Corrigendum: The Regulation of Ruminal Short-Chain Fatty Acids on the Functions of Rumen Barriers (Frontiers in Physiology, (2019), 10, (1305) 10.3389/fphys.2019.01305);The Regulation of Ruminal Short-Chain Fatty Acids on the Functions of Rumen Barriers

Frontiers in Physiology

Volumn 10, Issue , 2019, Pages

  Shen, Hong ^a   Xu, Zhihui ^a   Shen, Zanming ^a   Lu, Zhongyan ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

Author keywords

epimural microbiota; epithelium physiology; microbe host interactions; rumen barrier; short chain fatty acids

Indexed keywords

RNA 16S; SHORT CHAIN FATTY ACID;

ACINETOBACTER; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BACTERIAL GROWTH; CELL GROWTH; CELL MEMBRANE PERMEABILITY; CONTROLLED STUDY; EPITHELIUM; GENE SEQUENCE; LIPID HOMEOSTASIS; MALE; METAGENOME; MICROFLORA; NONHUMAN; PH; RUMEN; SIGNAL TRANSDUCTION; SPHINGOBIUM; STREPTOCOCCUS; TIGHT JUNCTION; UPREGULATION;

EID: 85074641615     PISSN: None     EISSN: 1664042X     Source Type: Journal    
DOI: 10.3389/fphys.2021.770061     Document Type: Erratum

References (50)

1. Belkaid Y., Hand T. W., (2014). Role of the microbiota in immunity and inflammation. Cell 157 121–141. 10.1016/j.cell.2014.03.011 24679531
2. Bennink M. R., Tyler T. R., Ward G. M., Johnson D. E., (1978). Ionic milieu of bovine and ovine rumen as affected by diet. J. Dairy Sci. 61 315–323. 10.3168/jds.s0022-0302(78)83600-5 659685
3. Caporaso J. G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F. D., Costello E. K., (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7 335–336.
4. Cario E., Gerken G., Podolsky D. K., (2004). Toll-like receptor 2 enhances ZO-1-associated intestinal epithelial barrier integrity via protein kinase C. Gastroenterology 127 224–238. 10.1053/j.gastro.2004.04.015 15236188
5. Cheng K. J., Mccowan R. P., Costerton J. W., (1979). Adherent epithelial bacteria in ruminants and their roles in digestive tract function. Am. J. Clin. Nutr. 32 139–148. 10.1093/ajcn/32.1.139 367141
6. Emmanuel D. G., Madsen K. L., Churchill T. A., Dunn S. M., Ametaj B. N., (2007). Acidosis and lipopolysaccharide from Escherichia coli B:055 cause hyperpermeability of rumen and colon tissues. J. Dairy Sci. 90 5552–5557. 10.3168/jds.2007-0257 18024746
7. Fukuda S., Toh H., Hase K., Oshima K., Nakanishi Y., Yoshimura K., (2011). Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469 543–547. 10.1038/nature09646 21270894
8. Gordon A., Hannon G., (2010). FASTX-Toolkit: FASTQ/A Short-reads Preprocessing Tools. Avaiable at: http://hannonlab.cshl.edu/fastx_toolkit/ (accessed February 2, 2010).
9. Greco G., Hagen F., Meissner S., Shen Z., Lu Z., Amasheh S., (2018). Effect of individual SCFA on the epithelial barrier of sheep rumen under physiological and acidotic luminal pH conditions. J. Anim. Sci. 96 126–142. 10.1093/jas/skx017 29378000
10. Gui H., Shen Z., (2016). Concentrate diet modulation of ruminal genes involved in cell proliferation and apoptosis is related to combined effects of short-chain fatty acid and pH in rumen of goats. J. Dairy Sci. 99 6627–6638. 10.3168/jds.2015-10446 27236768
11. Guilloteau P., Zabielski R., Hammon H. M., Metges C. C., (2010). Nutritional programming of gastrointestinal tract development. Is the pig a good model for man? Nutr. Res. Rev. 23 4–22. 10.1017/S0954422410000077 20500926
12. Hu F., Xue Y., Guo C., Liu J., Mao S., (2018). The response of ruminal fermentation, epithelium-associated microbiota, and epithelial barrier function to severe feed restriction in pregnant ewes. J. Anim. Sci. 96 4293–4305. 10.1093/jas/sky306 30272228
13. Jumpertz R., Le D. S., Turnbaugh P. J., Trinidad C., Bogardus C., Gordon J. I., (2011). Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am. J. Clin. Nutr. 94 58–65. 10.3945/ajcn.110.010132 21543530
14. Kilian M., Riley D. R., Jensen A., Bruggemann H., Tettelin H., (2014). Parallel evolution of Streptococcus pneumoniae and Streptococcus mitis to pathogenic and mutualistic lifestyles. mBio 5:e1490-14. 10.1128/mBio.01490-14 25053789
15. Kim D., Pertea G., Trapnell C., Pimentel H., Kelley R., Salzberg S. L., (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14:R36. 10.1186/gb-2013-14-4-r36 23618408
16. Kleen J. L., Hooijer G. A., Rehage J., Noordhuizen J. P., (2003). Subacute ruminal acidosis (SARA): a review. J. Vet. Med. A Physiol. Pathol. Clin. Med. 50 406–414. 10.1046/j.1439-0442.2003.00569.x 14633219
17. Langmead B., Salzberg S. L., (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 357–359. 10.1038/nmeth.1923 22388286
18. Langmead B., Trapnell C., Pop M., Salzberg S. L., (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25. 10.1186/gb-2009-10-3-r25 19261174
19. Li C. J., Li R. W., Baldwin R. L. T., Blomberg Le A., Wu S., Li W., (2016). Transcriptomic sequencing reveals a set of unique genes activated by butyrate-induced histone modification. Gene Regul. Syst. Biol. 10 1–8. 10.4137/GRSB.S35607 26819550
20. Liu J. H., Xu T. T., Liu Y. J., Zhu W. Y., Mao S. Y., (2013). A high-grain diet causes massive disruption of ruminal epithelial tight junctions in goats. Am. J. Physiol. Regul. Integr. Comp. Physiol. 305 R232–R241. 10.1152/ajpregu.00068.2013 23739344
21. Livak K. J., Schmittgen T. D., (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25 402–408. 10.1006/meth.2001.1262 11846609
22. Lodemann U., Martens H., (2006). Effects of diet and osmotic pressure on Na+ transport and tissue conductance of sheep isolated rumen epithelium. Exp. Physiol. 91 539–550. 10.1113/expphysiol.2005.032078 16452124
23. Love M. I., Huber W., Anders S., (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15:550. 10.1186/s13059-014-0550-8 25516281
24. Magoc T., Salzberg S. L., (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27 2957–2963. 10.1093/bioinformatics/btr507 21903629
25. Malhi M., Gui H., Yao L., Aschenbach J. R., Gabel G., Shen Z., (2013). Increased papillae growth and enhanced short-chain fatty acid absorption in the rumen of goats are associated with transient increases in cyclin D1 expression after ruminal butyrate infusion. J. Dairy Sci. 96 7603–7616. 10.3168/jds.2013-6700 24119813
26. Malmuthuge N., Li M., Fries P., Griebel P. J., Guan L. L., (2012). Regional and age dependent changes in gene expression of Toll-like receptors and key antimicrobial defence molecules throughout the gastrointestinal tract of dairy calves. Vet. Immunol. Immunopathol. 146 18–26. 10.1016/j.vetimm.2012.01.010 22321738
27. McMurdie P. J., Holmes S., (2013). phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217. 10.1371/journal.pone.0061217 23630581
28. Moriya Y., Itoh M., Okuda S., Yoshizawa A. C., Kanehisa M., (2007). KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35 W182–W185. 17526522
29. Nadell C. D., Xavier J. B., Foster K. R., (2009). The sociobiology of biofilms. FEMS Microbiol. Rev. 33 206–224. 10.1111/j.1574-6976.2008.00150.x 19067751
30. NRC (2000). Nutrient Requirements of Beef Cattle: Seventh Revised Edition: Update 2000. Washington, DC: The National Academies Press.
31. Ohland C. L., Jobin C., (2015). Microbial activities and intestinal homeostasis: a delicate balance between health and disease. Cell Mol. Gastroenterol. Hepatol. 1 28–40. 10.1016/j.jcmgh.2014.11.004 25729763
32. Oksanen J., Blanchet G. F., Friendly M., Kindt R., Legendre P., Mcglinn D., (2016). Vegan: Community Ecology Package. R Package Version 2.4-0. Available at: https://CRAN.R-project.org/package=vegan (accessed June 15, 2016).
33. Pacheco A. R., Curtis M. M., Ritchie J. M., Munera D., Waldor M. K., Moreira C. G., (2012). Fucose sensing regulates bacterial intestinal colonization. Nature 492 113–117. 10.1038/nature11623 23160491
34. Peng Y., Leung H. C., Yiu S. M., Chin F. Y., (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28 1420–1428. 10.1093/bioinformatics/bts174 22495754
35. Perry R. J., Peng L., Barry N. A., Cline G. W., Zhang D., Cardone R. L., (2016). Acetate mediates a microbiome-brain-beta-cell axis to promote metabolic syndrome. Nature 534 213–217. 10.1038/nature18309 27279214
36. Puertollano E., Kolida S., Yaqoob P., (2014). Biological significance of short-chain fatty acid metabolism by the intestinal microbiome. Curr. Opin. Clin. Nutr. Metab. Care 17 139–144. 10.1097/MCO.0000000000000025 24389673
37. Rho M., Tang H., Ye Y., (2010). FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 38:e191. 10.1093/nar/gkq747 20805240
38. Schmieder R., Edwards R., (2011). Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 6:e17288. 10.1371/journal.pone.0017288 21408061
39. Schweigel M., Freyer M., Leclercq S., Etschmann B., Lodemann U., Bottcher A., (2005). Luminal hyperosmolarity decreases Na transport and impairs barrier function of sheep rumen epithelium. J. Comp. Physiol. B 175 575–591. 10.1007/s00360-005-0021-3 16177895
40. Shannon P., Markiel A., Ozier O., Baliga N. S., Wang J. T., Ramage D., (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13 2498–2504. 10.1101/gr.1239303 14597658
41. Shen H., Lu Z., Chen Z., Wu Y., Shen Z., (2016). Rapid fermentable substance modulates interactions between ruminal commensals and toll-like receptors in promotion of immune tolerance of goat rumen. Front. Microbiol. 7:1812. 10.3389/fmicb.2016.01812 27909428
42. Sun D. M., Mao S. Y., Zhu W. Y., Liu J. H., (2018). Effect of starter diet supplementation on rumen epithelial morphology and expression of genes involved in cell proliferation and metabolism in pre-weaned lambs. Animal 12 2274–2283. 10.1017/S1751731118000290 29477152
43. Trapnell C., Williams B. A., Pertea G., Mortazavi A., Kwan G., Van Baren M. J., (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28 511–515. 10.1038/nbt.1621 20436464
44. Wetzels S. U., Mann E., Metzler-Zebeli B. U., Wagner M., Klevenhusen F., Zebeli Q., (2015). Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats. J. Dairy Sci. 98 5572–5587. 10.3168/jds.2014-9166 26051320
45. Wickham H., (2009). ggplot2: Elegant Graphics for Data Analysis. New York, NY: Springer-Verlag.
46. Yan L., Zhang B., Shen Z., (2014). Dietary modulation of the expression of genes involved in short-chain fatty acid absorption in the rumen epithelium is related to short-chain fatty acid concentration and pH in the rumen of goats. J. Dairy Sci. 97 5668–5675. 10.3168/jds.2013-7807 24996270
47. Yang W., Shen Z., Martens H., (2012). An energy-rich diet enhances expression of Na(+)/H(+) exchanger isoform 1 and 3 messenger RNA in rumen epithelium of goat. J. Anim. Sci. 90 307–317. 10.2527/jas.2011-3854 21856899
48. Yu G., Wang L. G., Han Y., He Q. Y., (2012). clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16 284–287. 10.1089/omi.2011.0118 22455463
49. Zelante T., Iannitti R. G., Cunha C., De Luca A., Giovannini G., Pieraccini G., (2013). Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 39 372–385. 10.1016/j.immuni.2013.08.003 23973224
50. Zhao S., Guo Y., Sheng Q., Shyr Y., (2014). Heatmap3: an improved heatmap package with more powerful and convenient features. BMC Bioinformatics 15(Suppl. 10):16. 10.1186/1471-2105-15-S10-P16