Comparative metagenomics of cellulose- and poplar hydrolysate-degrading microcosms from gut microflora of the Canadian Beaver (Castor canadensis) and North American moose (Alces americanus) after long-term enrichment

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Comparative metagenomics of cellulose- and poplar hydrolysate-degrading microcosms from gut microflora of the Canadian Beaver (Castor canadensis) and North American moose (Alces americanus) after long-term enrichment. / Wong, Mabel T.; Wang, Weijun; Couturier, Marie; Razeq, Fakhria M.; Lombard, Vincent; Lapebie, Pascal; Edwards, Elizabeth A.; Terrapon, Nicolas; Henrissat, Bernard; Master, Emma R.

julkaisussa: Frontiers in Microbiology, Vuosikerta 8, Nro DEC, 2504, 20.12.2017.

Tutkimustuotos: Lehtiartikkeli

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Wong, Mabel T. ; Wang, Weijun ; Couturier, Marie ; Razeq, Fakhria M. ; Lombard, Vincent ; Lapebie, Pascal ; Edwards, Elizabeth A. ; Terrapon, Nicolas ; Henrissat, Bernard ; Master, Emma R. / Comparative metagenomics of cellulose- and poplar hydrolysate-degrading microcosms from gut microflora of the Canadian Beaver (Castor canadensis) and North American moose (Alces americanus) after long-term enrichment. Julkaisussa: Frontiers in Microbiology. 2017 ; Vuosikerta 8, Nro DEC.

Bibtex - Lataa

@article{4acd572810cb4983b0cd33ec6fa5bf2c,
title = "Comparative metagenomics of cellulose- and poplar hydrolysate-degrading microcosms from gut microflora of the Canadian Beaver (Castor canadensis) and North American moose (Alces americanus) after long-term enrichment",
abstract = "To identify carbohydrate-active enzymes (CAZymes) that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver (Castor canadensis) and North American moose (Alces americanus) following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs) were identified, with up to half predicted to originate from Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria phyla, and up to 17{\%} from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH) distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF) as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs). Interestingly, DUF362, identified in iron-sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from digestive systems of mammals known for fiber-rich diets, and highlights the value of enrichment to select new CAZymes from metagenome sequences for future biochemical characterization.",
keywords = "Beaver, Carbohydrate-active enzymes (CAZymes), Comparative metagenomics, Digestive microbiome, Lignocellulose degradation, Microbial enrichment, Moose, Polysaccharide utilization loci (PULs)",
author = "Wong, {Mabel T.} and Weijun Wang and Marie Couturier and Razeq, {Fakhria M.} and Vincent Lombard and Pascal Lapebie and Edwards, {Elizabeth A.} and Nicolas Terrapon and Bernard Henrissat and Master, {Emma R.}",
note = "| openaire: EC/H2020/33947/EU//BHIVE",
year = "2017",
month = "12",
day = "20",
doi = "10.3389/fmicb.2017.02504",
language = "English",
volume = "8",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Research Foundation",
number = "DEC",

}

RIS - Lataa

TY - JOUR

T1 - Comparative metagenomics of cellulose- and poplar hydrolysate-degrading microcosms from gut microflora of the Canadian Beaver (Castor canadensis) and North American moose (Alces americanus) after long-term enrichment

AU - Wong, Mabel T.

AU - Wang, Weijun

AU - Couturier, Marie

AU - Razeq, Fakhria M.

AU - Lombard, Vincent

AU - Lapebie, Pascal

AU - Edwards, Elizabeth A.

AU - Terrapon, Nicolas

AU - Henrissat, Bernard

AU - Master, Emma R.

N1 - | openaire: EC/H2020/33947/EU//BHIVE

PY - 2017/12/20

Y1 - 2017/12/20

N2 - To identify carbohydrate-active enzymes (CAZymes) that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver (Castor canadensis) and North American moose (Alces americanus) following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs) were identified, with up to half predicted to originate from Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria phyla, and up to 17% from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH) distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF) as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs). Interestingly, DUF362, identified in iron-sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from digestive systems of mammals known for fiber-rich diets, and highlights the value of enrichment to select new CAZymes from metagenome sequences for future biochemical characterization.

AB - To identify carbohydrate-active enzymes (CAZymes) that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver (Castor canadensis) and North American moose (Alces americanus) following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs) were identified, with up to half predicted to originate from Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria phyla, and up to 17% from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH) distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF) as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs). Interestingly, DUF362, identified in iron-sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from digestive systems of mammals known for fiber-rich diets, and highlights the value of enrichment to select new CAZymes from metagenome sequences for future biochemical characterization.

KW - Beaver

KW - Carbohydrate-active enzymes (CAZymes)

KW - Comparative metagenomics

KW - Digestive microbiome

KW - Lignocellulose degradation

KW - Microbial enrichment

KW - Moose

KW - Polysaccharide utilization loci (PULs)

UR - http://www.scopus.com/inward/record.url?scp=85038417016&partnerID=8YFLogxK

U2 - 10.3389/fmicb.2017.02504

DO - 10.3389/fmicb.2017.02504

M3 - Article

VL - 8

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - DEC

M1 - 2504

ER -

ID: 16790205