modelling of methane production in cattle. J Agr Sci 146, 213-233 (2008).
22. Belanche, A., Ramos-Morales, E. & Newbold, C. J. In vitro screening of natural feed additives from crustaceans, diatoms, seaweeds and plant extracts to manipulate rumen fermentation. Journal of the science of food and agriculture (2015).
23. Hart, K. J., Yanez-Ruiz, D. R., Duval, S. M., McEwan, N. R. & Newbold, C. J. Plant extracts to manipulate rumen fermentation. Anim Feed Sci Tech 147, 8-35 (2008).
24. Patra, A. K. & Saxena, J. Dietary phytochemicals as rumen modifiers: a review of the effects on microbial populations. Antonie van Leeuwenhoek 96, 363-375 (2009).
25. Wanapat, M. & Cherdthong, A. Use of real-time PCR technique in studying rumen cellulolytic bacteria population as affected by level of roughage in swamp buffalo. Current microbiology 58, 294-299 (2009).
26. Li, R. W., Connor, E. E., Li, C., Baldwin Vi, R. L. & Sparks, M. E. Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environmental microbiology 14, 129-139 (2012).
27. Hristov, A. N., Callaway, T. R., Lee, C. & Dowd, S. E. Rumen bacterial, archaeal, and fungal diversity of dairy cows in response to ingestion of lauric or myristic acid. Journal of animal science 90, 4449-4457 (2012).
28. Chen, Y., Penner, G. B., Li, M., Oba, M. & Guan, L. L. Changes in bacterial diversity associated with epithelial tissue in the beef cow rumen during the transition to a high-grain diet. Applied and environmental microbiology 77, 5770-5781 (2011).
29. Jiao, J., Huang, J., Zhou, C. & Tan, Z. Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats. Applied and environmental microbiology 81, 3502-3509 (2015).
30. Baldwin Vi, R. L., McLeod, K. R., Klotz, J. L. & Heitmann, R. N. Rumen development, intestinal growth and hepatic metabolism in the pre-and postweaning ruminant. Journal of dairy science 87, 55-65 (2004).
31. Wang, Y. H. et al. Effect of dietary starch on rumen and small intestine morphology and digesta pH in goats. Livest Sci 122, 48-52 (2009).
32. Reynolds, C. K., Durst, B., Lupoli, B., Humphries, D. J. & Beever, D. E. Visceral tissue mass and rumen volume in dairy cows during the transition from late gestation to early lactation. Journal of dairy science 87, 961-971 (2004).
33. Faubladier, C., Julliand, V., Danel, J. & Philippeau, C. Bacterial carbohydrate-degrading capacity in foal faeces: changes from birth to pre-weaning and the impact of maternal supplementation with fermented feed products. The British journal of nutrition 110, 1040-1052 (2013).
34. Rey, M., Enjalbert, F. & Monteils, V. Establishment of ruminal enzyme activities and fermentation capacity in dairy calves from birth through weaning. Journal of dairy science 95, 1500-1512 (2012).
35. Fouts, D. E. et al. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PloS one 7, e48289 (2012).
36. Fonty, G., Gouet, P., Jouany, J. P. & Senaud, J. Establishment of the microflora and anaerobic fungi in the rumen of lambs. Microbioloy 133, 1835-1843 (1987).
37. Duffield, T. et al. Comparison of techniques for measurement of rumen pH in lactating dairy cows. Journal of dairy science 87, 59-66 (2004).
38. Garrett, E. F. et al. Diagnostic methods for the detection of subacute ruminal acidosis in dairy cows. Journal of dairy science 82, 1170-1178 (1999).
39. Li, S. et al. Effects of subacute ruminal acidosis challenges on fermentation and endotoxins in the rumen and hindgut of dairy cows. Journal of dairy science 95, 294-303 (2012).
40. Suarez, B. J. et al. Effects of supplementing concentrates differing in carbohydrate composition in veal calf diets: I. Animal performance and rumen fermentation characteristics. Journal of dairy science 89, 4365-4375 (2006).
41. Naeem, A., Drackley, J. K., Stamey, J. & Loor, J. J. Role of metabolic and cellular proliferation genes in ruminal development in response to enhanced plane of nutrition in neonatal Holstein calves. Journal of dairy science 95, 1807-1820 (2012).
42. Lane, M. A., Baldwin, R. L. t. & Jesse, B. W. Developmental changes in ketogenic enzyme gene expression during sheep rumen development. Journal of animal science 80, 1538-1544 (2002).
43. Pennington, R. J. & Sutherland, T. M. The production of succinate from propionate by carbon dioxide fixation in sheep rumen epithelial tissue. The Biochemical journal 60, xxxvii (1955).
44. Zhang, Q., Koser, S. L. & Donkin, S. S. Propionate induces mRNA expression of gluconeogenic genes in bovine calf hepatocytes. Journal of dairy science (2016).
45. Bobik, T. A. & Rasche, M. E. Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome. The Journal of biological chemistry 276, 37194-37198 (2001).
46. Bikker, H. et al. A homozygous nonsense mutation in the methylmalonyl-CoA epimerase gene (MCEE) results in mild methylmalonic aciduria. Human mutation 27, 640-643 (2006).
47. Liu, H., Vaddella, V. & Zhou, D. Effects of chestnut tannins and coconut oil on growth performance, methane emission, ruminal fermentation, and microbial populations in sheep. Journal of dairy science 94, 6069-6077 (2011).
48. Jami, E., Israel, A., Kotser, A. & Mizrahi, I. Exploring the bovine rumen bacterial community from birth to adulthood. The ISME journal 7, 1069-1079 (2013).
49. Petri, R. M. et al. Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge. PloS one 8, e83424 (2013).
50. Sadet, S., Martin, C., Meunier, B. & Morgavi, D. P. PCR-DGGE analysis reveals a distinct diversity in the bacterial population attached to the rumen epithelium. Animal: an international journal of animal bioscience 1, 939-944 (2007).
51. Rey, M. et al. Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential. Journal of applied microbiology 116, 245-257 (2014).
52. Stevenson, D. M. & Weimer, P. J. 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 (2007).
53. Purushe, J. et al. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microbial ecology 60, 721-729 (2010).
54. Jiao, J. et al. In vitro evaluation on neutral detergent fiber and cellulose digestion by post-ruminal microorganisms in goats. Journal of the science of food and agriculture 94, 1745-1752 (2014).
55. Jiao, J. et al. Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation. The British journal of nutrition 113, 888-900 (2015).
56. Eun, J. S. & Beauchemin, K. A. Effects of a proteolytic feed enzyme on intake, digestion, ruminal fermentation, and milk production. Journal of dairy science 88, 2140-2153 (2005).
57. Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols 7, 562-578 (2012).
58. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology 28, 511-515 (2010).
59. Audic, S. & Claverie, J. M. The significance of digital gene expression profiles. Genome research 7, 986-995 (1997).
60. Li, H. et al. RNA-Seq derived identification of differential transcription in the chrysanthemum leaf following inoculation with Alternaria tenuissima. BMC genomics 15, 9 (2014).
61. Young, N. D. et al. Whole-genome sequence of Schistosoma haematobium. Nature genetics 44, 221-225 (2012).
62. Buschmann, T., Zhang, R., Brash, D. E. & Bystrykh, L. V. Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate. BMC bioinformatics 15, 264 (2014).
63. Saldanha, A. J. Java Treeview-extensible visualization of microarray data. Bioinformatics 20, 3246-3248 (2004).
64. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25, 25-29 (2000).
65. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic acids research 32, D277-D280 (2004).
66. Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402-408 (2001).
67. Zhao, L. et al. Quantitative genetic background of the host influences gut microbiomes in chickens. Scientific reports 3, 1163 (2013).
68. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature methods 7, 335-336 (2010).
69. Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and environmental microbiology 75, 7537-7541 (2009).
70. Cole, J. R. et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic acids research 37, D141-D145 (2009).
71. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200 (2011).
72. Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and environmental microbiology 71, 8228-8235 (2005).
73. Zhou, M., Hernandez-Sanabria, E. & Guan, L. L. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Applied and environmental microbiology 75, 6524-6533 (2009).