Use of Gifu Anaerobic Medium for culturing 32 dominant species of human gut microbes and its evaluation based on short-chain fatty acids fermentation profiles

Figures & data

Table 1. List of bacterial species/strains and description of the media used for culture.

Rank^a	Species	Strain	Recommended medium^b	Growth in GAM	Growth in MegaMedium 1.0^31^)
1	Bacteroides uniformis	JCM 5828	JCM medium 13, EG, GAM	+	+
2	Alistipes putredinis	JCM 16772	EG	‒	n/a^c
3	Parabacteroides merdae	JCM 9497	EG	+	n/a
4	Dorea longicatena	DSM 13814	DSM medium 104	+	+
5	Ruminococcus bromii	ATCC 27255	ATCC medium 1016	‒	n/a
6	Bacteroides caccae	JCM 9498	EG	+	+
8	Bacteroides thetaiotaomicron	JCM 5897	JCM medium 12, GAM*	+	+
9	Eubacterium hallii	ATCC 27751	ATCC medium 1869, 260	‒	n/a
10	Ruminococcus torques	ATCC 27756	ATCC medium 1589, 260	+	n/a
14	Ruminococcus lactaris	ATCC 29176	ATCC medium 1490, 260	+	n/a
15	Collinsella aerofaciens	JCM 7790	EG	+	+
16	Dorea formicigenerans	ATCC 27755	ATCC medium 158, 260, 735*	+	n/a
17	Bacteroides vulgatus	JCM 5826	JCM medium 13, EG, GAM	+	+
18	Roseburia intestinalis	DSM 14610	DSM medium 330	+	n/a
20	Eubacterium siraeum	ATCC 29066	ATCC medium 1016	+	n/a
21	Parabacteroides distasonis	JCM 5825	JCM medium 13, EG, GAM	+	+
23	Bacteroides ovatus	JCM 5824	JCM medium 13, EG, GAM	+	+
26	Eubacterium rectale	JCM 17463	JCM medium 465	‒	n/a
27	Bacteroides xylanisolvens	JCM 15633	EG, JCM medium 461	+	n/a
28	Coprococcus comes	ATCC 27758	ATCC medium 1102	+	n/a
31	Eubacterium ventriosum	ATCC 27560	ATCC medium 1528, 1589*	+	n/a
32	Bacteroides dorei	JCM 13471	EG	+	n/a
33	Ruminococcus obeum	DSM 25238	DSM medium 104	+	+
34	Subdoligranulum variabile	DSM 15176	DSM medium 339a	‒	n/a
35	Pseudoflavonifractor capillosus	ATCC 29799	ATCC medium 1490, 260, GAM*	+	n/a
36	Streptococcus thermophilus	JCM 17834	JCM medium 13, 28, 156, 282	‒	n/a
37	Clostridium leptum	ATCC 29065	ATCC medium 2751, 260	‒	n/a
38	Holdemania filiformis	DSM 12042	DSM medium 104	‒	n/a
39	Bacteroides stercoris	JCM 9496	EG	+	n/a
40	Coprococcus eutactus	ATCC 27759	ATCC medium 1015, 260, 735*	‒	n/a
42	Bacteroides eggerthii	JCM 12986	EG	‒	n/a
43	Butyrivibrio crossotus	DSM 2876	DSM medium 330	‒	n/a
44	Bacteroides finegoldii	JCM 13345	EG	+	n/a
45	Parabacteroides johnsonii	JCM 13406	EG	+	n/a
47	Clostridium nexile	ATCC 27757	ATCC medium 1490	+	n/a
48	Bacteroides pectinophilus	ATCC 43243	ATCC medium 1547, 260	‒	n/a
49	Anaerotruncus colihominis	JCM 15631	EG, JCM medium 676	+	n/a
50	Ruminococcus gnavus	ATCC 29149	ATCC medium 1490, 260	+	n/a
51	Bacteroides intestinalis	JCM 13265	EG	+	n/a
52	Bacteroides fragilis	JCM 11019	EG	+	n/a
53	Clostridium asparagiforme	DSM 15981	DSM medium 104b	+	n/a
54	Enterococcus faecalis	ATCC 700802	ATCC medium 44, MRS*	+	n/a
55	Clostridium scindens	JCM 6567	EG	+	+
56	Blautia hansenii	JCM 14655	JCM medium 676	+	n/a

^a Rank order established in the “human gut microbial gene catalogue.”²⁸

^b Medium recommended by microbial resource collections. Underlined medium was used for recovery and storage. Media noted with asterisks (*) were used although they are not recommended by the resource collections.

^c There was no description about growth in reference.³¹

Table 2. List of proteins used as the query sequences for Blastp analysis.

	Source	Accession ID	Reference
Lactic acid synthesis
(1) d-lactate dehydrogenase (d-LDH)	Bacteroides thetaiotaomicron	NP_810488	Uniprot*
(2) l-lactate dehydrogenase (l-LDH)	Enterococcus faecalis	NP_814049	Uniprot
Acetic acid synthesis
(3) acetate kinase (AcK)	Bacteroides thetaiotaomicron	NP_812604	Uniprot
Propionic acid synthesis
(4) propionate kinase (ProK)	Clostridium neopropionicum	KXL51791	Uniprot
(5) propionyl-CoA:succinate CoA transferase (PCoAT)	Escherichia coli	WP_061359559	^35^)
(6) methylmalonyl-CoA decarboxylase (MmdA)	Veillonella parvula	ACZ24924	^33^)
(7) lactoyl-CoA dehydratase (LcdA)	Clostridium propionicum	AEM62994	^33^)
(8) CoA-dependent propionaldehyde dehydrogenase (PduP)	Roseburia inulinivorans	ABC25529	^33^)
Butyric acid synthesis
(9) butyrate kinase (ButK)	butyrate-producing bacterium	AAR19758	^34^)
(10) butyryl-CoA:acetate CoA-transferase (BCoAT)	Roseburia sp. A2-183	AAX19660	^40^)

* Protein sequence data were obtained from “Uniprot” (https://www.uniprot.org/).

Fig. 1. Concentration of SCFAs in culture supernatants.

Notes: SCFAs (lactic acid, acetic acid, propionic acid, and butyric acid) in culture supernatants after 60 h of culture of the dominant human gut bacteria. The number before the name of the species indicates the rank order listed in the “human gut microbial gene catalogue.” Dashed lines on the panel of lactic acid and acetic acid show the concentration of each acid originally contained in GAM.

Fig. 2. Pathways responsible for the biosynthesis of SCFAs from glucose in gut microbes.

Notes: The key enzymes are indicated: (1, 2) LDH, lactate dehydrogenase; (3) Ack, acetate kinase; (4) ProK, propionate kinase; (5) PCoAT, propionyl CoA:succinate CoA transferase; (6) MmdA, methylmalonyl CoA decarboxylase; (7) LcdA, lactoyl-CoA dehydratase subunit alpha; (8) PduP, CoA-dependent propionaldehyde dehydrogenase; (9) ButK, butyrate kinase; and (10) BCoAT, butyryl CoA:acetyl CoA transferase.

Fig. 3. Occurrence of homologous proteins responsible for SCFA synthesis from glucose in the genomes of dominant human gut bacteria.

Notes: The results shown are based on the Blastp analysis of genomes in the NCBI database. The color of each columns indicates the score from the Blastp analysis: (black) > 300 bit, (grey) 100–300 bit, and (white) < 100 bit. The number before the name of the species indicates the rank order listed in the “human gut microbial gene catalogue.”

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