Table 1.

First colonizers isolated from stools of 1–10-day-old infants

Systematic groups	Species	Ecology	Potential opportunistic pathogen	References
Proteobacteria
Enterobacteriaceae	E. coli	Gut commensal	Yes	4., 5., 7., 9., 10., 11., 16., 17., 20., 23., 24.
	Enterobacter sp.			4., 5., 6., 17., 22., 23., 28.
	E. cloacae	Gut commensal, environment	Yes	5., 7., 9., 10., 16.
	E. aerogenes	Gut commensal, environment	?	9., 16.
	E. asburiae	Environment	Yes	24
	Pantoea agglomerans	Plants, insects	Yes	5
	Serratia sp.			4., 16.
	S. liquefaciens	Environment	Yes	5
	Shigella sp.	Primate gut commensal	Yes	17
	Klebsiella sp.			4., 11., 17., 20.
	K. pneumoniae	Gut, oral, skin commensal; environment	Yes	3., 5., 9., 10., 28.
	K. oxytoca	Soil	Yes	5., 10., 31.
	Raoultella planticola	Plants	Yes	10., 23.
	Proteus sp.			7., 11.
	P. mirabilis	Gut commensal, environment	Yes	4
	Morganella morganii	Environment	Yes	4., 5.
	Rahnella aquatilis	Environment	Yes	5
	Ewingella americana	Environment	Yes	7
	Citrobacter sp.			16
	C. freundii	Environment	No	4., 5., 9.
	Cronobacter muytjensii	Environment	?	28
Pasteurellaceae	Haemophilus sp.	Airway commensal	Yes	17
	H. parainfluenzae	Airway commensal	Yes	5
Moraxellaceae	Acinetobacter sp.	Soil	Yes	4
Pseudomonadaceae	Pseudomonas sp.			4., 5., 11., 17., 20.
	P. aeruginosa	Environment, gut commensal	Yes	7., 9., 16.
Firmicutes
Enterococcaceae	Enterococcus sp.			3., 4., 5., 6., 7., 9., 15., 17., 20., 22., 23.
	E. faecalis	Major gut commensal	Yes	10., 16.
	E. faecium	Major gut commensal	?	10., 16.
	E. gallinarum	Gut commensal of birds	Yes	10
	E. avium	Gut commensal of birds	Yes	24
	E. raffinosus	Gut commensal of animals	Yes	24
Closrtidiaceae	Clostridium sp.			3., 4., 6., 7., 15., 22., 25., 31.
	C. perfringens	Ubiquitous	Yes	11., 31.
	C. butyricum	Soil, gut commensal	Yes	10., 11.
	C. difficile	Soil	Yes	10., 11.
	C. neonatale	Environment	Yes	10
	C. disporicum	Environment	?	24
	C. paraputrificum	Environment	Yes	24
	Ruminococcus gnavus	Gut commensal	?	24
	R. productus	Environment	?	10
Staphylococcaceae	Staphylococcus sp.			3., 4., 6., 7., 17., 20., 22., 25.
	S. aureus	Skin commensal, soil	Yes	9., 11., 16., 23., 31.
	S. haemolyticus	Skin commensal	?	16
	S. epidermidis	Skin commensal	Yes	9., 10., 11., 16., 28., 31.
Streptococcaceae	Streptococcus sp.			3., 4., 5., 11., 15., 20.
	S. salivarius	Oral commensal	No	10
	S. viridis	Oral commensal	No	11
	S. parasanguinis	Oral commensal	No	10
	S. bovis	Ruminal commensal	Yes	10
Lactobacillaceae	Lactobacillus sp.	Vaginal, oral, gut commensal, environment	Yes	3., 11., 15., 16., 22., 23., 25.
Bacillaceae	Bacillus sp.			5., 20.
	B. cereus	Soil, gut commensal	Yes	4
Leukonostocaceae	Weissella sp.	Environment	Yes	3
Veillonellaceae	Veillonella sp.			6., 15., 17., 22.
	V. parvula	Oral commensal	No	10
	V. dispar	Oral commensal	No	24
	Megasphaera sp.	Vaginal commensal	No	10
Actinobacteria
Bifidobacteriaceae	Bifidobacterium sp.			3., 6., 15., 20., 22., 23., 25., 26.
	B. bifidum	Major gut, vaginal commensal	No	10
	B. breve	Major gut, vaginal commensal	No	10
	B. longum	Major gut, vaginal commensal	No	10
	B. dentium	Oral commensal	No	10
Coriobacteriaceae	Atopobium sp.	Vaginal commensal	?	3
	A. parvulum	Vaginal commensal	Yes	10
Corynebacteriaceae	Corynebacterium sp.	Environment	No	5., 16.
Bacteroidetes
Bacteroidaceae	Bacteroides sp.	Major gut commensal	No	11., 15., 16., 22., 23., 25.
	B. fragilis	Major gut commensal	No	4
	B. thetaiotaomicron	Gut commensal	No	24
	Parabacteroides sp.	Gut commensal	No	15
Fungi	Candida sp.	Environment	Yes	4., 5., 20.