title: Gut microbial gene expression in mother-fed and formula-fed piglets.
abstract: BACKGROUND
  Effects of diet on the structure and function of gut microbial communities in newborn infants are poorly understood. High-resolution molecular studies are needed to definitively ascertain whether gut microbial communities are distinct in milk-fed and formula-fed infants.
  
  
  RESULTS
  Pyrosequencing-based whole transcriptome shotgun sequencing (RNA-seq) was used to evaluate community wide gut microbial gene expression in 21 day old neonatal piglets fed either with sow's milk (mother fed, MF; n = 4) or with artificial formula (formula fed, FF; n = 4). Microbial DNA and RNA were harvested from cecal contents for each animal. cDNA libraries and 16S rDNA amplicons were sequenced on the Roche 454 GS-FLX Titanium system. Communities were similar at the level of phylum but were dissimilar at the level of genus; Prevotella was the dominant genus within MF samples and Bacteroides was most abundant within FF samples. Screened cDNA sequences were assigned functional annotations by the MG-RAST annotation pipeline and based upon best-BLASTX-hits to the NCBI COG database. Patterns of gene expression were very similar in MF and FF animals. All samples were enriched with transcripts encoding enzymes for carbohydrate and protein metabolism, as well as proteins involved in stress response, binding to host epithelium, and lipopolysaccharide metabolism. Carbohydrate utilization transcripts were generally similar in both groups. The abundance of enzymes involved in several pathways related to amino acid metabolism (e.g., arginine metabolism) and oxidative stress response differed in MF and FF animals.
  
  
  CONCLUSIONS
  Abundant transcripts identified in this study likely contribute to a core microbial metatranscriptome in the distal intestine. Although microbial community gene expression was generally similar in the cecal contents of MF and FF neonatal piglets, several differentially abundant gene clusters were identified. Further investigations of gut microbial gene expression will contribute to a better understanding of normal and abnormal enteric microbiology in animals and humans.
authors.affiliation: Department of Surgery, The University of Chicago Pritzker School of Medicine, Chicago, Illinois, United States of America.
authors.forename: Valeriy
authors.initials: V
authors.lastname: Poroyko
authors.forename: James Robert
authors.initials: JR
authors.lastname: White
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.forename: Sharon
authors.initials: S
authors.lastname: Donovan
authors.forename: John
authors.initials: J
authors.lastname: Alverdy
authors.forename: Donald C
authors.initials: DC
authors.lastname: Liu
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Morowitz
mesh_terms: D000821:Animal Feed; D000818:Animals; D000831:Animals, Newborn; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D002432:Cecum / Q000382:microbiology*; D004269:DNA, Bacterial / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling; D041943:Infant Formula; D009035:Mothers; D017422:Sequence Analysis, DNA; D013552:Swine / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D018076:DNA, Complementary
references.citation: Nutrition. 2006 Jun;22(6):616-9
references.pmid: 16635560
references.citation: Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8
references.pmid: 20363958
references.citation: DNA Res. 2007 Aug 31;14(4):169-81
references.pmid: 17916580
references.citation: Nat Protoc. 2006;1(2):870-3
references.pmid: 17406319
references.citation: Br J Nutr. 1992 Jul;68(1):195-207
references.pmid: 1390604
references.citation: Appl Environ Microbiol. 2008 Feb;74(4):1264-7
references.pmid: 18065633
references.citation: J Pediatr. 2002 Apr;140(4):425-31
references.pmid: 12006956
references.citation: Lancet. 2006 Oct 7;368(9543):1271-83
references.pmid: 17027734
references.citation: Curr Opin Gastroenterol. 2008 Jan;24(1):4-10
references.pmid: 18043225
references.citation: Science. 2001 May 11;292(5519):1115-8
references.pmid: 11352068
references.citation: PLoS Pathog. 2009 Jun;5(6):e1000487
references.pmid: 19557163
references.citation: Pediatr Res. 1997 Jul;42(1):78-86
references.pmid: 9212041
references.citation: Pediatr Res. 2002 May;51(5):612-8
references.pmid: 11978886
references.citation: PLoS Comput Biol. 2009 Apr;5(4):e1000352
references.pmid: 19360128
references.citation: J Inorg Biochem. 2006 Apr;100(4):679-93
references.pmid: 16504301
references.citation: J Mol Microbiol Biotechnol. 2009;17(3):158-62
references.pmid: 19672048
references.citation: Infect Immun. 1996 Nov;64(11):4549-56
references.pmid: 8890205
references.citation: FEMS Microbiol Ecol. 2005 Sep 1;54(1):77-85
references.pmid: 16329974
references.citation: Infect Immun. 2001 Oct;69(10):6179-85
references.pmid: 11553558
references.citation: Nature. 2006 Aug 17;442(7104):806-9
references.pmid: 16915287
references.citation: J Proteome Res. 2008 Jan;7(1):352-60
references.pmid: 18052033
references.citation: Cochrane Database Syst Rev. 2007 Jul 18;(3):CD004339
references.pmid: 17636753
references.citation: Semin Perinatol. 2007 Apr;31(2):83-8
references.pmid: 17462492
references.citation: FEMS Microbiol Lett. 2005 Feb 1;243(1):141-7
references.pmid: 15668012
references.citation: Infect Immun. 2004 Apr;72(4):2160-9
references.pmid: 15039339
references.citation: Infect Immun. 2010 Jan;78(1):348-57
references.pmid: 19841081
references.citation: J Bacteriol. 1993 Mar;175(6):1605-11
references.pmid: 8449870
references.citation: PLoS Biol. 2007 Jul;5(7):e177
references.pmid: 17594176
references.citation: Infect Immun. 2004 Nov;72(11):6748-52
references.pmid: 15501816
references.citation: Nat Rev Microbiol. 2008 Aug;6(8):613-24
references.pmid: 18628769
references.citation: BMC Bioinformatics. 2008 Sep 19;9:386
references.pmid: 18803844
references.citation: PLoS One. 2008 Aug 22;3(8):e3042
references.pmid: 18725995
references.citation: Nature. 2010 Mar 4;464(7285):59-65
references.pmid: 20203603
references.citation: Proc Natl Acad Sci U S A. 1971 Aug;68(8):1673-7
references.pmid: 4942911
references.citation: Trends Biochem Sci. 2008 Mar;33(3):101-3
references.pmid: 18276143
references.citation: Appl Environ Microbiol. 2007 Aug;73(16):5261-7
references.pmid: 17586664
references.citation: Pediatr Allergy Immunol. 2010 Jun;21(4 Pt 2):e772-9
references.pmid: 19573144
references.citation: Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10
references.pmid: 18316740
references.citation: Environ Microbiol. 2009 Jun;11(6):1358-75
references.pmid: 19207571
references.citation: FEMS Microbiol Lett. 2010 Jan;302(1):1-7
references.pmid: 19735299
references.citation: PLoS One. 2009 Jul 28;4(7):e6386
references.pmid: 19636438
references.citation: Appl Environ Microbiol. 2008 Aug;74(15):4686-94
references.pmid: 18539808
references.citation: Infect Immun. 2010 Apr;78(4):1482-94
references.pmid: 20123708
references.citation: J Bacteriol. 2007 Aug;189(16):5929-36
references.pmid: 17557824
references.citation: Nucleic Acids Res. 2007;35(21):7188-96
references.pmid: 17947321
references.citation: Acta Paediatr Scand. 1985 Jan;74(1):45-51
references.pmid: 3984727
references.citation: Science. 1997 Oct 24;278(5338):631-7
references.pmid: 9381173
references.citation: Science. 2001 Feb 2;291(5505):881-4
references.pmid: 11157169
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1698-703
references.pmid: 18230719
references.citation: PLoS One. 2008 Jul 30;3(7):e2836
references.pmid: 18665274
references.citation: Nature. 2009 Jan 22;457(7228):480-4
references.pmid: 19043404
references.citation: Int J Biochem Cell Biol. 2007;39(6):1190-203
references.pmid: 17449317
references.citation: Microbiology (Reading). 2009 Oct;155(Pt 10):3294-3303
references.pmid: 19574304
references.citation: J Nutr. 2008 Oct;138(10):2032S-2039S
references.pmid: 18806120
references.citation: Appl Environ Microbiol. 2007 Feb;73(4):1388-92
references.pmid: 17158612
references.citation: Anaerobe. 2005 Oct;11(5):247-51
references.pmid: 16701579
references.citation: Nat Rev Microbiol. 2005 Jun;3(6):489-98
references.pmid: 15931167
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Microbiology (Reading). 2009 Dec;155(Pt 12):4058-4068
references.pmid: 19762447
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3976-81
references.pmid: 19234113
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11070-5
references.pmid: 16033867
references.citation: Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13780-5
references.pmid: 17699621
references.citation: Nature. 2008 Apr 3;452(7187):629-32
references.pmid: 18337718
references.citation: Sci Transl Med. 2009 Nov 11;1(6):6ra14
references.pmid: 20368178
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5
references.pmid: 19004872
references.citation: J Biol Chem. 2009 Sep 11;284(37):24673-7
references.pmid: 19553672
references.citation: J Bacteriol. 2009 Jun;191(12):3804-10
references.pmid: 19376872
references.citation: Am J Clin Nutr. 1999 May;69(5):1035S-1045S
references.pmid: 10232646
references.citation: ISME J. 2009 Feb;3(2):179-89
references.pmid: 18971961
references.citation: Nature. 2009 May 14;459(7244):266-9
references.pmid: 19444216
references.citation: Pediatrics. 2006 Aug;118(2):511-21
references.pmid: 16882802
references.citation: Nat Med. 2009 Sep;15(9):1016-22
references.pmid: 19701202
references.citation: PLoS One. 2008 Jun 25;3(6):e2527
references.pmid: 18575584