A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes

Maruthamuthu, Mukil; Jiménez, Diego Javier; Stevens, Patricia; van Elsas, Jan Dirk

doi:10.1186/s12864-016-2404-0

Table 4 Comparison of functional metagenomic approaches to screen for (hemi)cellulases

From: A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes

Microbial source (enrichment bred from)	Vector / Host	Screened clones	Substrates for (hemi)cellulases screening	Hit rate ^f	Reference
Cow rumen	pCCl-BAC ^a/ E. coli EPI300	15360	Xylan	1/853	Zhao et al. (2010) [38]
Termite gut	pCC1FOS ^b /E. coli EPI100	40000	5-Bromo-3-indolyl-beta-D-xylopyranoside	1/740	Bastien et al. (2013) [32]
		40000	5-bromo-4-chloro-3-indolyl-alpha-L-arabinofuranoside	1/1.212
		40000	Oat AZCl-xylan	1/4.444
Cow rumen	pCCFOS ^b / E. coli EPI300-T1	17000	pNP-beta-D-glucopyranoside + pNP-beta-D-cellobioside	1/5.666	Del Pozo et al. (2012) [16]
Buffalo rumen	pCCFOS1 ^b / EPI300-T1	10000	AZCL-HE-cellulose	1:108	Nguyen et al. (2012) [39]
Buffalo rumen	pCCFOS1 ^b / EPI300-T1	10000	AZCL-xylan	1:2.500	Nguyen et al. (2012) [39]
Avicel- enrichment culture (soil)	pUC19 ^c / E. coli DH5α	57000	Rimazol brilliant blue dyed-CMC	1/7.125	Mori et al. (2014) [29]
Pulp- enrichment culture (soil)	pUC19 ^c / E. coli DH5α	63000	Rimazol brilliant blue dyed-xylan	1/63.000	Mori et al. (2014) [29]
Ikaite tufa columns	pGNS-BAC ^a / E.coli DH10B	2843	5-bromo-4-chloro-3-indolyl-beta-d-galactopyranoside	1/1.421	Vester et al. (2014) [49]
Grassland soil	pCC1FOS ^b / E. coli EPI300	4600	Dye-labeled hydroxyethyl xylan	1/4.600	Nacke et al. (2012) [28]
Grassland soil	pCC1FOS ^b / E. coli EPI300	4600	Dye-labeled hydroxyethyl cellulose	1/2.300	Nacke et al. (2012) [28]
Human gut	pCC1FOS ^b / E. coli EPI300	156000	AZCL-xylan	1/4.588	Tasse et al. (2010) [50]
		156000	AZCL-beta-glucan	1/1.772
		136000	AZCL-galactan	1/1.271
Filter paper -enrichment culture (Earthworm)	pCCFOS ^b / E. coli EPI300	115000	pNP-beta-D-glucopyranoside	1/2.090	Beloqui et al. (2010) [30]
Compost from pig manure	pCC2FOS ^b / E. coli EPI300	12380	Xylan	1/2.476	Jeong et al. (2012) [51]
Forest soil	Lambda ZAP Express ^c / E. coli XL1 blue	10000	CMC	1/10.000	Wang et al. (2009) [52]
Elephant dung	Lambda ZAP Express ^c / E. coli XL1 blue	10000	CMC	1/5.000	Wang et al. (2009) [52]
Cow rumen	pCCFOS ^b / E. coli EPI300	12288	pNP-alpha-galactopyranoside	1/12.288	Ferrer et al. (2012) [27]
		12288	pNP-alpha-L-arabinofuranoside	1/4.096
		12288	CMC	1/6.144
Alkaline-polluted soil	pGEM-3Zf ^c / E. coli DH5a	30000	Esculine	1/15.000	Jiang et al. (2011) [53]
Soil	pHBM803 ^c / E. coli XL10-Gold	24000	Remazol brilliant blue dyed-xylan	1/24.000	Hu et al. (2008) [54]
¹³C-cellulose-enriched DNA (soil) ^e	pJC8 ^d / E. coli HB101	2876	CMC	1/360	Verastegui et al. (2014) [40]
Wheat straw- enrichment culture (soil)	pCC2FOS ^b / E. coli EPI300	22000	Mixture of 6 indolyl-monosaccharides	1/440	This study
Torrefied wheat straw- enrichment culture (soil)	pCC2FOS ^b / E. coli EPI300	22000	Mixture of 6 indolyl-monosaccharides	1/1,047	This study

^aBacterial artificial chromosome
^bFosmid
^cPlasmid
^dCosmid
^eHigh-molecular weight DNA from the ¹³C-cellulose-enriched SIP incubations for the three soils
^fHit rate was determined based on the number positives clones in the initial screening / total of screened clones
AZCL (azurine cross-linked)
CMC (carboxymethylcellulose)
pNP (para-nitrophenyl)

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