@article{fdi:010070955,
  title = {{O}ptimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome},
  author = {{M}arynowska, {M}. and {G}oux, {X}. and {S}illam-{D}uss{\`e}s, {D}avid and {R}ouland {L}ef{\`e}vre, {C}orinne and {R}oisin, {Y}. and {D}elfosse, {P}. and {C}alusinska, {M}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {T}hanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose utilizing environments. {E}specially, the examination of its symbiotic microbes should reveal interesting carbohydrate-active enzymes, which are of primary interest for the industry. {P}revious metatranscriptomic reports (high-throughput m{RNA} sequencing) highlight the high representation and overexpression of cellulose and hemicelluloses degrading genes in the termite hindgut digestomes, indicating the potential of this technology in search for new enzymes. {N}evertheless, several factors associated with the material sampling and library preparation steps make the metatranscriptomic studies of termite gut prokaryotic symbionts challenging. {M}ethods: {I}n this study, we first examined the influence of the sampling strategy, including the whole termite gut and luminal fluid, on the diversity and the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. {S}econdly, we evaluated different commercially available kits combined in two library preparative pipelines for the best bacterial m{RNA} enrichment strategy. {R}esults: {W}e showed that the sampling strategy did not significantly impact the generated results, both in terms of the representation of the microbes and their transcriptomic profiles. {N}evertheless collecting luminal fluid reduces the co-amplification of unwanted {RNA} species of host origin. {F}urthermore, for the four studied higher termite species, the library preparative pipeline employing {R}ibo-{Z}ero {G}old r{RNA} {R}emoval {K}it "{E}pidemiology" in combination with {P}oly({A}) {P}urist {MAG} kit resulted in a more efficient r{RNA} and poly-{A}-m{RNA}depletion (up to 98.44% r{RNA} removed) than the pipeline utilizing {MICROBE}xpress and {MICROBE}nrich kits. {H}igh correlation of both {R}ibo-{Z}ero and {MICROBE}xpresse depleted gene expression profiles with total non-depleted {RNA}-seq data has been shown for all studied samples, indicating no systematic skewing of the studied pipelines. {C}onclusions: {W}e have extensively evaluated the impact of the sampling strategy and library preparation steps on the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. {T}he presented methodological approach has great potential to enhance metatranscriptomic studies of the higher termite intestinal flora and to unravel novel carbohydrate-active enzymes.},
  keywords = {{C}arbohydrate-active enzymes ({CAZ}ymes) ; {I}soptera ; {M}etatranscriptomics ; {M}icrobiome ; m{RNA} enrichment ; {T}ermite gut ; {GUYANE} {FRANCAISE}},
  booktitle = {},
  journal = {{BMC} {G}enomics},
  volume = {18},
  numero = {},
  pages = {art. 681 [ 14 p.]},
  ISSN = {1471-2164},
  year = {2017},
  DOI = {10.1186/s12864-017-4076-9},
  URL = {https://www.documentation.ird.fr/hor/fdi:010070955},
}