@article{PAR00012819,
  title = {{W}hole-genome assembly of {A}kkermansia muciniphila sequenced directly from human stool},
  author = {{C}aputo, {A}. and {D}ubourg, {G}. and {C}roce, {O}. and {G}upta, {S}. and {R}obert, {C}. and {P}apazian, {L}. and {R}olain, {J}. {M}. and {R}aoult, {D}idier},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {A}lterations in gut microbiota composition under antibiotic pressure have been widely studied, revealing a restricted diversity of gut flora, including colonization by organisms such as {E}nterococci, while their impact on bacterial load is variable. {H}igh-level colonization by {A}kkermansia muciniphila, ranging from 39% to 84% of the total bacterial population, has been recently reported in two patients being treated with broad-spectrum antibiotics, although attempts to cultivate this microorganism have been unsuccessful. {R}esults: {H}ere, we propose an original approach of genome sequencing for {A}kkermansia muciniphila directly from the stool sample collected from one of these patients. {W}e performed and assembly using metagenomic data obtained from the stool sample. {W}e used a mapping method consisting of aligning metagenomic sequencing reads against the reference genome of the {A}kkermansia muciniphila {M}uc({T}) strain, and a {D}e novo assembly to support this mapping method. {W}e obtained draft genome of the {A}kkermansia muciniphila strain {U}rmite with only 56 gaps. {T}he absence of particular metabolic requirement as possible explanation of our inability to culture this microorganism, suggests that the bacterium was dead before the inoculation of the stool sample. {A}dditional antibiotic resistance genes were found following comparison with the reference genome, providing some clues pertaining to its survival and colonization in the gut of a patient treated with broad-spectrum antimicrobial agents. {H}owever, no gene coding for imipenem resistance was detected, although this antibiotic was a part of the patient's antibiotic regimen. {C}onclusions: {T}his work highlights the potential of metagenomics to facilitate the assembly of genomes directly from human stool.},
  keywords = {{A}kkermansia muciniphila ; {G}enome ; {G}ut microbiota ; {M}etagenomics ; {A}ntibiotics},
  booktitle = {},
  journal = {{B}iology {D}irect},
  volume = {10},
  numero = {},
  pages = {art. 5 [11 p.]},
  ISSN = {1745-6150},
  year = {2015},
  DOI = {10.1186/s13062-015-0041-1},
  URL = {https://www.documentation.ird.fr/hor/{PAR}00012819},
}