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Human Microbiome

Gut Microbe
Scanning electron microscope images of B. thetaiotaomicron, a prominent human gut bacterium, and the intestine.

A human being can be viewed as a biological eco-system that includes distinctly human cells and tissues as well as thousands of microbial species that co-exist in various parts of the body.

In fact, "within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one. These communities, however, remain largely unstudied, leaving almost entirely unknown their influence upon human development, physiology, immunity, and nutrition. To take advantage of recent technological advances and to develop new ones, the NIH Roadmap has initiated the Human Microbiome Project (HMP) with the mission of generating resources enabling comprehensive characterization of the human microbiota and analysis of its role in human health and disease." [http://nihroadmap.nih.gov/hmp/]

The BCM-HGSC, with Genome Sequencing Center at Washington University, the Broad Institute of MIT and Harvard, and the J. Craig Venter Institute addressed some early goals of this project. The HMP metagenomic sample sequencing compared microbial communities between individuals, body sites, and states (e.g., disease, diet, age).1 Pilot projects determined the appropriate sequencing platforms, quality controls, and annotation pipelines for generating reference genomes3 and sequencing metagenomic samples.2

Resources

HMPP_Proposal.pdf

Entry # Reference strains Center
1 Acidaminococcus sp. 2_2_8 Broad
2 Acidovorax AM084006 JCVI
3 Acinetobacter haemolyticus JCVI
4 Acinetobacter schindleri BCM-HGSC
5 Acinetobacter sp. ATCC#27244 BCM-HGSC
6 Actinobacterium M28 BCM-HGSC
7 Actinomyces coleocanis BCM-HGSC
8 Actinomyces naeslundii JCVI
9 Actinomyces urogenitalis BCM-HGSC
10 Aerococcus christensenii BCM-HGSC
11 Aeromicrobium marinum BCM-HGSC
12 Alistipes putredinis DSM 17216 WUGSC
13 Alistipes sp. 1_2_47A Broad
14 Alistipes sp. 10_1_37_FAA Broad
15 Allochromatium vinosum BCM-HGSC
16 Anaerococcus hydrogenalis DSM 7454 WUGSC
17 Anaerococcus lactolyticus BCM-HGSC
18 Anaerococcus lactolyticus (additional) BCM-HGSC
19 Anaerococcus lactolyticus ATCC#51172 BCM-HGSC
20 Anaerococcus tetradius JCVI
21 Anaerococcus tetradius BCM-HGSC
22 Anaerofustis stercorihominis DSM 17244 WUGSC
23 Anaerostipes caccae DSM14662 WUGSC
24 Anaerotruncus colihominis DSM 17241 WUGSC
25 Aneurinibacillus aneurinolyticus DSM 5562 WUGSC
26 Arcobacter cryaerophilus ATCC 49615 JCVI
27 Atopobium vaginae JCVI
28 Atopobium vaginae ATCC#BAA-55 BCM-HGSC
29 Bacteroides pectinophilus ATCC 43243 WUGSC
30 Bacteroides coprocola DSM 17136 WUGSC
31 Bacteroides dorei DSM 17855 WUGSC
32 Bacteroides eggerthii DSM 20697 WUGSC
33 Bacteroides finegoldii DSM 17565 WUGSC
34 Bacteroides galacturonicus ATCC 43244 WUGSC
35 Bacteroides intestinalis DSM 17393 WUGSC
36 Bacteroides plebeius DSM 17135 WUGSC
37 Bacteroides heparinolytica JCVI
38 Bacteroides merdae ATCC 43184 WUGSC
39 Bacteroides sp. 1_1_11 Broad
40 Bacteroides sp. 1_1_14 Broad
41 Bacteroides sp. 1_1_30 Broad
42 Bacteroides sp. 1_1_6 Broad
43 Bacteroides sp. 2_1_16 Broad
44 Bacteroides sp. 2_1_22 Broad
45 Bacteroides sp. 2_1_33B Broad
46 Bacteroides sp. 2_1_7 Broad
47 Bacteroides sp. 2_2_4 Broad
48 Bacteroides sp. 20_3 Broad
49 Bacteroides sp. 3_1_12 Broad
50 Bacteroides sp. 3_1_13 Broad
51 Bacteroides sp. 3_1_19 Broad
52 Bacteroides sp. 3_1_23 Broad
53 Bacteroides sp. 3_1_33FAA Broad
54 Bacteroides sp. 3_1_40A Broad
55 Bacteroides sp. 3_2_5 Broad
56 Bacteroides sp. 4_1_36 Broad
57 Bacteroides sp. 4_3_47FAA Broad
58 Bacteroides sp. 9_1_42FAA Broad
59 Bacteroides stercoris ATCC 43183 WUGSC
60 Bacteroides uniformis DSM 6597 WUGSC
61 Bdellovibrio AF148938 JCVI
62 Bifidobacterium dentium ATCC 27678 WUGSC
63 Bifidobacterium angulatum DSM 20098 WUGSC
64 Bifidobacterium bifidum DSM 20456 WUGSC
65 Bifidobacterium breve DSM 20213 WUGSC
66 Bifidobacterium catenulatum DSM 16992 WUGSC
67 Bifidobacterium gallicum DSM 20093 WUGSC
68 Bifidobacterium bifidum NCIMB 41171 Broad
69 Bifidobacterium dentium JCVI
70 Bifidobacterium longum infantis strain 52484 Broad
71 Bifidobacterium pseudocatenulatum DSM 20438 WUGSC
72 Bifidobacterium sp. 12_1_47BFAA Broad
73 Brachybacterium sp.C3H-211 JCVI
74 Brevibacterium mcbrellneri ATCC#49030 BCM-HGSC
75 Brevibacterium paucivorans JCVI
76 Brevundimonas aurantiaca JCVI
77 Bryantella formatexigens DSM 14469 WUGSC
78 Butyrivibrio crossotus DSM 2876 WUGSC
79 Campylobacter Bacterioides ureolyticus ATCC 33387 (type) JCVI
80 Capnocytophaga gingivalis JCVI
81 Carnobacterium AJ427446 JCVI
82 Catenibacterium mitsuokai DSM 15897 WUGSC
83 Cedecea davisae DSM 4568 WUGSC
84 Cetobacterium somerae ATCC N/A WUGSC
85 Chitinophaga AJ318177 JCVI
86 Chryseobacterium gleum ATCC#35910 BCM-HGSC
87 Citrobacter youngae ATCC29220 WUGSC
88 Citrobacter sp. 30_2 Broad
89 Clostridium celatum DSM 1785 WUGSC
90 Clostridium sporogenes ATCC 15579 WUGSC
91 Clostridium asparagiforme DSM 15981 WUGSC
92 Clostridium bartlettii DSM 16795 WUGSC
93 Clostridium celatum DSM 1785 WUGSC
94 Clostridium hathewayi DSM 13479 WUGSC
95 Clostridium hiranonis DSM 13275 WUGSC
96 Clostridium hylemonae DSM 15053 WUGSC
97 Clostridium leptum DSM 753 WUGSC
98 Clostridium methylpentosum DSM 5476 WUGSC
99 Clostridium nexile DSM 1787 WUGSC
100 Clostridium nexile-related A2-232 WUGSC
101 Clostridium orbiscindens DSM 6740 WUGSC
102 Clostridium scatologenes DSM 757 WUGSC
103 Clostridium scindens ATCC 35704 WUGSC
104 Clostridium sp. 1_1_41A1FAA Broad
105 Clostridium boltaea ATCC BAA-613 WUGSC
106 Clostridium eutactus-related L2-50 WUGSC
107 Clostridium indolis-related SS2/1 WUGSC
108 Clostridium inocuum 6_1_30 Broad
109 Clostridium ramosum DSM 1402 WUGSC
110 Clostridium saccharolyticum-related M62/1 WUGSC
111 Clostridium sp A2-166 WUGSC
112 Clostridium sp DSM 4029 WUGSC
113 Clostridium sp SR1/1 WUGSC
114 Clostridium sp. ATCC BAA-442 WUGSC
115 Clostridium sp. 7_2_43FAA Broad
116 Clostridium spiroforme DSM 1552 WUGSC
117 Clostridium symbiosum ATCC 14940 WUGSC
118 Collinsella intestinalis DSM 13280 WUGSC
119 Collinsella stercoris DSM 13279 WUGSC
120 Coprobacillus sp. 29_1 Broad
121 Coprobacillus sp. 8_1_38FAA Broad
122 Coprobacillus sp. 8_2_54BFAA Broad
123 Coprococcus comes ATCC 27758 WUGSC
124 Coprococcus eutactus ATCC 27759 WUGSC
125 Corynebacterium ammoniagenes DSM 20306 WUGSC
126 Corynebacterium accolens JCVI
127 Corynebacterium accolens ATCC#49725 BCM-HGSC
128 Corynebacterium aurimucosum BCM-HGSC
129 Corynebacterium efficiens BCM-HGSC
130 Corynebacterium genitalium ATCC#33030 BCM-HGSC
131 Corynebacterium glutamicum BCM-HGSC
132 Corynebacterium jelkelum BCM-HGSC
133 Corynebacterium lipophiloflavum BCM-HGSC
134 Corynebacterium nigricans ATCC#700975 BCM-HGSC
135 Corynebacterium pseudogenitalium ATCC#33035 BCM-HGSC
136 Corynebacterium seminale ATCC#51866 BCM-HGSC
137 Corynebacterium seminale ATCC#51867 BCM-HGSC
138 Corynebacterium striatum BCM-HGSC
139 Corynebacterium sundsvallense BCM-HGSC
140 Cryptobacterium curtum1 JCVI
141 Deinococcus AE002076 JCVI
142 Delftia acidovorans1 JCVI
143 Desulfomicrobium orale JCVI
144 Desulfovibrio fairfieldensis4 JCVI
145 Desulfovibrio piger DSM 749 WUGSC
146 Desulfovibrio sp. 3_1_syn3 Broad
147 Dialister invisus JCVI
148 Diaphorobacter nitroreducens JCVI
149 Dietzia sp. E9_21 JCVI
150 Dorea formicigenerans ATCC 27755 WUGSC
151 Dorea sp. 1_1_29AFAA Broad
152 Dorea sp. 4_1_36FAA Broad
153 Edwardsiella tarda ATCC 23685 WUGSC
154 Enterobacter cancerogenus ATCC 35316 WUGSC
155 Enterobacter asburiae JCVI
156 Enterococcus faecalis JCVI
157 Enterococcus faecalis ATCC#29200 BCM-HGSC
158 Enterococcus faecalis HH22 BCM-HGSC
159 Enterococcus faecalis OG1RF BCM-HGSC
160 Enterococcus faecalis TX0104 BCM-HGSC
161 Enterococcus faecalis TX1322 BCM-HGSC
162 Enterococcus faecium DO BCM-HGSC
163 Enterococcus faecium TX1330 BCM-HGSC
164 Erysipelothrix rhusiopathiae BCM-HGSC
165 Escherichia sp. 1_1_43 Broad
166 Escherichia sp. 3_2_53FAA Broad
167 Escherichia sp. 4_1_40B Broad
168 Eschericia coli MG1655 BCM-HGSC
169 Eschericia coli Trautner BCM-HGSC
170 Eubacterium biforme DSM 3989 WUGSC
171 Eubacterium cylindroides DSM 3983 WUGSC
172 Eubacterium dolichum DSM 3991 WUGSC
173 Eubacterium hadrum DSM 3319 WUGSC
174 Eubacterium halii-related DSM 17630 WUGSC
175 Eubacterium ramulus DSM 3995 WUGSC
176 Eubacterium brachy4 JCVI
177 Eubacterium hallii DSM 3353 WUGSC
178 Eubacterium plautii ATCC 29863 WUGSC
179 Eubacterium siraeum DSM 15702 WUGSC
180 Eubacterium sp. 3_1_31 Broad
181 Eubacterium sp. L2-7 WUGSC
182 Faecalibacterium prausnitzii M21/2 WUGSC
183 Faecalibacterium prausnitzii A2-165 WUGSC
184 Falcivibrio vaginalis ATCC#43063 BCM-HGSC
185 Finegoldia magna ATCC#53516 BCM-HGSC
186 Fusobacterium prausnitzii DSM 17677 WUGSC
187 Fusobacterium prausnitzii L2-6 WUGSC
188 Fusobacterium gonidiaformans ATCC 25563 Broad
189 Fusobacterium mortiferum ATCC 9817 Broad
190 Fusobacterium nucleatum ATCC#10953 BCM-HGSC
191 Fusobacterium nucleatum ATCC#23726 BCM-HGSC
192 Fusobacterium sp 1_1_41FAA Broad
193 Fusobacterium sp 11_3_2 Broad
194 Fusobacterium sp. 12_1B Broad
195 Fusobacterium sp. 2_1_31 Broad
196 Fusobacterium sp. 2_1_37FAA Broad
197 Fusobacterium sp. 21_1A Broad
198 Fusobacterium sp. 3_1_27 Broad
199 Fusobacterium sp. 3_1_33 Broad
200 Fusobacterium sp. 3_1_36A2 Broad
201 Fusobacterium sp. 3_1_5R Broad
202 Fusobacterium sp. 4_1_13 Broad
203 Fusobacterium sp. 4_8 Broad
204 Fusobacterium sp. 7_1 Broad
205 Fusobacterium ulcerans ATCC 49185, NCTC 12111 Broad
206 Fusobacterium varium ATCC 27725 Broad
207 Gardnerella vaginalis ATCC#14019 BCM-HGSC
208 Gordonia sputi JCVI
209 Grimontia hollisae DSM 15132 WUGSC
210 Haemophilus AF224309 JCVI
211 Haemophilus ducreyi ATCC#700724 BCM-HGSC
212 Helicobacter canadensis BCM-HGSC
213 Helicobacter canadensis MIT 98-5491 (LCDC 16143, ATCC 700968) Broad
214 Helicobacter cinaedi ATCC BAA-847 JCVI
215 Helicobacter cinaedi CCUG 18818 (NCTC 12423) Broad
216 Helicobacter pullorum BCM-HGSC
217 Helicobacter pullorum MIT 98-5489 (LCDC 15115) Broad
218 Helicobacter pylori 35A BCM-HGSC
219 Helicobacter pylori 74B BCM-HGSC
220 Helicobacter rappini taxon 8 (ATCC 49309) Broad
221 Helicobacter winghamensis (ATCC BAA-430) Broad
222 Holdemania filiformis DSM 12042 WUGSC
223 Hyphomicrobium facile JCVI
224 Janibacter melonis JCVI
225 Janthinobacterium lividum JCVI
226 Klebsiella sp. 1_1_55 Broad
227 Kocuria marina JCVI
228 Lactobacillus brevis DSM 20054 WUGSC
229 Lactobacillus acidophilus BCM-HGSC
230 Lactobacillus amylolyticus BCM-HGSC
231 Lactobacillus antri BCM-HGSC
232 Lactobacillus coleohominis BCM-HGSC
233 Lactobacillus crispatus JCVI
234 Lactobacillus crispatus JVV01 BCM-HGSC
235 Lactobacillus delbrueckii BCM-HGSC
236 Lactobacillus gasseri JVV03 BCM-HGSC
237 Lactobacillus helveticus BCM-HGSC
238 Lactobacillus iners BCM-HGSC
239 Lactobacillus jensenii JVV16 BCM-HGSC
240 Lactobacillus johnsonii BCM-HGSC
241 Lactobacillus lactis subsp. cremoris BCM-HGSC
242 Lactobacillus paracasei 362.501388888889 Broad
243 Lactobacillus reuteri CF48-3A BCM-HGSC
244 Lactobacillus rhamnosus BCM-HGSC
245 Lactobacillus sakei BCM-HGSC
246 Lactobacillus suntoryeus BCM-HGSC
247 Lactobacillus ultunensis BCM-HGSC
248 Leptothrix sp. strain DhA-711 JCVI
249 Leptotrichia amnionii JCVI
250 Leuconostoc argentinum JCVI
251 Leuconostoc mesenteroides BCM-HGSC
252 Listeria grayi BCM-HGSC
253 Megasphaera micronucliformis1 JCVI
254 Mesorhizobium AP0030011 JCVI
255 Methanobrevibacter smithii DSM 11975 WUGSC
256 Methanobrevibacter oralis1 JCVI
257 Methanobrevibacter smithii DSM 2374 WUGSC
258 Methanobrevibacter smithii DSM 2375 WUGSC
259 Methylobacillus AF289159 JCVI
260 Methylobacterium AY741717 JCVI
261 Micrococcus luteus4 JCVI
262 Micromonas micros1 JCVI
263 Mitsuokella multacida DSM 20544 WUGSC
264 Mobiluncus curtisii BCM-HGSC
265 Mobiluncus mulieris BCM-HGSC
266 Mogibacterium timidum1 JCVI
267 Moraxella osloensis4 JCVI
268 Mycobacterium chlorophenolicum JCVI
269 Mycobacterium parascrofulaceum ATCC#BAA-614 BCM-HGSC
270 Mycoplasma fermentans ATCC#15474 BCM-HGSC
271 Mycoplasma hominis ATCC#14268 BCM-HGSC
272 Mycoplasma hominis ATCC#43519 BCM-HGSC
273 Mycoplasma salivarum4 JCVI
274 Mycoplasma spermatophilum ATCC#49695 BCM-HGSC
275 Neisseria DQ409137 JCVI
276 Neisseria gonorrhoeae ATCC#43070 BCM-HGSC
277 Paenibacillus sp. JCVI
278 Papillibacter sp. 4_1_38B Broad
279 Pediococcus sp. 7_4A Broad
280 Pedomicrobium australicum JCVI
281 Peptostreptococcus anaerobius JCVI
282 Peptostreptococcus micros ATCC 33270 WUGSC
283 Phascolarctobacterium sp. 3_1_syn4 Broad
284 Porphyromonas L16493 JCVI
285 Prevotella AY207061 JCVI
286 Prevotella bergensis BCM-HGSC
287 Propionibacterium acnes JCVI
288 Propionibacterium sp. 5_U_42AFAA Broad
289 Proteus penneri ATCC 35198 WUGSC
290 Proteus mirabilis BCM-HGSC
291 Providencia rustigianii DSM 4541 WUGSC
292 Providencia stuartii ATCC 25827 WUGSC
293 Pseudomonas aeruginosa JCVI
294 Rhodococcus corynebacterioides JCVI
295 Rhodococcus equi BCM-HGSC
296 Roseburia faecis DSM 16840 WUGSC
297 Roseburia intestinalis DSM 14610 WUGSC
298 Roseburia inulinivorans DSM 16841 WUGSC
299 Roseburia inulinivorans L1-83 WUGSC
300 Roseomonas cervicalis ATCC#49957 BCM-HGSC
301 Ruminococcus callidus ATCC 27760 WUGSC
302 Ruminococcus gnavus-related GM2/1 WUGSC
303 Ruminococcus hansenii DSM 20583 WUGSC
304 Ruminococcus luti DSM 14534 WUGSC
305 Ruminococcus hydrogenotrophicus DSM 10507 WUGSC
306 Ruminococcus lactaris ATCC 29176 WUGSC
307 Ruminococcus sp. JCVI
308 Ruminococcus sp. 4_1_47 FAA Broad
309 Ruminococcus sp. 5_1_39AFAA Broad
310 Ruminococcus sp. 5_1_39B FAA Broad
311 Ruminococcus sp. 8_1_37 FAA Broad
312 Selenomonas dianae2 JCVI
313 Serratia liquefaciens JCVI
314 Slackia exigua JCVI
315 Sphingobacterium spiritivorum ATCC#33300 BCM-HGSC
316 Sphingobacterium spiritivorum ATCC#33861 BCM-HGSC
317 Sphingobium amiens JCVI
318 Sphingopyxis AY328823 JCVI
319 Staphylococcus aureus MN8 BCM-HGSC
320 Staphylococcus aureus MRSA BCM-HGSC
321 Staphylococcus aureus USA300 BCM-HGSC
322 Staphylococcus capitis JCVI
323 Staphylococcus epidermidis BCM-HGSC
324 Stenotrophomonas maltophilia JCVI
325 Streptococcus infantarius ATCC BAA-102 WUGSC
326 Streptococcus agalactiae JCVI
327 Streptococcus equinus BCM-HGSC
328 Streptococcus pneumoniae BCM-HGSC
329 Streptococcus sp. 2_1_36FAA Broad
330 Subdoligranulum variabile DSM 15176 WUGSC
331 Synergistes phyla sp. E1 E3_33 JCVI
332 Synergistes sp. 3_1_syn1 Broad
333 Thermomicrobium AY250886 JCVI
334 Treponema amylovorum JCVI
335 Tsukamurella tyrosinosolvens JCVI
336 unclassified bacterium 1_1_47 Broad
337 unclassified bacterium 1_7_47FAA Broad
338 unclassified bacterium 4_1_31 Broad
339 unclassified bacterium 4_1_37 FAA Broad
340 unclassified bacterium 5_2_54FAA Broad
341 unclassified bacterium 6_1_37FAA Broad
342 unclassified bacterium 4_1_31 Broad
343 unclassified_Desulfovibrionaceae bacterium 3_1_6 Broad
344 unclassified_Desulfovibrionaceae bacterium 4_1_30 Broad
345 unclassified_Enterobacteriaceae bacterium 9_2_54FAA Broad
346 unclassified_Erysipelotrichaceae bacterium 2_2_44A Broad
347 unclassified_Erysipelotrichaceae bacterium 6_1_45 Broad
348 Ureaplasma urealyticum parvum JCVI
349 Variovorax paradoxus2 JCVI
350 Veillonella AF186071 JCVI
351 Veillonella sp. 3_1_44 Broad
352 Veillonella sp. 6_1_27 Broad
353 Weissella paramesenteroides BCM-HGSC

 



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