Palaeomicrobiology: current issues and perspectives, Nat Rev Microbiol, vol.3, pp.23-35, 2005. ,
Sequence analysis of bacterial DNA in the colon of an Andean mummy, Am J Phys Anthropol, vol.107, pp.285-295, 1998. ,
Old parasites for a new world: the future of paleoparasitological research. a review, J Parasitol, vol.95, pp.365-371, 2009. ,
Insights from characterizing extinct human gut microbiomes, PLoS One, vol.7, p.51146, 2012. ,
Phylotyping and functional analysis of two ancient human microbiomes, PLoS One, vol.3, p.3703, 2008. ,
Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach, J Archaeol Sci, vol.40, pp.3060-3066, 2013. ,
Molecular characterization of a pre-Columbian mummy and in situ coprolite, Am J Phys Anthropol, vol.129, pp.620-629, 2006. ,
Studies on the preservation of the intestinal microbiota's DNA in human mummies from cold environments, Med Secoli, vol.18, pp.725-740, 2006. ,
Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman, Am J Phys Anthropol, vol.112, pp.297-309, 2000. ,
Microbial communities in pre-columbian coprolites, PLoS One, vol.8, p.65191, 2013. ,
DOI : 10.1371/journal.pone.0065191
URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0065191&type=printable
Molecular identification by ''suicide PCR'' of Yersinia pestis as the agent of medieval black death, Proc Natl Acad Sci U S A, vol.97, pp.12800-12803, 2000. ,
URL : https://hal.archives-ouvertes.fr/hal-00157003
, Manual of Clinical Microbiology, vol.10, pp.2200-2212, 2011.
Belgium: a biostatistics analysis of trichurid eggs between the Old and New World, Rev Bras Parasitol Vet, vol.18, pp.70-74, 2009. ,
Pathogenic and opportunistic freeliving amoebae: Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri, and Sappinia diploidea, FEMS Immunol Med Microbiol, vol.50, pp.1-26, 2007. ,
DOI : 10.1016/b978-0-7020-5101-2.00051-0
Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrixassisted laser desorption ionization-time of flight mass spectrometry, J Clin Microbiol, vol.51, pp.2182-2194, 2013. ,
16 S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates, J Clin Microbiol, vol.38, pp.3623-3630, 2000. ,
A bioinformatician's guide to metagenomics, Microbiol Mol Biol Rev, vol.72, pp.557-578, 2008. ,
DOI : 10.1128/mmbr.00009-08
URL : https://mmbr.asm.org/content/72/4/557.full.pdf
A core gut microbiome in obese and lean twins, Nature, vol.457, pp.480-484, 2009. ,
DOI : 10.1038/nature07540
URL : http://europepmc.org/articles/pmc2677729?pdf=render
Microorganisms resistant to free-living amoebae, Clin Microbiol Rev, vol.17, pp.413-433, 2004. ,
DOI : 10.1128/cmr.17.2.413-433.2004
URL : https://cmr.asm.org/content/17/2/413.full.pdf
Ancient DNA from Ascaris: extraction amplification and sequences from eggs collected in coprolites, Int J Parasitol, vol.31, pp.1101-1106, 2001. ,
DOI : 10.1016/s0020-7519(01)00214-4
Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample, Mem Inst Oswaldo Cruz, vol.105, pp.225-228, 2010. ,
DOI : 10.1590/s0074-02762010000200020
URL : http://www.scielo.br/pdf/mioc/v105n2/20.pdf
Use of subgenic 18 S ribosomal DNA PCR and sequencing for genus and genotype identification of Acanthamoebae from humans with keratitis and from sewage sludge, J Clin Microbiol, vol.39, pp.1903-1911, 2001. ,
Ancient DNA: do it right or not at all, Science, vol.289, p.1139, 2000. ,
DOI : 10.1126/science.289.5482.1139b
Ancient DNA, Nat Rev Genet, vol.2, pp.353-359, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-01673468
, Ancient DNA. Proc Biol Sci, vol.272, pp.3-16, 2005.
Genetic analyses from ancient DNA, Annu Rev Genet, vol.38, pp.645-679, 2004. ,
Critical analysis of coprolite evidence of medicinal plant use, Palaeogeography, Palaeoclimatology, Palaeoecology, vol.237, pp.110-118, 2006. ,
Hostbacterial mutualism in the human intestine, Science, vol.307, pp.1915-1920, 2005. ,
DOI : 10.1126/science.1104816
Molecular evidence for the presence of Rickettsia felis in the feces of wildliving African apes, PLoS One, vol.8, p.54679, 2013. ,
Detection of Plasmodium spp. in human feces, Emerg Infect Dis, vol.18, pp.634-636, 2012. ,
Detection of Mycobacterium tuberculosis complex organisms in the stools of patients with pulmonary tuberculosis, Microbiology, vol.155, pp.2384-2389, 2009. ,
, Manual of Clinical Microbiology, 10 th Edition, pp.786-799, 2011.
Bordetella and Related Genera, Manual of Clinical Microbiology, vol.10, pp.739-751, 2011. ,
SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in preColumbian human coprolites, Int J Parasitol, vol.36, pp.1419-1425, 2006. ,
Microbial culturomics: paradigm shift in the human gut microbiome study, Clin Microbiol Infect, vol.18, pp.1185-1193, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00964466
Reducing the effects of PCR amplification and sequencing artifacts on 16 S rRNA-based studies, PLoS One, vol.6, p.27310, 2011. ,
Ironing out the wrinkles in the rare biosphere through improved OTU clustering, Environ Microbiol, vol.12, pp.1889-1898, 2010. ,
TaxCollector: Modifying Current 16 S rRNA Databases for the Rapid Classification at Six Taxonomic Levels, Diversity, vol.2, pp.1015-1025, 2010. ,
A systematic approach for discovering novel, clinically relevant bacteria, Emerg Infect Dis, vol.18, pp.422-430, 2012. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004. ,
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments, Syst Biol, vol.56, pp.564-577, 2007. ,
Estimating maximum likelihood phylogenies with PhyML, Methods Mol Biol, vol.537, pp.113-137, 2009. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511830
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, J Mol Evol, vol.22, pp.160-174, 1985. ,
Phylogeny.fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Res, vol.36, pp.465-469, 2008. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00324099
TreeDyn: towards dynamic graphics and annotations for analyses of trees, BMC Bioinformatics, vol.7, p.439, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00321061
Bayesian community-wide culture-independent microbial source tracking, Nat Methods, vol.8, pp.761-763, 2011. ,
Microbial biogeography of public restroom surfaces, PLoS One, vol.6, p.28132, 2011. ,
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale, Appl Environ Microbiol, vol.75, pp.5111-5120, 2009. ,
Bacterial community variation in human body habitats across space and time, Science, vol.326, pp.1694-1697, 2009. ,
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa, Proc Natl Acad Sci U S A, vol.107, pp.14691-14696, 2010. ,
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans, Science, vol.332, pp.970-974, 2011. ,
Changes in bacterial communities accompanied by aggregation in a fed-batch composting reactor, Curr Microbiol, vol.56, pp.458-467, 2008. ,
QIIME allows analysis of high-throughput community sequencing data, Nat Methods, vol.7, pp.335-336, 2010. ,
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource, Nucleic Acids Res, vol.39, pp.546-551, 2011. ,
Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, vol.11, p.119, 2010. ,
Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes, Cold Spring Harb Protoc, p.5368, 2010. ,
A novel bacterium associated with lymphadenitis in a patient with chronic granulomatous disease, PLoS Pathog, vol.2, p.28, 2006. ,
Parachlamydia acanthamoebae, an emerging agent of pneumonia, Clin Microbiol Infect, vol.15, pp.18-28, 2009. ,