TABLE 2

Additional factors exhibiting at least a 2-log decrease in abundance from chicken cecal samples relative to the input

LocusAnnotation/predicted functionaFitness ratiob
CJJ81176_1449Hypothetical protein0.00027
CJJ81176_0310cheA0.00028
CJJ81176_1411Hypothetical protein0.00034
CJJ81176_0025flgE flagellar hook protein0.00037
CJJ81176_0311cheV0.00037
CJJ81176_1452Hypothetical protein0.00053
CJJ81176_0283Sulfatase, putative0.00056
CJJ81176_0305carB carbamoyl phosphate synthase large subunit0.00056
CJJ81176_0246Pathogenicity domain-containing protein0.00072
CJJ81176_0573fliD flagellar capping protein0.00095
CJJ81176_0343dxs 1-deoxy-d-xylulose-5-phosphate synthase0.00096
CJJ81176_0038rbr rubrerythrin0.00119
CJJ81176_1567Peptide ABC transporter, permease protein0.00133
CJJ81176_0290zupT zinc transporter0.00144
CJJ81176_0764Putative outer membrane protein0.00148
CJJ81176_0098fliM flagellar motor switch protein0.00155
CJJ81176_0356Antioxidant AhpCTSA family protein0.00157
CJJ81176_0918Hypothetical protein0.00168
CJJ81176_1062Hypothetical protein0.00168
CJJ81176_1087Hypothetical protein0.00175
CJJ81176_1242htrA protease DO0.00178
CJJ81176_0389cmeB RND efflux system, inner membrane transporter CmeB0.00184
CJJ81176_12142OG-Fe(II) oxygenase family oxidoreductase0.00188
CJJ81176_1457Hypothetical protein0.00237
CJJ81176_1341Hypothetical protein0.00238
CJJ81176_0671cbrR response regulator/GGDEF domain-containing protein0.00246
CJJ81176_0444Hypothetical protein0.00248
CJJ81176_0079Hypothetical protein0.00265
CJJ81176_0083Hypothetical protein0.00272
CJJ81176_0357flhB flagellar biosynthesis protein0.00276
CJJ81176_1598rpsT 30S ribosomal protein S200.00277
CJJ81176_1061Putative transmembrane transport protein0.00296
CJJ81176_0813Hypothetical protein0.00298
CJJ81176_1206Methyl-accepting chemotaxis protein0.00302
CJJ81176_1548Methyl-accepting chemotaxis protein0.00303
CJJ81176_0508rplL 50S ribosomal protein L7/L120.00305
CJJ81176_1433Putative sugar transferase0.00307
CJJ81176_0040Inner membrane protein YagU0.00311
CJJ81176_0215Ser/Thr protein phosphatase family protein0.00313
CJJ81176_1438kpsD capsular polysaccharide ABC transporter, periplasmic polysaccharide-binding protein0.00316
CJJ81176_1675gltA citrate synthase0.00324
CJJ81176_0414Hypothetical protein0.00346
CJJ81176_0080flgD flagellar basal body rod modification protein0.00347
CJJ81176_0109Hypothetical protein0.00352
CJJ81176_0574fliS flagellar protein0.00356
CJJ81176_0294Hypothetical protein0.00365
CJJ81176_0906pheS phenylalanyl-tRNA synthetase subunit alpha0.00367
CJJ81176_1415Putative sugar-1-phosphate nucleotidyltransferase0.00367
CJJ81176_0589Hypothetical protein0.00374
CJJ81176_0236OPT family oligopeptide transporter0.00379
CJJ81176_0359motA flagellar motor protein0.00390
CJJ81176_1462Hypothetical protein0.00391
CJJ81176_1602Hemin ABC transporter, permease protein, putative0.00399
CJJ81176_1541Hypothetical protein0.00400
CJJ81176_1050Hypothetical protein0.00402
CJJ81176_1203gidA tRNA uridine 5-carboxymethylaminomethyl modification enzyme0.00416
CJJ81176_0307tal transaldolase0.00435
CJJ81176_1413kpsC capsule polysaccharide export protein0.00451
CJJ81176_0299Hypothetical protein0.00454
CJJ81176_0273MCP-domain-containing signal transduction protein0.00459
CJJ81176_1335Motility accessory factor0.00462
CJJ81176_1529Integral membrane protein0.00462
CJJ81176_0602ilvB acetolactate synthase 3 catalytic subunit0.00463
CJJ81176_1455flgI flagellar basal body P-ring protein0.00468
CJJ81176_1459flgK flagellar hook-associated protein0.00468
CJJ81176_0032Na+/H+ antiporter family protein0.00479
CJJ81176_0641ftn nonheme iron-containing ferritin0.00493
CJJ81176_1337pseE0.00493
CJJ81176_1012argF ornithine carbamoyltransferase0.00495
CJJ81176_0219Hypothetical protein0.00519
CJJ81176_1416Class I glutamine amidotransferase, putative0.00525
CJJ81176_0590Hypothetical protein0.00537
CJJ81176_0892rpsO 30S ribosomal protein S150.00542
CJJ81176_1652ABC transporter, permease protein0.00550
CJJ81176_0251argB acetylglutamate kinase0.00559
CJJ81176_0296ilvE branched-chain amino acid aminotransferase0.00564
CJJ81176_0674rlpA rare lipoprotein A0.00566
CJJ81176_0005ksgA dimethyladenosine transferase0.00571
CJJ81176_1238Hypothetical protein0.00576
CJJ81176_1606kgtP alpha-ketoglutarate permease0.00587
CJJ81176_1143pglB general glycosylation pathway protein0.00588
CJJ81176_1679Major facilitator superfamily protein0.00590
CJJ81176_1436Putative glycosyl transferase0.00593
CJJ81176_0245Hypothetical protein0.00596
CJJ81176_1136cheY chemotaxis protein0.00603
CJJ81176_1147wlaB ABC transporter, permease/ATP-binding protein0.00668
CJJ81176_1605Hypothetical protein0.00668
CJJ81176_0366uvrA excinuclease ABC subunit A0.00674
CJJ81176_0585MATE efflux family protein, authentic frameshift0.00677
CJJ81176_0801napA nitrate reductase catalytic subunit0.00702
CJJ81176_0386Coproporphyrinogen III oxidase0.00713
CJJ81176_1654ABC transporter, ATP-binding protein0.00720
CJJ81176_0185hom homoserine dehydrogenase0.00724
CJJ81176_0274Hypothetical protein0.00728
CJJ81176_0730waaA 3-deoxy-d-manno-octulosonic-acid transferase0.00728
CJJ81176_0119cydB cytochrome d ubiquinol oxidase, subunit II0.00736
CJJ81176_1417Hypothetical protein0.00737
CJJ81176_1392metC cystathionine beta-lyase0.00752
CJJ81176_1547MerR family transcriptional regulator0.00752
CJJ81176_1154Beta-1,4-N-acetylgalactosaminyltransferase0.00756
CJJ81176_1405Hypothetical protein0.00760
CJJ81176_0252argD acetylornithine aminotransferase0.00764
CJJ81176_1550pflA paralyzed flagellar protein0.00766
CJJ81176_0543Hypothetical protein0.00769
CJJ81176_0572flaG flagellar protein0.00777
CJJ81176_1458Hypothetical protein0.00786
CJJ81176_0223clpP ATP-dependent Clp protease proteolytic subunit0.00791
CJJ81176_0295SPFH domain-containing protein0.00795
CJJ81176_0076Hypothetical protein0.00800
CJJ81176_0107Hypothetical protein0.00805
CJJ81176_1421Putative glycosyltransferase0.00814
CJJ81176_1336pseD0.00816
CJJ81176_0534alaS alanyl-tRNA synthetase0.00829
CJJ81176_1519Bacterioferritin, putative0.00829
CJJ81176_0856Hypothetical protein0.00839
CJJ81176_0802napG quinol dehydrogenase periplasmic component0.00865
CJJ81176_0661Hypothetical protein0.00882
CJJ81176_1431Putative sugar transferase0.00882
CJJ81176_0202Hypothetical protein0.00893
CJJ81176_0893Cell division protein FtsK, putative0.00936
CJJ81176_0110Hypothetical protein0.00955
CJJ81176_1352ceuC enterochelin ABC transporter, permease protein0.00955
CJJ81176_1387katA catalase0.00962
CJJ81176_1530Flavodoxin-like fold domain-containing protein0.00962
CJJ81176_0024Hypothetical protein0.00969
CJJ81176_0339hisC histidinol-phosphate aminotransferase0.00969
CJJ81176_0483miaB (dimethylallyl)adenosine tRNA methylthiotransferase0.00969
CJJ81176_0210Iron ABC transporter, permease protein0.00983
CJJ81176_1569Peptide ABC transporter, periplasmic peptide-binding protein0.00983
CJJ81176_1063AraC family transcriptional regulator0.00997
  • a MATE, multiantimicrobial extrusion protein; OPT, oligopeptide transporter; RND, resistance-nodulation-cell division.

  • b Fitness ratio data were calculated by dividing normalized sequence abundance in output by normalized input abundance. All genes listed are significantly decreased in abundance (P < 0.05).