Table 4 The differentially expressed genes of BF compared with Δpga

Up-regulated genes/operons (log₂FC ≥ 1, FDR < 0.05)

 Carbohydrate metabolism

APPSER1_RS05460-APPSER1_RS05465

galT/K

galactokinase

APPSER1_RS07965-APPSER1_RS07970

mglAC

galactose/methyl galactoside ABC transporter

APPSER1_RS09115-APPSER1_RS09120

manYZ

mannose PTS system

APPSER1_RS09135

idnK

gluconokinase

APPSER1_RS06715-APPSER1_RS06725

malM-APPSER1_RS06720-malK

maltose/maltodextrin ABC transporter

APPSER1_RS06730, APPSER1_RS06740

malE-malG

maltose/maltodextrin ABC transporter

APPSER1_RS05415

APPSER1_RS05415

glycosyltransferase

APPSER1_RS09220

fucRIKU

L-fucose isomerase; L-fuculokinase;

L-fucose mutarotase

APPSER1_RS09580-APPSER1_RS09605

APPSER1_RS09580-nanEKA-nagBA

N-acetylmannosamine kinase;

N-acetylneuraminate lyase;

glucosamine-6-phosphate deaminase;

N-acetylglucosamine-6-phosphate deacetylase

 Fermentation

APPSER1_RS02385-APPSER1_RS02390

lldEF

L-lactate dehydrogenase

APPSER1_RS02395

lctP

L-lactate permease

APPSER1_RS10140

lldD

FMN-dependent L-lactate dehydrogenase LldD

APPSER1_RS10665

adhP

alcohol dehydrogenase AdhP

 Transporter

APPSER1_RS07470-APPSER1_RS07490

ccmEDCBA

cytochrome c maturation protein;

heme exporter protein

APPSER1_RS04515-APPSER1_RS04525

APPSER1_RS04515-APPSER1_RS04525

dipeptide/oligopeptide/nickel ABC transporter

APPSER1_RS09260-APPSER1_RS09265

APPSER1_RS09260-APPSER1_RS09265

amino acid ABC transporter

APPSER1_RS09375

ulaAB

PTS ascorbate transporter

APPSER1_RS07040-APPSER1_RS07045

mlaEF

phospholipid ABC transporter

APPSER1_RS10020

glpT

glycerol-3-phosphate transporter

APPSER1_RS10940-APPSER1_RS10945

fhuCD

iron-siderophore ABC transporter

APPSER1_RS10115-APPSER1_RS10130

sbp-cysTW-cysA

sulfate ABC transporter

 Reductase

APPSER1_RS10085-APPSER1_RS10090

cysJI

assimilatory sulfite reductase;

assimilatory sulfite reductase

APPSER1_RS10095-APPSER1_RS10110

cysGHDN

phosphoadenylyl-sulfate reductase

 Others

APPSER1_RS10595

cpdA

3',5'-cyclic-AMP phosphodiesterase

APPSER1_RS02045-APPSER1_RS02050

ribDE

uracil reductase RibD; riboflavin synthase

APPSER1_RS05435

katE

catalase

APPSER1_RS10970

hisG, hisD, hisC

ATP phosphoribosyltransferase;

histidinol dehydrogenase;

histidinol-phosphate transaminase

Down-regulated genes/operons (log₂FC ≤ -1, FDR < 0.05)

 Reductase

APPSER1_RS00525-APPSER1_RS00530

nrfAB

nitrite reductase

APPSER1_RS07905-APPSER1_RS07915

napFDA

nitrate reductase

APPSER1_RS09175-APPSER1_RS09190

dmsABCD

anaerobic dimethyl sulfoxide reductase

APPSER1_RS03675

torY

trimethylamine-N-oxide reductase

APPSER1_RS07240

hyaA

hydrogenase 2