TABLE 2.
Additional factors exhibiting at least a 2-log decrease in abundance from chicken cecal samples relative to the input
| Locus | Annotation/predicted functiona | Fitness ratiob |
|---|---|---|
| CJJ81176_1449 | Hypothetical protein | 0.00027 |
| CJJ81176_0310 | cheA | 0.00028 |
| CJJ81176_1411 | Hypothetical protein | 0.00034 |
| CJJ81176_0025 | flgE flagellar hook protein | 0.00037 |
| CJJ81176_0311 | cheV | 0.00037 |
| CJJ81176_1452 | Hypothetical protein | 0.00053 |
| CJJ81176_0283 | Sulfatase, putative | 0.00056 |
| CJJ81176_0305 | carB carbamoyl phosphate synthase large subunit | 0.00056 |
| CJJ81176_0246 | Pathogenicity domain-containing protein | 0.00072 |
| CJJ81176_0573 | fliD flagellar capping protein | 0.00095 |
| CJJ81176_0343 | dxs 1-deoxy-d-xylulose-5-phosphate synthase | 0.00096 |
| CJJ81176_0038 | rbr rubrerythrin | 0.00119 |
| CJJ81176_1567 | Peptide ABC transporter, permease protein | 0.00133 |
| CJJ81176_0290 | zupT zinc transporter | 0.00144 |
| CJJ81176_0764 | Putative outer membrane protein | 0.00148 |
| CJJ81176_0098 | fliM flagellar motor switch protein | 0.00155 |
| CJJ81176_0356 | Antioxidant AhpCTSA family protein | 0.00157 |
| CJJ81176_0918 | Hypothetical protein | 0.00168 |
| CJJ81176_1062 | Hypothetical protein | 0.00168 |
| CJJ81176_1087 | Hypothetical protein | 0.00175 |
| CJJ81176_1242 | htrA protease DO | 0.00178 |
| CJJ81176_0389 | cmeB RND efflux system, inner membrane transporter CmeB | 0.00184 |
| CJJ81176_1214 | 2OG-Fe(II) oxygenase family oxidoreductase | 0.00188 |
| CJJ81176_1457 | Hypothetical protein | 0.00237 |
| CJJ81176_1341 | Hypothetical protein | 0.00238 |
| CJJ81176_0671 | cbrR response regulator/GGDEF domain-containing protein | 0.00246 |
| CJJ81176_0444 | Hypothetical protein | 0.00248 |
| CJJ81176_0079 | Hypothetical protein | 0.00265 |
| CJJ81176_0083 | Hypothetical protein | 0.00272 |
| CJJ81176_0357 | flhB flagellar biosynthesis protein | 0.00276 |
| CJJ81176_1598 | rpsT 30S ribosomal protein S20 | 0.00277 |
| CJJ81176_1061 | Putative transmembrane transport protein | 0.00296 |
| CJJ81176_0813 | Hypothetical protein | 0.00298 |
| CJJ81176_1206 | Methyl-accepting chemotaxis protein | 0.00302 |
| CJJ81176_1548 | Methyl-accepting chemotaxis protein | 0.00303 |
| CJJ81176_0508 | rplL 50S ribosomal protein L7/L12 | 0.00305 |
| CJJ81176_1433 | Putative sugar transferase | 0.00307 |
| CJJ81176_0040 | Inner membrane protein YagU | 0.00311 |
| CJJ81176_0215 | Ser/Thr protein phosphatase family protein | 0.00313 |
| CJJ81176_1438 | kpsD capsular polysaccharide ABC transporter, periplasmic polysaccharide-binding protein | 0.00316 |
| CJJ81176_1675 | gltA citrate synthase | 0.00324 |
| CJJ81176_0414 | Hypothetical protein | 0.00346 |
| CJJ81176_0080 | flgD flagellar basal body rod modification protein | 0.00347 |
| CJJ81176_0109 | Hypothetical protein | 0.00352 |
| CJJ81176_0574 | fliS flagellar protein | 0.00356 |
| CJJ81176_0294 | Hypothetical protein | 0.00365 |
| CJJ81176_0906 | pheS phenylalanyl-tRNA synthetase subunit alpha | 0.00367 |
| CJJ81176_1415 | Putative sugar-1-phosphate nucleotidyltransferase | 0.00367 |
| CJJ81176_0589 | Hypothetical protein | 0.00374 |
| CJJ81176_0236 | OPT family oligopeptide transporter | 0.00379 |
| CJJ81176_0359 | motA flagellar motor protein | 0.00390 |
| CJJ81176_1462 | Hypothetical protein | 0.00391 |
| CJJ81176_1602 | Hemin ABC transporter, permease protein, putative | 0.00399 |
| CJJ81176_1541 | Hypothetical protein | 0.00400 |
| CJJ81176_1050 | Hypothetical protein | 0.00402 |
| CJJ81176_1203 | gidA tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 0.00416 |
| CJJ81176_0307 | tal transaldolase | 0.00435 |
| CJJ81176_1413 | kpsC capsule polysaccharide export protein | 0.00451 |
| CJJ81176_0299 | Hypothetical protein | 0.00454 |
| CJJ81176_0273 | MCP-domain-containing signal transduction protein | 0.00459 |
| CJJ81176_1335 | Motility accessory factor | 0.00462 |
| CJJ81176_1529 | Integral membrane protein | 0.00462 |
| CJJ81176_0602 | ilvB acetolactate synthase 3 catalytic subunit | 0.00463 |
| CJJ81176_1455 | flgI flagellar basal body P-ring protein | 0.00468 |
| CJJ81176_1459 | flgK flagellar hook-associated protein | 0.00468 |
| CJJ81176_0032 | Na+/H+ antiporter family protein | 0.00479 |
| CJJ81176_0641 | ftn nonheme iron-containing ferritin | 0.00493 |
| CJJ81176_1337 | pseE | 0.00493 |
| CJJ81176_1012 | argF ornithine carbamoyltransferase | 0.00495 |
| CJJ81176_0219 | Hypothetical protein | 0.00519 |
| CJJ81176_1416 | Class I glutamine amidotransferase, putative | 0.00525 |
| CJJ81176_0590 | Hypothetical protein | 0.00537 |
| CJJ81176_0892 | rpsO 30S ribosomal protein S15 | 0.00542 |
| CJJ81176_1652 | ABC transporter, permease protein | 0.00550 |
| CJJ81176_0251 | argB acetylglutamate kinase | 0.00559 |
| CJJ81176_0296 | ilvE branched-chain amino acid aminotransferase | 0.00564 |
| CJJ81176_0674 | rlpA rare lipoprotein A | 0.00566 |
| CJJ81176_0005 | ksgA dimethyladenosine transferase | 0.00571 |
| CJJ81176_1238 | Hypothetical protein | 0.00576 |
| CJJ81176_1606 | kgtP alpha-ketoglutarate permease | 0.00587 |
| CJJ81176_1143 | pglB general glycosylation pathway protein | 0.00588 |
| CJJ81176_1679 | Major facilitator superfamily protein | 0.00590 |
| CJJ81176_1436 | Putative glycosyl transferase | 0.00593 |
| CJJ81176_0245 | Hypothetical protein | 0.00596 |
| CJJ81176_1136 | cheY chemotaxis protein | 0.00603 |
| CJJ81176_1147 | wlaB ABC transporter, permease/ATP-binding protein | 0.00668 |
| CJJ81176_1605 | Hypothetical protein | 0.00668 |
| CJJ81176_0366 | uvrA excinuclease ABC subunit A | 0.00674 |
| CJJ81176_0585 | MATE efflux family protein, authentic frameshift | 0.00677 |
| CJJ81176_0801 | napA nitrate reductase catalytic subunit | 0.00702 |
| CJJ81176_0386 | Coproporphyrinogen III oxidase | 0.00713 |
| CJJ81176_1654 | ABC transporter, ATP-binding protein | 0.00720 |
| CJJ81176_0185 | hom homoserine dehydrogenase | 0.00724 |
| CJJ81176_0274 | Hypothetical protein | 0.00728 |
| CJJ81176_0730 | waaA 3-deoxy-d-manno-octulosonic-acid transferase | 0.00728 |
| CJJ81176_0119 | cydB cytochrome d ubiquinol oxidase, subunit II | 0.00736 |
| CJJ81176_1417 | Hypothetical protein | 0.00737 |
| CJJ81176_1392 | metC cystathionine beta-lyase | 0.00752 |
| CJJ81176_1547 | MerR family transcriptional regulator | 0.00752 |
| CJJ81176_1154 | Beta-1,4-N-acetylgalactosaminyltransferase | 0.00756 |
| CJJ81176_1405 | Hypothetical protein | 0.00760 |
| CJJ81176_0252 | argD acetylornithine aminotransferase | 0.00764 |
| CJJ81176_1550 | pflA paralyzed flagellar protein | 0.00766 |
| CJJ81176_0543 | Hypothetical protein | 0.00769 |
| CJJ81176_0572 | flaG flagellar protein | 0.00777 |
| CJJ81176_1458 | Hypothetical protein | 0.00786 |
| CJJ81176_0223 | clpP ATP-dependent Clp protease proteolytic subunit | 0.00791 |
| CJJ81176_0295 | SPFH domain-containing protein | 0.00795 |
| CJJ81176_0076 | Hypothetical protein | 0.00800 |
| CJJ81176_0107 | Hypothetical protein | 0.00805 |
| CJJ81176_1421 | Putative glycosyltransferase | 0.00814 |
| CJJ81176_1336 | pseD | 0.00816 |
| CJJ81176_0534 | alaS alanyl-tRNA synthetase | 0.00829 |
| CJJ81176_1519 | Bacterioferritin, putative | 0.00829 |
| CJJ81176_0856 | Hypothetical protein | 0.00839 |
| CJJ81176_0802 | napG quinol dehydrogenase periplasmic component | 0.00865 |
| CJJ81176_0661 | Hypothetical protein | 0.00882 |
| CJJ81176_1431 | Putative sugar transferase | 0.00882 |
| CJJ81176_0202 | Hypothetical protein | 0.00893 |
| CJJ81176_0893 | Cell division protein FtsK, putative | 0.00936 |
| CJJ81176_0110 | Hypothetical protein | 0.00955 |
| CJJ81176_1352 | ceuC enterochelin ABC transporter, permease protein | 0.00955 |
| CJJ81176_1387 | katA catalase | 0.00962 |
| CJJ81176_1530 | Flavodoxin-like fold domain-containing protein | 0.00962 |
| CJJ81176_0024 | Hypothetical protein | 0.00969 |
| CJJ81176_0339 | hisC histidinol-phosphate aminotransferase | 0.00969 |
| CJJ81176_0483 | miaB (dimethylallyl)adenosine tRNA methylthiotransferase | 0.00969 |
| CJJ81176_0210 | Iron ABC transporter, permease protein | 0.00983 |
| CJJ81176_1569 | Peptide ABC transporter, periplasmic peptide-binding protein | 0.00983 |
| CJJ81176_1063 | AraC family transcriptional regulator | 0.00997 |
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).