@article{fdi:010079708,
  title = {{C}omparison of environmental and culture-derived bacterial communities through 16s metabarcoding : a powerful tool to assess media selectivity and detect rare taxa},
  author = {{P}edron, {J}. and {G}uyon, {L}. and {L}ecomte, {A}. and {B}lottiere, {L}. and {C}handeysson, {C}. and {R}ochelle-{N}ewall, {E}mma and {R}aynaud, {X}. and {B}erge, {O}. and {B}arny, {M}. {A}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}o compare environmental and culture-derived microbial communities, we performed 16{S} metabarcoding of uncultured samples and their culture-derived bacterial lawns. {M}icrobial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. {T}heir culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. {T}he {V}3-{V}4 16{S} r{RNA} region was amplified and sequenced. {T}he bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. {O}verall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. {C}omparison of treatments indicated that the culture selected both detected and rare undetected environmental species. {A}ccurate detection of rare environmental bacteria of the{P}ectobacteriumgenus by 16{S} metabarcoding of the culture lawn was demonstrated. {I}nterestingly, for abundant taxa, such as those of the {P}seudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. {F}inally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.},
  keywords = {16{S} barcoding ; {P}ectobacterium ; {P}seudomonas ; river ; bacterial communities ; medium selectivity ; cultivation ; microbial ecology},
  booktitle = {},
  journal = {{M}icroorganisms},
  volume = {8},
  numero = {8},
  pages = {1129 [17 p.]},
  year = {2020},
  DOI = {10.3390/microorganisms8081129},
  URL = {https://www.documentation.ird.fr/hor/fdi:010079708},
}