@article{fdi:010078392,
  title = {{U}se of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels},
  author = {{L}okmer, {A}. and {C}ian, {A}. and {F}roment, {A}lain and {G}antois, {N}. and {V}iscogliosi, {E}. and {C}hab{\'e}, {M}. and {S}{\'e}gurel, {L}.},
  editor = {},
  language = {{ENG}},
  abstract = {{P}rotozoa have long been considered undesirable residents of the human gut, but recent findings suggest that some of them may positively affect the gut ecosystem. {T}o better understand the role and ecological dynamics of these commensal and potentially beneficial protozoan symbionts, we need efficient methods to detect them, as well as accurate estimates of their prevalence across human populations. {M}etagenomics provides such an opportunity, allowing simultaneous detection of multiple symbionts in a single analytical procedure. {I}n this study, we collected fecal samples of 68 individuals from three {C}ameroonian populations with different subsistence modes and compared metagenomics-based and targeted methods of detection for two common protozoan genera: {B}lastocystis and {E}nt-amoeba. {I}n addition, we analyzed our data along with publicly available fecal metagenomes from various worldwide populations to explore the prevalence and association patterns of ten protozoan genera. {R}egarding the detection method, microscopy was much less sensitive than metagenomics for {E}ntamoeba, whereas q{PCR} was at least as sensitive as meta-genomics for {B}lastocystis sp. {H}owever, metagenomics was more likely to detect co-colonizations by multiple subtypes. {O}ut of the ten examined genera in 127 individuals from {C}ameroon, {T}anzania, {P}eru, {I}taly or {USA}, only three ({B}lastocystis, {E}ntamoeba and {E}ntero-monas) had an overall prevalence exceeding 10%. {A}ll three genera were more common in less industrialized populations and their prevalence differed between continents and subsistence modes, albeit not in a straightforward manner. {T}he majority (72.5%) of colonized individuals carried at least two protozoan species, indicating that mixed-species colonizations are common. {I}n addition, we detected only positive and no negative association patterns between different protozoa. {D}espite the pitfalls of the metagenomic approach, ranging from the availability of good-quality sequencing data to the lack of standard analytical procedures, we demonstrated its utility in simultaneous detection of multiple protozoan genera, and especially its ability to efficiently detect mixed-species colonizations. {O}ur study corroborates and expands prevalence results previously obtained for {B}lastocystis sp. and provides novel data for {E}ntamoeba spp. and several other protozoan genera. {F}urthermore, it indicates that multiple protozoa are common residents of the healthy human gut worldwide.},
  keywords = {{CAMEROUN} {SUD} {OUEST}},
  booktitle = {},
  journal = {{PL}o{S} {O}ne},
  volume = {14},
  numero = {2},
  pages = {art. no e0211139 [20 ]},
  year = {2019},
  DOI = {10.1371/journal.pone.0211139},
  URL = {https://www.documentation.ird.fr/hor/fdi:010078392},
}