. 2015 Jan;28(1):237–264. doi: 10.1128/CMR.00014-14

TABLE 3.

New bacterial species and genera isolated from human gut by culturomics and culture conditions used, 2011 to 2014

Phylum	New bacterial species	Stool sample type^a	Culture method^c	Atmosphere	Temp (°C)	Reference(s)
Firmicutes	Oceanobacillus massiliensis	A	Active filtration (0.45-μm filter) and then inoculation in brain heart infusion agar with 5% sheep blood	Aerobic	37	4, 244
	Bacillus timonensis	A	Brain heart infusion agar with 5% sheep blood	Aerobic	37	4, 223
	Kurthia massiliensis	B	CNA agar	Aerobic, 2.5% CO₂	37	4, 232
	Kurthia senegalensis	B	Active filtration (1.2-μm filter) and then inoculation in 5% sheep blood agar	Aerobic	37	4
	Kurthia timonensis	B	Haemophilus test medium	Aerobic, 2.5% CO₂	37	4
	Anaerococcus senegalensis	B	Brucella agar	Anaerobic	37	4, 226
	Paenibacillus senegalensis	B	Schaedler agar + kanamycin and vancomycin	Aerobic	37	4, 230
	Bacillus massiliosenegalensis	B	5% sheep blood agar	Aerobic	28	4, 239
	Clostridium senegalense	B	Inoculation for 5 days in blood culture bottle with sheep blood and then 5% sheep blood agar	Anaerobic	37	4, 228
	Peptoniphilus senegalensis	B	Inoculation for 10 days in blood culture bottle with sheep blood and then 5% sheep blood agar	Anaerobic	37	4, 221
	Peptoniphilus timonensis	B	Inoculation for 14 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	4, 229
	Ruminococcus massiliensis	B	Inoculation for 14 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	4 ^b
	Dielma fastidiosa	B	Inoculation for 10 days in blood culture bottle and then brain heart infusion agar	Anaerobic	37	4, 237
	Anaerococcus obesiensis	C	Inoculation for 5 days in blood culture bottle with thioglycolate and then 5% sheep blood agar	Anaerobic	37	4
	Brevibacillus massiliensis	C	M17 agar	Aerobic	37	4, 233
	Peptoniphilus grossensis	C	Inoculation for 26 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	4, 247
	Peptoniphilus obesi	C	Inoculation for 26 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	4, 222
	Kallipyga massiliensis	C	Inoculation for 26 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	4, 241
	Paenibacillus antibioticophila	D	Inoculation for 21 days in blood culture bottle with cow rumen and sheep blood and then 5% sheep blood agar	Aerobic	37	7
	Pytheasella massiliensis	F	5% sheep blood agar during 14 days	Aerobic	28	7
	Paenibacillus reamassiliensis	H	Inoculation for 14 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Aerobic	37	7
	Soleaferrea massiliensis	E	Inoculation in blood culture bottle and then 5% sheep blood agar	Anaerobic	37	6
	Stoquefichus massiliensis	E	5% sheep blood agar	Anaerobic	28	6
	Dorea massiliensis	E	Inoculation in blood culture bottle with rumen fluid and then 5% sheep blood agar	Anaerobic	37	6
	Holdemania massiliensis	E	Inoculation in blood culture bottle with thioglycolate and then 5% sheep blood agar	Anaerobic	37	6, 246
	Clostridium ihumii	E	Inoculation in blood culture bottle with sheep blood and then 5% sheep blood agar	Anaerobic	37	6
	Bacillus massilioanorexius	E	Inoculation in blood culture bottle for 1 mo with rumen fluid and then 5% sheep blood agar	Anaerobic	37	6, 240
	Clostridium polynesiense	I	Active filtration (0.45-μm filter) and then inoculation in 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Bacillus saudii	K	Inoculation in blood culture bottle with sheep blood and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Polynesia massiliensis	I	Inoculation for 5 days in blood culture bottle and then inoculation in 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Bacillus jeddahense	K	Inoculation in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Clostridium saudii	K	5% sheep blood agar	Anaerobic cabinet	37	Our unpublished data
	Clostridium jeddahense	K	Inoculation in blood culture bottle with rumen fluid and then 5% sheep blood agar	Anaerobic	37	286
	Clostridium massilioamazoniensis	J	Inoculation for 5 days in blood culture bottle and then Schaedler agar with neomycin + vancomycin	Anaerobic	37	Our unpublished data
	Anaerosalibacter massiliensis	J	Thermic shock (20 min, 65°C) and then inoculation for 3 days in blood culture bottle and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Nosocomiicoccus massiliensis	L	Inoculation for 14 days in blood culture bottle with rumen fluid and then 5% sheep blood agar	Aerobic	37	243
	Megasphaera massiliensis	L	Inoculation for 7 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	242
	Bacillus casamancensis	M	5% sheep blood agar	Anaerobic	37	Our unpublished data
	Clostridium dakarense	M	5% sheep blood agar	Anaerobic	37	245
	Bacillus numidis	O	Inoculation for 21 days in liquid brain heart infusion broth with 5% sheep blood then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Numidum massiliensis	O	Inoculation for 21 days in liquid brain heart infusion broth with 5% sheep blood and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Bacillus rubiinfantis	P	Inoculation for 21 days in blood culture bottle with sheep blood and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Amazonia massiliensis	Q	Inoculation in Columbia broth during 30 days and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Clostridium culturomicsense	S	Inoculation for 7 days in blood culture bottle with rumen fluid and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Clostridium jeddahtimonense	S	Inoculation for 7 days in blood culture bottle with rumen fluid and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Oceanobacillus jeddahense	S	Inoculation for 15 days in Columbia broth medium with 100 g/liter NaCl and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Bacillus jeddahtimonense	T	Inoculation for 15 days in Columbia broth medium with 100 g/liter NaCl and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Paraliobacillus massiliensis	U	Inoculation for 21 days in Columbia broth medium with 100 g/liter NaCl and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Thalassobacillus massiliensis	U	Inoculation for 21 days in Columbia broth medium with 100 g/liter NaCl and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Peptoniphilus ihumii	V	Inoculation for 21 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Bacillus andreraoultii	Y	Inoculation for 10 days in blood culture bottle with sheep blood and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Rubiinfantum massiliensis	X	Inoculation in marine liquid medium during 3 days and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Bacillus massilioamazoniensis	Y	Inoculation for 10 days in blood culture bottle with sheep blood and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Clostridium amazonitimonense	Y	Inoculation for 15 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Guyana massiliensis	Y	Inoculation for 15 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Virgibacillus senegalensis	Z	Inoculation for 3 days in Columbia broth medium with 100 g/liter NaCl and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Virgibacillus massiliensis	Y2	Inoculation for 21 days in Columbia broth medium with 100 g/liter NaCl and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Planomicrobium massiliensis	Z2	Inoculation for 2 days in Columbia broth medium with 100 g/liter NaCl and then 5% sheep blood agar	Aerobic	37	Our unpublished data
Bacteroidetes	Alistipes senegalensis	B	Schaedler agar with kanamycin + vancomycin	Anaerobic	37	4, 227
	Alistipes timonensis	B	Inoculation for 5 days in blood culture bottle and then Schaedler agar with kanamycin + vancomycin	Anaerobic	37	4, 228
	Alistipes obesi	C	Inoculation for 11 days in blood culture bottle with rumen fluid and then 5% sheep blood agar	Anaerobic	37	4, 235
	Bacteroides timonensis	E	5% sheep blood agar for 1 mo	Anaerobic	37	6, 291
	Bacteroides neonati	N	Inoculation in blood culture bottle and then 5% sheep blood agar	Anaerobic	37	283
	Alistipes ihumii	E	Inoculation in blood culture bottle with thioglycolate and then 5% sheep blood agar	Anaerobic	37	6
	Butyricimonas massiliensis	G	Inoculation for 14 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	7 ^b
	Alistipes jeddahensis	S	Incubation 3 days in PolyViteX chocolate agar medium	Anaerobic	37	Our unpublished data
Actinobacteria	Timonella senegalensis	B	Inoculation for 14 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	4, 238
	Senegalemassilia anaerobia	B	Inoculation for 5 days in blood culture bottle and then 5% sheep blood agar	Anaerobic	37	4, 236
	Cellulomonas massiliensis	B	Passive filtration (0.4-μm filter) using Leptospira broth and then inoculation in 5% sheep blood agar	Aerobic	37	4, 197
	Aeromicrobium massiliense	B	5% sheep blood agar	Aerobic	37	4, 231
	Brevibacterium senegalense	B	Brucella agar	Aerobic	37	4, 224
	Actinomyces grossensis	C	Inoculation for 4 days in blood culture bottle with thioglycolate and then 5% sheep blood agar	Anaerobic	37	4
	Streptomyces massiliensis	E	Active filtration (0.45-μm filter) and then inoculation in brain heart infusion agar	Aerobic	37	6
	Blastococcus massiliensis	E	Brucella agar	Aerobic	37	6
	Collinsella massiliensis	G	Inoculation for 14 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	7
	Enorma massiliensis	C	Inoculation for 4 days in blood culture bottle with thioglycolate and then 5% sheep blood agar	Anaerobic	37	4, 234
	Enorma timonensis	G	Inoculation for 14 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	284
	Corynebacterium ihumii	H	PolyViteX chocolate agar during 21 days	Aerobic with 5% CO₂	37	287
	Nocardioides massiliensis	H	PolyViteX chocolate agar during 14 days	Aerobic	28	Our unpublished data
	Actinomyces polynesiense	I	Inoculation in blood culture bottle with coconut milk and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Nesterenkonia massiliensis	L	Inoculation for 14 days in blood culture bottle with rumen fluid and then 5% sheep blood agar	Aerobic	37	277
	Corynebacterium jeddahense	K	Inoculation for 14 days in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Aerobic	37	285
	Collinsella massilioamazoniensis	Q	Inoculation in marine liquid medium during 30 days and then 5% sheep blood agar	Anaerobic	37	Our unpublished data
	Jeddahella massiliensis	S	Inoculation for 3 days in blood culture bottle with TSA medium and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Nigerium massiliensis	W	Inoculation for 21 days in blood culture bottle with liquid brain heart infusion medium, yeast extract, and proteose peptone and then 5% sheep blood agar	Anaerobic	28	Our unpublished data
	Flaviflexus massiliensis	X	Inoculation in marine liquid medium during 3 days and then 5% sheep blood agar	Aerobic	37	Our unpublished data
	Tessaracoccus massiliensis	X	Inoculation in marine liquid medium during 10 days and then 5% sheep blood agar	Aerobic	37	Our unpublished data
Proteobacteria	Enterobacter massiliensis	B	Use of both T1 and T4 phage and then inoculation in 5% sheep blood agar	Aerobic	37	4, 206
	Herbaspirillum massiliense	B	Passive filtration (0.4-μm filter) using Leptospira broth and then inoculation in 5% sheep blood agar	Aerobic	37	4, 198
	Microvirga massiliensis	B	MOD 2	Aerobic	37	10
	Dakarella massiliensis	R	Inoculation for 1 day in blood culture bottle with rumen fluid and sheep blood and then 5% sheep blood agar	Anaerobic	37	Our unpublished data^b

A, N’Diop, Senegal (healthy individual A); B, Dielmo, Senegal, healthy individual; C, French obese patient; D, XDR tuberculosis patient; E, French anorexia nervosa patient; F, Q fever patient; G, intensive care unit (patient A); H, intensive care unit (patient B); I, Raiatea Island (French Polynesia) healthy individual; J, Amazonian (healthy individual A); K, obese Saudi (patient A); L, AIDS (patient A); M, Senegalese subjects (684 samples); N, preterm infant with necrotizing enterocolitis; O, Touareg healthy individual; P, Kwashiorkor malnutrition (patient A); Q, Amazonian (healthy individual B); R, fresh sample from French healthy individual; S, obese Saudi (patient B); T, lean Saudi; U, Amazonian (healthy individual C); V, AIDS (patient B); W, Kwashiorkor malnutrition (patient B); X, Kwashiorkor malnutrition (patient C); Y, Amazonian (healthy individual D); Z, N’Diop, Senegal (healthy individual B); Y2, Amazonian (healthy individual E); Z2, N’Diop, Senegal (healthy individual C).

Bacterial species were not characterized because subculturing was impossible.

TSA, Trypticase soy agar.