Table 1.

B. longum subspecies-specific core genes

B. longumsubsp.longum
Core gene	Prevalence across the subspecies	Function		Transporter classification database		HGT events
		Interpro Database	Refseq Database	Function	Family
B1_0665	99 %	Selenoprotein, putative	YbdD/YjiX family protein			Native
B1_0666	98 %	5TM C-terminal transporter carbon starvation CstA	Carbon starvation protein A	Peptide Transporter Carbon Starvation CstA (CstA) Family	2.A.114.-	Native
B1_1343	98 %	Protein of unknown function (DUF3073)	DUF3073 domain-containing protein			Native
B1_0094	98 %	NADH Oxidase	Nitroreductase			Native
B1_0106	98 %	Periplasmic binding protein-like II	Extracellular solute-binding protein			Native
B1_0884	98 %	–	Aldo/keto reductase family protein			Native
B1_1277	97 %	Glycosidases	Pullulanase type I			Native
B1_0628	97 %	l,d-transpeptidase YCIB-related	l,d-transpeptidase			Native
B1_0345	97 %	Metal-dependent hydrolase	Amidohydrolase family protein			Native
B1_1278	97 %		Alpha-amylase			Native
B1_0156	95 %	–	DUF2400 domain-containing protein			Native
B1_1275	95 %	ABC transporter permease protein MG189-related	ABC transporter permease subunit	It binds α-(1,6)-linked glucosides and galactosides	3.A.1.1.53	Native
B1_0738	94 %	–	DUF1846 domain-containing protein			Native
B1_1795	93 %	Acyl-CoA N-acyltransferases (Nat)	GNAT family N-acetyltransferase			Native
B1_0431	91 %	Uncharacterized protein conserved in bacteria C-term(DUF2220)	DUF3322 and DUF2220 domain-containing protein			Native
B1_1294	90 %	–	Substrate-binding domain-containing protein			Native
B1_0735	90 %	–	DUF87 domain-containing protein			Foreign
B1_0883	90 %	Transcriptional dual regulator hcar-related	LysR family transcriptional regulator			Native
B1_0737	89 %	Type VII secretion system protein EsaG-like	–			Foreign
134B_0607	88 %	–	DNA/RNA non-specific endonuclease			Native
134B_0472	88 %	MATE_MepA_like	MATE family efflux transporter			Native
B1_1296	88 %	K+potassium transporter	KUP/HAK/KT family potassium transporter			Native
B1_0107	86 %	Glycosidase family 31	Alpha-xylosidase			Native
B1_0786	86%	zinc-ribbon domain	Zinc ribbon domain-containing protein			Native
B. longum subsp. infantis
Core gene	Prevalence across the subspecies	Function		Transporter classification database		HGT events
		Interpro Database	Refseq Database	Function	Family
ACJ51545.1	100 %	MFS general substrate transporter domains	MFS transporter	Glucose Transporter (GT) Family	2.A.1.68.1	Native
ACJ53225.1	100 %	Tetratricopeptide-like helical domain	DUF4037 domain-containing protein			Native
ACJ52470.1	100 %	Ttransporter solute:sodium symporter family	Sodium/solute symporter	Glucose or galactose:Na +symporter	2.A.1.68.1	Native
ACJ52099.1	100%	Response regulator receiver domain	Response regulator transcription factor			Foreign
ACJ51227.1	100 %	–	–			Native
ACJ52098.1	100 %	Lantibiotic immunity protein Spa1	NisI/SpaI family lantibiotic immunity			Native
ACJ53071.1	100 %	Pyridoxal-phosphate dependent enzyme	Pyridoxal-phosphate dependent enzyme			Native
ACJ51238.1	100 %	High-affinity nickel-transport protein	Nickel/cobalt transporter			Native
ACJ51551.1	100 %	Bacteriocin (Lactococcin_972)	Lactococcin 972 family bacteriocin			Foreign
ACJ51549.1	100 %	Nitrate/nitrite sensor protein narx-related	Histidine kinase			Native
ACJ53072.1	100 %	metallo-dependent hydrolases	Guanine deaminase			Native
ACJ52052.1	100 %	GDSL-like Lipase/Acylhydrolase family	Lipase			Native
ACJ53073.1	100 %	MFS multidrug transporter	MFS transporter	Tet38 tetracycline-resistance protein	2.A.1.3.22	Native
ACJ51151.1	100 %	–	–			Foreign
ACJ53179.1	100 %	RecG, C-terminal domain superfamily	Transcriptional regulator, partial			Native
ACJ52471.1	100 %	–	–			Native
ACJ51149.1	100 %	RelB antitoxin/Antitoxin DinJ	Type II toxin-antitoxin system family			Foreign
ACJ51552.1	100 %	–	–			Native
ACJ53224.1	100 %	–	5'-nucleotidase C-terminal domain			Native
ACJ51550.1	100 %	Response regulatory domain profile.	Response regulator transcription factor			Native
ACJ51553.1	100 %	Nucleoside triphosphate hydrolases	ATP-binding domain-containing protein			Foreign
ACJ52096.1	100 %	Lantibiotic protection ABC transporter permease	Lantibiotic immunity ABC transporter permease	3-component subtilin immunity exporter	3.A.1.124.2	Foreign
ACJ52097.1	100 %	ABC-2 family transporter protein	Lantibiotic immunity permease	CprABC antimicrobial peptide resistance ABC exporter	3.A.1.124.6	Foreign
ACJ51554.1	100 %	–	–			Native
ACJ51425.1	90 %	Antitoxin	–			Foreign
ACJ51673.1	90 %	ABC superfamily metabolite uptake	ABC transporter permease	Putative macrolide-specific efflux system, MacAB	3.A.1.122.16	Native
ACJ53183.1	90 %	Metallophosphoesterase, calcineurin family	Metallophosphoesterase			Native
ACJ53406.1	90 %	Sialidase	Exo-alpha-sialidase			Native
ACJ52932.1	90 %	MFS_MefA_like	MFS transporter	The tetracycline resistance determinant, TetV	2.A.1.21.3	Native
ACJ52100.1	90 %	HAMP domain-containing histidine kinase	–	–		Native
ACJ52095.1	90 %	lantibiotic, protection ABC transporter ATP binding protein	–	–		Foreign
ACJ51226.1	90 %	Protein/nucleic acid deglycase dj-1-related	DJ-1/PfpI family protein			Native
ACJ53416.1	90 %	Beta-lactamase superfamily domain	MBL fold metallo-hydrolase			Native
ACJ53415.1	90 %	PBP2_UgpB	ABC transporter substrate-binding protein	Involved in maltose and maltodextrin uptake	CEF11988.1	Native
ACJ51154.1	90 %	ABC transporter integral membrane type-1	Phosphonate ABC transporter, permease	Putative phosphonate/phosphite/phosphate porter	3.A.1.9.2	Native
ACJ51426.1	90 %	type II toxin-antitoxin system	BrnT family toxin			Native
ACJ51156.1	90 %	ABC transporter-type domain profile	Phosphonate ABC transporter ATP-binding	Putative phosphonate/phosphite/phosphate porter	3.A.1.9.2	Native
ACJ53417.1	90%	Transport system inner membrane component	Carbohydrate ABC transporter permease	ABC transporters for maltose/maltotriose and trehalose	3.A.1.1.23	Native
ACJ51155.1	90 %	phosphonate ABC transporter, permease	ABC transporter, permease protein	Putative phosphonate/phosphite/phosphate porter	3.A.1.9.2	Native
ACJ51158.1	90 %	SIS_RpiR	MurR/RpiR family transcriptional regulator			Native
ACJ51157.1	90  %	Periplasmatic phosphonate-binding protein	ABC transporter substrate-binding protein	Putative phosphonate/phosphite/phosphate porter, PhnDCE	3.A.1.9.2	Native
ACJ51374.1	90 %	MFS_MdtG_SLC18_like	MFS transporter	Copper Uptake Porter	2.A.1.81.-	Native
ACJ51159.1	90  %	HAD-like superfamily	HAD family hydrolase			Native
ACJ51153.1	90 %	5′-Nucleotidase/apyrase	Metallophosphoesterase			Native
ACJ53414.1	90 %	Haloacid dehalogenase-like hydrolase	HAD family hydrolase			Native
ACJ53419.1	90 %	ABC transporter-type domain profile.	ABC transporter ATP-binding protein	Involved in the uptake of pectin oligosaccharides	3.A.1.1.34	Native
ACJ53418.1	90 %	ABC transporter integral membrane type-1	Sugar ABC transporter permease	The fructooligosaccharide porter	3.A.1.1.20	Native
ACJ51575.1	90 %	Glycosidases	Family 20 glycosylhydrolase			Native
ACJ51984.1	90 %	MetI-like	Sugar ABC transporter permease	The xylobiose porter; BxlEFG(K)	3.A.1.1.21	Native
ACJ51567.1	90%	–	Tyrosine-type recombinase/integrase			Foreign
ACJ51985.1	90 %	Maltose transport system permease	ABC transporter permease subunit	N-Acetylglucosamine/N,N'-diacetyl chitobiose porter	3.A.1.1.18	Native
ACJ53244.1	90 %	Duplicated hybrid motif	PTS glucose transporter subunit IIA			Native
ACJ51983.1	90 %	Carbohydrate substrate-binding protein	Carbohydrate ABC transporter	xylobiose porter	3.A.1.1.21	Native
B. longum subsp. suis
Core gene	Prevalence across the subspecies	Function		Transporter classification database		HGT events
		Interpro Database	Refseq Database	Function	Family
AIF90321.1	100 %	ABC transporter, atp-binding protein	ABC transporter ATP-binding protein	The Macrolide Exporter (MacB) Family	3.A.1.122.-	Native
AIF90322.1	100 %	ABC transporter permease	MacB-like periplasmic core domain	Exports macrolide antibiotics	3.A.1.122.18	Native
SDO34397.1	70 %	Heavy metal transporter	ABC transporter ATP-binding protein			Native
SDO30658.1	70 %	ABC-2 type transporter	FHA domain-containing protein	ABC exporter involved in bacterial competitiveness	3.A.1.105.19	Native
AIF89665.1	70 %	vWA-like	VWA domain-containing protein			Native