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. 2016 Aug 11;9:171. doi: 10.1186/s13068-016-0581-3

Table 3.

Summary of pure isolates obtained from the thermophilic biogas plant applying different isolation strategies (1)–(11) assigned to characterized reference species by means of their 16S rRNA gene sequence similarity using the EzTaxon identification tool; metagenomic and metatranscriptomic sequences were mapped on a reference strain 16S rRNA gene sequence applying the gsMapper program

Closest related NCBI GenBank entry Isolates from the thermophilic biogas plant Number of metagenome sequences mapped on the 16S rRNAb Number of metatranscriptome sequences mapped on the 16S rRNAc
Class Family Species Accession number 16S rRNA identity (%) Number of isolates and/or colony forming units (CFU) Isolate designation NCBI Genbank entry Cellulose degrader Main substrate Fermentation products Isolation strategya
Cellulolytic Bacteria
 Clostridia Lachnospiraceae Herbinix hemicellulosilytica LN626355 100.0  1 isolate T3/55T LN626355 Yes Cellobiose Et, Ac, Pr 4 17 1552
96.4  8 isolates SD1D LN626359 Yes Cellobiose Et, Ac, Pr 4, 5 17 858
Ruminococcaceae Clostridium cellulosi L09177 98.9  14 isolates DG5 LN881577 Yes Cellobiose Et, Ac 3, 4 0 1831
Clostridium clariflavum CP003065 100.0  34 isolates K50/5 LN881585 Yes Cellulose NAd 3, 4 862 9152
Clostridium stercorarium CP004044 99.3  13 isolates Neu14 LN881576 Yes Cellobiose NA 3 28 12,099
Clostridium thermocellum CP000568 99.9  27 isolates HAW2/1 HG917924 Yes Cellulose Et, Ac, Ip 3, 4, 5 1279 7814
Acidogenic/acetogenic Bacteria
 Bacilli Bacillaceae Bacillus cereus NA 2 × 107 CFU g−1 (No) NA NA 1 NA NA
Bacillus licheniformis AE017333 99.9  5 × 107 CFU g−1, 9 isolates L2C KT351634 (No) NA NA 1, 8a, 8b, 9 2 2696
Bacillus oleronius NA 1 × 107 CFU g−1 (No) NA NA 2 NA NA
Bacillus thermoamylovorans L27478 99.5  1 × 107 CFU g−1, 7 isolates Neu19 LN881587 No Starch Et, Ac, Fo 2, 3, 4, 8c, 8d 1 5070
Bacillus coagulans AB271752 99.6  2 isolates M1A KT351636 NA NA NA 8a 3 2566
Bacillus infernus U20385 99.9  3 isolates E2C KT351638 NA NA NA 8d 3 3989
Geobacillus thermodenitrificans CP000557 100.0  2 isolates J2B KT351633 NA NA NA 8a, 8b 0 4181
Enterococcaceae Enterococcus faecium NA <102 CFU g−1 (No) NA NA 2 NA NA
Paenibacillaceae Aneurinibacillus spp. NA <103 CFU g−1 (No) NA NA 2 NA NA
Paenibacillus barengoltzii AY167814 99.1  6 isolates YP4-6A KT351639 NA NA NA 8a 0 1788
Planococcaceae Ureibacillus thermosphaericus AB101594 100.0  3 × 107 CFU g−1, 3 isolates A6A KT351635 NA NA NA 1, 9 2 4376
 Clostridia Clostridiaceae Clostridium isatidis X98395 99.9  13 isolates MV1 LN881568 No Glucose NA 3, 4 738 2404
99.3  2 isolates RX1 LN881572 No Glucose NA 3 65 2027
Clostridium perfringens NA <105 CFU g−1 (No) NA NA 1 NA NA
Clostridium putrefaciens Y18177 94.2  7 isolates Neu23 LN881581 No Cellobiose NA 4, 8a 286 4415
94.2  17 isolates N1F KT351631 NA NA NA 8a, 8b 281 4347
Clostridium sporogenes NA <105 CFU g−1 (No) NA NA 1 NA NA
Clostridium thermopalmarium X72869 99.5  1 isolate Neu4 LN881579 No Glucose NA 4 11 1180
Lutispora thermophila AB186360 100.0  1 isolate XV1 LN881567 No Glucose NA 3 3 2000
Tepidimicrobium ferriphilum AY656718 97.4  1 isolate GRX2 LN881569 No Glucose NA 3 9 6191
97.4  1 isolate GRM1 LN881570 No Glucose NA 3 10 6204
97.5  1 isolate Z2-16 KT351637 NA NA NA 8a 9 6123
98.7  1 isolate GRC5 LN881575 No Glucose NA 3 20 5958
96.2  1 isolate D1 KT274718 NA Glucosee Ac 6 5 6609
94.4  1 isolate GRC3 LN890940 No Glucose NA 3 12 7329
Tepidimicrobium xylanilyticum EF522948 99.7  1 isolate GRC4 LN881574 No Glucose NA 3 27 4322
96.7  2 isolates GRC1 LN881571 No Glucose NA 3 13 8131
96.3  1 isolate XV2 LN881586 No Glucose NA 3 22 5549
Defluviitaleaceae Defluviitalea saccharophila HQ020487 96.5  1 isolate GRX3 LN881573 No Glucose NA 3 12 2923
Peptococcaceae Desulfotomaculum australicum M96665 99.5  1 isolate L14 KT274713 No Lactic acid Ac 6 1 3784
Ruminococcaceae Clostridium straminisolvens BAVR01000144 98.3  3 isolates Neu18 LN881580 No Cellobiose NA 4 37 9436
Clostridium caenicola AB221372 97.6  3 isolates Neu21 LN881582 No Glucose NA 3, 4 9 8238
Clostridium thermosuccinogenes Y18180 99.8  14 isolates Iso4/1b LN881583 No Glucose NA 3, 4 7 6742
Thermoanaerobacteraceae Tepidanaerobacter syntrophicus AB106353 96.6  1 isolate AS34 KT274714 NA Amino acidsf Ac, Pr 6 23 8696
96.2  1 isolate AS46 KT274715 NA Amino acidsf Ac, Pr 6 43 12,295
Incertae sedis Sporanaerobacter acetigenes AF358114 98.7  1 isolate XP2-13-3 KT351640 NA NA NA 8b 0 1715
Thermoanaerobacterium thermosaccharolyticum CP002171 99.2  24 isolates Iso6/1b LN881584 No Glucose NA 3 0 1838
99.9  1 isolate Gluc2 KT274716 NA Glucose Ac, Bu, La 7 0 3000
99.9  1 isolate Gluc4 KT274717 No Glucose Ac, Bu, La 7 0 2881
Tissierella creatinini FR749955 96.2  1 isolate DG3 LN881578 No Glucose NA 3 1 2229
Unclassified Proteiniborus ethanoligenes EF116488 95.9  2 isolates BA2-13 KT351641 NA NA NA 8e 0 1809
 Thermotogae Petrotogaceae Defluviitoga tunisiensis FR850164 99.9  7 isolates L3 KT274706 No Lactic acid Ac 6 968 115,754
99.3  1 isolate AS30 KT274709 NA Amino acidsf Ac 6 201 39,551
Methanogenic Archaea
 Methanobacteria Methanobacteriaceae Methanothermobacter marburgensis CP001710 99.7  1 isolate Viersen-HAW KU667127 (No) H2/CO2 NA 10 13 32
Methanothermobacter wolfeii AB104858 100.0  1 isolate SIV6 KT368944 (No) H2/CO2 NA 11 39 60
 Methanomicrobia Methano-microbiaceae Methanoculleus thermophilus AB065297 100.0  3 isolates V2.1 KT368945 (No) H2/CO2 NA 11 389 35,733

Et ethanol; Ac acetic acid; Pr propionic acid; Ip isopropanol; Fo formic acid; Bu butyric acid; La lactic acid

aFor details, refer “Methods” section

bIn total, 18,817 16S rRNA gene sequences

cIn total, 532,381 16S rRNA sequences

dNot analyzed

eFormation of acetic acid in medium DSMZ 1328 [104] with 0.5 % (w/v) glucose

fMinimal medium (modified DSMZ 287 [36]) containing alanine, threonine, serine, glutamic acid, cysteine and methionine