Development, validation and application of specific primers for analyzing the clostridial diversity in dark fermentation pit mud by PCR-DGGE

Bacchetti De Gregoris, 2011, Improvement of phylum-and class-specific primers for real-time PCR quantification of bacterial taxa, J. Microbiol. Methods, 86, 351, 10.1016/j.mimet.2011.06.010 Carver, 2012, Hydrogen and volatile fatty acid production during fermentation of cellulosic substrates by a thermophilic consortium at 50 and 60 degrees C, Bioresour. Technol., 104, 424, 10.1016/j.biortech.2011.11.013 Cheng, 2012, High yield bio-butanol production by solvent-producing bacterial microflora, Bioresour. Technol., 113, 58, 10.1016/j.biortech.2011.12.133 Claesson, 2010, Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions, Nucleic Acids Res., 38, e200, 10.1093/nar/gkq873 Cole, 2009, The ribosomal database project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res., 37, D141, 10.1093/nar/gkn879 Collins, 1994, The phylogeny of the genus clostridium: proposal of five new genera and eleven new species combinations, 44, 812 Ding, 2013, Characterization of eubacterial and archaeal community diversity in the pit mud of Chinese Luzhou-flavor liquor by nested PCR-DGGE, World J. Microbiol. Biotechnol., 1 Franks, 1998, Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes, Appl. Environ. Microbiol., 64, 3336, 10.1128/AEM.64.9.3336-3345.1998 Garde, 2012, Enhanced PFGE protocol to study the genomic diversity of Clostridium spp. isolated from Manchego cheeses with late blowing defect, Food Control, 28, 392, 10.1016/j.foodcont.2012.05.024 Greppi, 2013, Yeast dynamics during spontaneous fermentation of mawè and tchoukoutou, two traditional products from Benin, Int. J. Food Microbiol., 165, 200, 10.1016/j.ijfoodmicro.2013.05.004 Heilig, 2002, Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA, Appl. Environ. Microbiol., 68, 114, 10.1128/AEM.68.1.114-123.2002 Hernandez-Eugenio, 2002, Sporanaerobacter acetigenes gen. nov., sp. nov., a novel acetogenic, facultatively sulfur-reducing bacterium, Int. J. Syst. Evol. Microbiol., 52, 1217 Hung, 2008, Application of Clostridium-specific PCR primers on the analysis of dark fermentation hydrogen-producing bacterial community, Int. J. Hydrogen Energy, 33, 1586, 10.1016/j.ijhydene.2007.09.037 Jang, 2012, Butanol production from renewable biomass by clostridia, Bioresour. Technol., 653, 10.1016/j.biortech.2012.07.104 Lazarevic, 2009, Metagenomic study of the oral microbiota by Illumina high-throughput sequencing, J. Microbiol. Methods, 79, 266, 10.1016/j.mimet.2009.09.012 Le Bourhis, 2005, Development and validation of PCR primers to assess the diversity of Clostridium spp. in cheese by temporal temperature gradient gel electrophoresis, Appl. Environ. Microbiol., 71, 29, 10.1128/AEM.71.1.29-38.2005 Li, 2010, DNA extraction and removing humic substance from wetland soil, 08, 1130 Marchandin, 2010, Int. J. Syst. Evol. Microbiol., 60, 1271, 10.1099/ijs.0.013102-0 Martínez-Blanch, 2009, Development of a real-time PCR assay for detection and quantification of enterotoxigenic members of Bacillus cereus group in food samples, Int. J. Food Microbiol., 135, 15, 10.1016/j.ijfoodmicro.2009.07.013 Muyzer, 1993, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA, Appl. Environ. Microbiol., 59, 695, 10.1128/AEM.59.3.695-700.1993 Steinbusch, 2011, Biological formation of caproate and caprylate from acetate: fuel and chemical production from low grade biomass, Energy Environ. Sci., 4, 216, 10.1039/C0EE00282H Takii, 2007, Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with casamino acids, Int. J. Syst. Evol. Microbiol., 57, 2320, 10.1099/ijs.0.64882-0 Thirumale, 2001, Control of cellulase formation by trehalose in Clostridium papyrosolvens CFR-703, 37, 241 Thompson, 2002, Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by ‘reconditioning PCR’, Nucleic Acids Res., 30, 2083, 10.1093/nar/30.9.2083 Throbäck, 2004, Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE, FEMS Microbiol. Ecol., 49, 401, 10.1016/j.femsec.2004.04.011 Tracy, 2012, Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications, Curr. Opin. Biotechnol., 23, 364, 10.1016/j.copbio.2011.10.008 Van Dyke, 2002, Molecular biological detection and characterization of Clostridium populations in municipal landfill sites, Appl. Environ. Microbiol., 68, 2049, 10.1128/AEM.68.4.2049-2053.2002 Wang, 2008, Analysis and comparison of the bacterial community in fermented grains during the fermentation for two different styles of Chinese liquor, J. Ind. Microbiol. Biotechnol., 35, 603, 10.1007/s10295-008-0323-z Warnick, 2002, Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil, Int. J. Syst. Evol. Microbiol., 52, 1155, 10.1099/00207713-52-4-1155 Yang, 2009, Substrate utilization by Clostridium estertheticum cultivated in meat juice medium, Int. J. Food Microbiol., 128, 501, 10.1016/j.ijfoodmicro.2008.10.024 Youssef, 2009, Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys, Appl. Environ. Microbiol., 75, 5227, 10.1128/AEM.00592-09 Yu, 2013, Design and application of specific 16S rDNA-targeted primers for assessing endophytic diversity in Dendrobium officinale using nested PCR-DGGE, Appl. Microbiol. Biotechnol., 97, 9825, 10.1007/s00253-013-5294-y Zhao, 2013, Enhancement effect of silver nanoparticles on fermentative biohydrogen production using mixed bacteria, Bioresour. Technol., 142, 240, 10.1016/j.biortech.2013.05.042 Zheng, 2013, Characterization of microbial communities in strong aromatic liquor fermentation pit muds of different ages assessed by combined DGGE and PLFA analyses, Food Res. Int., 54, 660, 10.1016/j.foodres.2013.07.058 Zoetendal, 2004, Molecular ecological analysis of the gastrointestinal microbiota: a review, J. Nutr., 134, 465, 10.1093/jn/134.2.465