Mining biomass-degrading genes through Illumina-based de novo sequencing and metagenomic analysis of free-living bacteria in the gut of the lower termite Coptotermes gestroi harvested in Vietnam

Huyen, Thi; Nguyen, Thi Thao; Nguyen, Thanh N.; Le, Quynh Giang; Nguyen, Charlene; Kimura, Keitarou; Truong, Nam Hai

doi:10.1016/j.jbiosc.2014.05.010

Cited by 67 publications

(71 citation statements)

References 44 publications

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“…also are involved in degradation of soluble fibers (57). Recent studies also have identified abundant Treponema in a termite gut metagenome (58) and enriched in the gut microbiomes of humans with highly fibrous hunter-gatherer diets (59). Bacteria from this genus likely are able to metabolize exopolysaccharides produced by the primary cellulolytic bacteria, functioning as fermenters (15).…”

Section: Discussionmentioning

confidence: 99%

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

Jia

Wilkins

et al. 2016

Appl Environ Microbiol

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Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose-or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus Methanobacterium) and bacterial (order Clostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose-and xylan-digesting functions given appropriate enrichment conditions. C ellulose and xylan, two major structural components of plant cell walls, represent important resources for renewable energy (1-3). Cellulose, hemicellulose (the major component is xylan), and lignin make up 35 to 50%, 20 to 35%, and 10 to 25% of total lignocellulose by dry weight, respectively (4). Cellulose and xylan from lignocellulosic biomass not only represent new energy sources but also could reduce carbon dioxide emissions, as lignocellulosic biofuels are considered carbon neutral. However, digesting recalcitrant lignocellulosic components to fermentable sugars is a rate-limiting step (5), making lignocellulosic biofuels currently challenging to produce while being price competitive with fossil fuels (6, 7). Microbes have evolved strategies (8, 9) to digest lignocellulosic components concurrent with the evolution of plant cell walls, making the investigation of microbial cellulose and xylan digestion potentially important to this emerging energy source.Metagenomic and microbial diversity studies of ruminant animals (e.g., cow [10], sheep [11], and deer [12]) have revealed rich taxonomic and functional microbial diversity, including mechanisms for cellulose and xylan digestion. Microbial cellulose and xylan digestion systems have been ide...

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Section: Discussionmentioning

confidence: 99%

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

Jia

Wilkins

et al. 2016

Appl Environ Microbiol

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“…Furthermore, 5 % of sequences were identified as Bacteroidetes, which are involved in the degradation of complex polysaccharides [14]. It is the second-most abundant bacterial taxon in lignocellulose degradation cultures, and the thirdmost abundant bacteria in the gut of the lower termite Coptotermes [15]. Clostridium, which accounted for 5.0 % of the clones, is an anaerobic cellulolytic bacterium [16].…”

Section: Discussionmentioning

confidence: 99%

Diversity of archaea and bacteria in a biogas reactor fed with <i>Pennisetum sinese</i> Roxb by 16S rRNA sequence analysis

Zhao¹,

Ai²,

Li³

et al. 2017

Trop. J. Pharm Res

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“…Metagenomic DNA sequence data was analyzed using standard bioinformatics approach. A range of bioinformatic softwares such as BLAST, MEGAN, SOAP and the data in NCBI, KEGG, eggNOG were used to identify and account for ORFs [6].…”

Section: Methodsmentioning

confidence: 99%

In silico mining for alkaline enzymes from metagenomic dna data of gut microbes of the lower termite Coptotermes gestroi in Vietnam

Giang¹,

Huyen²,

Hải³

2016

V J Bio

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ASBTRACT:The high alkaline proteases, lipases, cellulases and hemicellulases are important enzymes in research and industries. In this study, using the Alcapred software, the metagenomic DNA sequences of the gut flora of Coptotermes gestroi were analyzed to identify the enzymes that were specifically adapted to alkaline condition. The results show that 737 of 943 ORFs (accounting for 72%) encoded proteases, 154 of 214 ORFs (holding 78%) encoded lipases and 338 of 575 ORFs (accounting for 59%) encoded cellulase and hemicelluase. All those enzymes were predicted to be alkaline enzymes. This study provide an overview picture of the alkaline enzyme groups of the gut flora of C. gestroi, and provide a good database for mining, isolation of the genes to produce recombinant enzymes.

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Mining biomass-degrading genes through Illumina-based de novo sequencing and metagenomic analysis of free-living bacteria in the gut of the lower termite Coptotermes gestroi harvested in Vietnam

Cited by 67 publications

References 44 publications

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

Diversity of archaea and bacteria in a biogas reactor fed with <i>Pennisetum sinese</i> Roxb by 16S rRNA sequence analysis

In silico mining for alkaline enzymes from metagenomic dna data of gut microbes of the lower termite Coptotermes gestroi in Vietnam

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