Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Coyne, Michael J.; Roelofs, Kevin G.; Comstock, Laurie E.

doi:10.1186/s12864-016-2377-z

Table 1 Summary of the 205 human gut Bacterodales strains analyzed and the T6SS loci present in each genome

From: Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

					T6SS architecture
number	genome	16S ID	NCBI Bioproject ID	loci initially identified	1	2	3	other	identified by HMM
1	Alistipes finegoldii DSM 17242	A. finegoldii	PRJNA40775	0
2	Alistipes indistinctus YIT 12060	A. indistinctus	PRJNA46373	0
3	Alistipes onderdonkii DSM 19147	A. onderdonkii	PRJNA199292	0
4	Alistipes putredinis DSM 17216	A. putredinis	PRJNA19655	0
5	Alistipes senegalensis JC50	A. senegalensis	PRJNA199660	0
6	Alistipes shahii WAL 8301	A. shahii	PRJNA45913	0
7	Alistipes sp. AL-1	A. onderdonkii	PRJNA224116	0
8	Alistipes sp. HGB5	A. finegoldii	PRJNA54031	0
9	Alistipes timonensis JC136	A. timonensis	PRJEA174622	0
10	Bacteroides caccae ATCC 43185	B. caccae	PRJNA18163	0
11	Bacteroides caccae CL03T12C61	B. caccae	PRJNA64801	1		1
12	Bacteroides cellulosilyticus CL02T12C19	B. cellulosilyticus	PRJNA64803	1	1
13	Bacteroides cellulosilyticus DSM 14838	B. cellulosilyticus	PRJNA30027	0
14	Bacteroides cellulosilyticus WH2	B. cellulosilyticus	PRJNA224116	0
15	Bacteroides sp. 14(A)	B. cellulosilyticus	PRJNA224116	0
16	Bacteroides clarus YIT 12056	B. clarus	PRJNA48509	0
17	Bacteroides coprocola DSM 17136	B. coprocola	PRJNA20521	0
18	Bacteroides coprophilus DSM 18228	B. coprophilus	PRJNA30371	1	1				1
19	Bacteroides dorei 5 1 36-D4	B. dorei	PRJNA32451	0
20	Bacteroides dorei CL02T00C15	B. dorei	PRJNA64805	1	1
21	Bacteroides dorei CL02T12C06	B. dorei	PRJNA64807	1	1
22	Bacteroides dorei CL03T12C01	B. dorei	PRJNA64809	0
23	Bacteroides dorei DSM 17855	B. dorei	PRJNA27831	1		1
24	Bacteroides dorei HS1 L 1 B 010	B. dorei	PRJNA232731	1	1
25	Bacteroides dorei HS1 L 3 B 079	B. dorei	PRJNA232731	0
26	Bacteroides sp. 3 1 33FAA	B. dorei	PRJNA38353	0
27	Bacteroides sp. 9 1 42FAA	B. dorei	PRJNA32445	0
28	Bacteroides eggerthii 1 2 48FAA	B. eggerthii	PRJNA40009	0
29	Bacteroides eggerthii DSM 20697	B. eggerthii	PRJNA27827	1		1
30	Bacteroides faecis MAJ27	B. faecis	PRJNA86875	0
31	Bacteroides finegoldii CL09T03C10	B. finegoldii	PRJNA64831	1	1
32	Bacteroides finegoldii DSM 17565	B. finegoldii	PRJNA27823	0
33	Bacteroides fluxus YIT 12057	B. fluxus	PRJNA48511	1				1
34	Bacteroides fragilis 3 1 12	B. fragilis	PRJNA32433	1	1
35	Bacteroides fragilis 638R	B. fragilis	PRJNA50405	1			1
36	Bacteroides fragilis CL03T00C08	B. fragilis	PRJNA64811	1			1
37	Bacteroides fragilis CL03T12C07	B. fragilis	PRJNA64813	1			1
38	Bacteroides fragilis CL05T00C42	B. fragilis	PRJNA64815	1		1
39	Bacteroides fragilis CL05T12C13	B. fragilis	PRJNA64817	1		1
40	Bacteroides fragilis CL07T00C01	B. fragilis	PRJNA64819	1			1
41	Bacteroides fragilis CL07T12C05	B. fragilis	PRJNA64821	1			1
42	Bacteroides fragilis DCMOUH0017B	B. fragilis	PRJNA244943	2			2
43	Bacteroides fragilis DCMOUH0018B	B. fragilis	PRJNA244944	0
44	Bacteroides fragilis DCMOUH0042B	B. fragilis	PRJNA253771	1			1
45	Bacteroides fragilis DCMOUH0067B	B. fragilis	PRJNA254401	0
46	Bacteroides fragilis DCMOUH0085B	B. fragilis	PRJNA254455	1			1
47	Bacteroides fragilis DCMSKEJBY0001B	B. fragilis	PRJNA244942	0
48	Bacteroides fragilis HMW 610	B. fragilis	PRJNA71525	0
49	Bacteroides fragilis HMW 615	B. fragilis	PRJNA71527	0
50	Bacteroides fragilis HMW 616	B. fragilis	PRJNA71529	1			1
51	Bacteroides fragilis JCM 11017	B. fragilis	PRJNA224116	0					1
52	Bacteroides fragilis NCTC 9343	B. fragilis	PRJNA46	1			1
53	Bacteroides fragilis YCH46	B. fragilis	PRJNA13067	2	1		1
54	Bacteroides fragilis str 1007-1-F #10	B. fragilis	PRJNA206138	1			1
55	Bacteroides fragilis str 1007-1-F #3	B. fragilis	PRJNA206180	1			1
56	Bacteroides fragilis str 1007-1-F #4	B. fragilis	PRJNA206181	1			1
57	Bacteroides fragilis str 1007-1-F #5	B. fragilis	PRJNA206182	1			1
58	Bacteroides fragilis str 1007-1-F #6	B. fragilis	PRJNA206183	1			1
59	Bacteroides fragilis str 1007-1-F #7	B. fragilis	PRJNA206135	1			1
60	Bacteroides fragilis str 1007-1-F #8	B. fragilis	PRJNA206136	1			1
61	Bacteroides fragilis str 1007-1-F #9	B. fragilis	PRJNA206137	1			1
62	Bacteroides fragilis str 1009-4-F #10	B. fragilis	PRJNA206140	1			1
63	Bacteroides fragilis str 1009-4-F #7	B. fragilis	PRJNA206139	1			1
64	Bacteroides fragilis str 2-F-2 #4	B. fragilis	PRJNA206111	1	1
65	Bacteroides fragilis str 2-F-2 #5	B. fragilis	PRJNA206112	1	1
66	Bacteroides fragilis str 2-F-2 #7	B. fragilis	PRJNA206113	1	1
67	Bacteroides fragilis str 20793-3	B. fragilis	PRJNA206110	0
68	Bacteroides fragilis str 3-F-2 #6	no call	PRJNA206178	0					1
69	Bacteroides fragilis str 3397 N2	B. fragilis	PRJNA206143	0
70	Bacteroides fragilis str 3397 N3	B. fragilis	PRJNA206144	0
71	Bacteroides fragilis str 3397 T10	B. xylanisolvens	PRJNA206115	0
72	Bacteroides fragilis str 3397 T14	B. fragilis	PRJNA206142	0
73	Bacteroides fragilis str 34-F-2 #13	B. fragilis	PRJNA206179	1	1
74	Bacteroides fragilis str 3719 A10	B. fragilis	PRJNA206150	0
75	Bacteroides fragilis str 3719 T6	B. fragilis	PRJNA206149	0
76	Bacteroides fragilis str 3725 D9(v)	B. fragilis	PRJNA206141	2	1		1
77	Bacteroides fragilis str 3725 D9 ii	B. ovatus	PRJNA206117	0
78	Bacteroides fragilis str 3774 T13	B. fragilis	PRJNA206151	2	1		1
79	Bacteroides fragilis str 3783 N1-2	B. fragilis	PRJNA206152	1	1
80	Bacteroides fragilis str 3783 N1-6	B. fragilis	PRJNA206153	1	1
81	Bacteroides fragilis str 3783 N1-8	B. fragilis	PRJNA206154	1	1
82	Bacteroides fragilis str 3783 N2-1	B. fragilis	PRJNA206155	1	1
83	Bacteroides fragilis str 3976 T7	B. fragilis	PRJNA206156	1	1
84	Bacteroides fragilis str 3976 T8	B. fragilis	PRJNA206157	0					1
85	Bacteroides fragilis str 3986 T(B)10	B. fragilis	PRJNA206145	1			1
86	Bacteroides fragilis str 3986 N(B)19	B. fragilis	PRJNA206120	0					1
87	Bacteroides fragilis str 3986 N(B)22	B. fragilis	PRJNA206148	1			1
88	Bacteroides fragilis str 3986 N3	no call	PRJNA206147	1			1
89	Bacteroides fragilis str 3986 T(B)13	no call	PRJNA206146	1			1
90	Bacteroides fragilis str 3986 T(B)9	B. fragilis	PRJNA206118	1			1
91	Bacteroides fragilis str 3988 T(B)14	B. fragilis	PRJNA206158	1	1
92	Bacteroides fragilis str 3988 T1	B. fragilis	PRJNA206119	1	1
93	Bacteroides fragilis str 3996 N(B) 6	B. fragilis	PRJNA206114	1	1
94	Bacteroides fragilis str 3998 T(B)3	B. fragilis	PRJNA206159	0					1
95	Bacteroides fragilis str 3998 T(B) 4	B. fragilis	PRJNA206116	0					1
96	Bacteroides fragilis str A7 (UDC12-2)	B. fragilis	PRJNA206105	1			1
97	Bacteroides fragilis str B1 (UDC16-1)	no call	PRJNA206104	1			1
98	Bacteroides fragilis str DS-166	B. fragilis	PRJNA206109	1			1
99	Bacteroides fragilis str DS-208	B. fragilis	PRJNA206107	0
100	Bacteroides fragilis str DS-71	B. fragilis	PRJNA206108	1			1
101	Bacteroides fragilis str Ds-233	B. fragilis	PRJNA206106	0					1
102	Bacteroides fragilis str I1345	B. fragilis	PRJNA206101	1			1
103	Bacteroides fragilis str J-143-4	B. fragilis	PRJNA206102	2	1		1
104	Bacteroides fragilis str J38-1	B. fragilis	PRJNA206103	1			1
105	Bacteroides fragilis str Korea 419	B. fragilis	PRJNA206100	1			1
106	Bacteroides fragilis str S13 L11	B. fragilis	PRJNA206121	1			1
107	Bacteroides fragilis str S23L17	B. fragilis	PRJNA206172	1			1
108	Bacteroides fragilis str S23L24	B. fragilis	PRJNA206173	1			1
109	Bacteroides fragilis str S23 R14	no call	PRJNA206122	1			1
110	Bacteroides fragilis str S24L15	B. fragilis	PRJNA206166	0					1
111	Bacteroides fragilis str S24L26	B. fragilis	PRJNA206167	1			1
112	Bacteroides fragilis str S24L34	B. fragilis	PRJNA206168	1			1
113	Bacteroides fragilis str S36L11	B. fragilis	PRJNA206170	1	1				1
114	Bacteroides fragilis str S36L12	B. fragilis	PRJNA206171	2	1		1
115	Bacteroides fragilis str S36L5	B. fragilis	PRJNA206169	2	1		1
116	Bacteroides fragilis str S38L3	B. fragilis	PRJNA206174	1			1
117	Bacteroides fragilis str S38L5	B. fragilis	PRJNA206175	1			1
118	Bacteroides fragilis str S6L3	B. fragilis	PRJNA206160	1			1
119	Bacteroides fragilis str S6L5	Chlamydia sp.	PRJNA206161	1			1
120	Bacteroides fragilis str S6L8	B. fragilis	PRJNA206162	1			1
121	Bacteroides fragilis str S6R5	B. fragilis	PRJNA206163	1			1
122	Bacteroides fragilis str S6R6	B. fragilis	PRJNA206164	2	1		1
123	Bacteroides fragilis str S6R8	B. fragilis	PRJNA206165	1			1
124	Bacteroides sp. 2 1 16	B. fragilis	PRJNA38347	2	1		1
125	Bacteroides sp. 2 1 56FAA	B. fragilis	PRJNA40013	3	2		1
126	Bacteroides sp. 3 2 5	B. fragilis	PRJNA32441	2	1		1
127	Bacteroides intestinalis DSM 17393	B. intestinalis	PRJNA20523	0
128	Bacteroides massiliensis B84634	no call	PRJNA199226	0					1
129	Bacteroides massiliensis dnLKV3	no call	PRJNA175977	0
130	Bacteroides nordii CL02T12C05	B. nordii	PRJNA64823	0
131	Bacteroides nordii JCM 12987	B. nordii	PRJNA224116	0
132	Bacteroides sp. HPS0048	B. nordii	PRJNA72497	0
133	Bacteroides oleiciplenus YIT 12058	B. oleiciplenus	PRJNA46377	0
134	Bacteroides ovatus 3 8 47FAA	B. ovatus	PRJNA40011	0
135	Bacteroides ovatus ATCC 8483	B. ovatus	PRJNA18191	0
136	Bacteroides ovatus CL02T12C04	B. ovatus	PRJNA64825	1	1
137	Bacteroides ovatus CL03T12C18	B. ovatus	PRJNA64827	0
138	Bacteroides ovatus SD CMC 3f	B. ovatus	PRJNA42769	1	1
139	Bacteroides ovatus str 3725 D1 iv	B. ovatus	PRJNA206123	0
140	Bacteroides ovatus str 3725 D9 iii	B. ovatus	PRJNA206124	0
141	Bacteroides sp. 3 1 23	B. ovatus	PRJNA38771	0
142	Bacteroides sp. D2	B. ovatus	PRJNA32449	0
143	Bacteroides plebeius DSM 17135	B. plebeius	PRJNA27829	0
144	Bacteroides salyersiae CL02T12C01	B. salyersiae	PRJNA64829	1	1
145	Bacteroides salyersiae WAL 10018	B. salyersiae	PRJNA170350	0
146	Bacteroides stercoris ATCC 43183	B. stercoris	PRJNA19859	0
147	Bacteroides stercoris CC31F	B. stercoris	PRJNA71531	1				1
148	Bacteroides thetaiotaomicron VPI-5482	B. thetaiotaomicron	PRJNA399	0
149	Bacteroides thetaiotaomicron dnLKV9	B. thetaiotaomicron	PRJNA175974	0
150	Bacteroides sp. 1 1 14	B. thetaiotaomicron	PRJNA38765	0
151	Bacteroides sp. 1 1 6	B. thetaiotaomicron	PRJNA32435	0
152	Bacteroides uniformis ATCC 8492	B. uniformis	PRJNA18195	0
153	Bacteroides uniformis CL03T00C23	B. uniformis	PRJNA64833	1	1
154	Bacteroides uniformis CL03T12C37	B. uniformis	PRJNA64835	1	1
155	Bacteroides uniformis dnLKV2	B. uniformis	PRJNA175976	0
156	Bacteroides uniformis str 3978 T3 i	B. uniformis	PRJNA206128	0
157	Bacteroides uniformis str 3978 T3 ii	B. uniformis	PRJNA206129	0
158	Bacteroides sp. 4 1 36	B. uniformis	PRJNA39357	0
159	Bacteroides sp. D20	B. uniformis	PRJNA38355	0
160	Bacteroides vulgatus ATCC 8482	B. vulgatus	PRJNA13378	0
161	Bacteroides vulgatus CL09T03C04	B. vulgatus	PRJNA64837	0
162	Bacteroides vulgatus PC510	B. vulgatus	PRJNA42763	0
163	Bacteroides vulgatus dnLKV7	B. vulgatus	PRJNA175975	1		1
164	Bacteroides vulgatus str 3775 SL(B) 10 (iv)	B. vulgatus	PRJNA206132	1	1
165	Bacteroides vulgatus str 3775 SR(B) 19	B. vulgatus	PRJNA206133	1	1
166	Bacteroides vulgatus str 3975 RP4	B. vulgatus	PRJNA206134	0
167	Bacteroides sp. 3 1 40A	B. vulgatus	PRJNA38773	0
168	Bacteroides sp. 4 3 47FAA	B. vulgatus	PRJNA32443	1	1
169	Bacteroides xylanisolvens CL03T12C04	B. xylanisolvens	PRJNA64839	0
170	Bacteroides xylanisolvens SD CC 1b	B. xylanisolvens	PRJNA42773	1	1
171	Bacteroides xylanisolvens SD CC 2a	B. xylanisolvens	PRJNA42771	1	1
172	Bacteroides sp. 1 1 30	B. xylanisolvens	PRJNA41955	1	1
173	Bacteroides sp. 2 1 22	B. xylanisolvens	PRJNA38349	0
174	Bacteroides sp. 2 2 4	B. xylanisolvens	PRJNA32439	1	1
175	Bacteroides sp. D1	B. xylanisolvens	PRJNA32447	0
176	Bacteroides sp. D22	B. xylanisolvens	PRJNA41953	1	1
177	Bacteroides xylanisolvens XB1A	no call	PRJNA39177	0
178	Parabacteroides distasonis ATCC 8503	P. distasonis	PRJNA13485	0
179	Parabacteroides distasonis CL03T12C09	P. distasonis	PRJNA64883	1		1
180	Parabacteroides distasonis CL09T03C24	P. distasonis	PRJNA64885	0
181	Parabacteroides distasonis str 3776 D15 i	P. distasonis	PRJNA206126	0
182	Parabacteroides distasonis str 3776 D15 iv	P. distasonis	PRJNA206127	0
183	Parabacteroides distasonis str 3776 Po2 i	P. distasonis	PRJNA206125	0
184	Parabacteroides distasonis str 3999B T(B) 4	P. distasonis	PRJNA206130	0					1
185	Parabacteroides distasonis str 3999B T(B) 6	P. distasonis	PRJNA206131	0					2
186	Bacteroides sp. 2 1 33B	P. distasonis	PRJNA38351	0
187	Parabacteroides sp. 20 3	P. distasonis	PRJNA38767	2		2
188	Parabacteroides sp. 2 1 7	P. distasonis	PRJNA55579	1	1
189	Parabacteroides sp. D13	P. distasonis	PRJNA38359	0
190	Parabacteroides sp. D25	P. distasonis	PRJNA39405	1	1
191	Bacteroides sp. 3 1 19	P. distasonis	PRJNA41951	0
192	Parabacteroides sp. ASF519	P. goldsteinii	PRJNA176004	0
193	Parabacteroides goldsteinii CL02T12C30	P. goldsteinii	PRJNA64887	0
194	Parabacteroides goldsteinii dnLKV18	P. goldsteinii	PRJNA175978	0
195	Parabacteroides gordonii DSM 23371	P. gordonii	PRJNA224116	1	1
196	Parabacteroides johnsonii CL02T12C29	P. johnsonii	PRJNA64889	1	1
197	Parabacteroides johnsonii DSM 18315	P. johnsonii	PRJNA30007	0
198	Parabacteroides merdae ATCC 43184	P. merdae	PRJNA18193	0
199	Parabacteroides merdae CL03T12C32	P. merdae	PRJNA64891	0
200	Parabacteroides merdae CL09T00C40	P. merdae	PRJNA64893	0
201	Prevotella copri DSM 18205	Pr. copri	PRJNA30025	0
202	Prevotella stercorea DSM 18206	Pr. stercorea	PRJNA65131	0					1
203	Bacteroides sp. VE202-11	C. hathewayi	PRJNA224116	0
204	Bacteroides sp. Ga6A1	no call	PRJNA224116	0
205	Bacteroides sp. Ga6A2	no call	PRJNA224116	0
				115	48	9	56	2	15

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