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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