Molecular studies neglect apparently gram-negative populations in the human gut microbiota
| Autor: | Didier Raoult, Laurent Papazian, Catherine Lepolard, Perrine Hugon, Catherine Robert, Didier Musso, Jean-Christophe Lagier, Bernard Vialettes |
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| Přispěvatelé: | Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Service de réanimation-Détresses respiratoires et infections sévères, Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Nutrition, obésité et risque thrombotique (NORT), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Hôpital nord, ProdInra, Archive Ouverte, Raoult, Didier, Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM) |
| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Male
microbiote intestinal Gut flora law.invention antibiotique Feces law être humain 0303 health sciences biology Microbiology and Parasitology santé humaine Middle Aged Biota Microbiologie et Parasitologie communauté bactérienne trouble métabolique Gram staining [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology étude moléculaire Female matière fécale ciblage génique microscopie électronique à transmission (MET) Adult Microbiology (medical) Firmicutes pcr quantitative cytométrie de flux Microbiology procaryote Young Adult 03 medical and health sciences flore intestinale séquençage arnr 16s intestin Humans [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology maladie humaine Aged 030304 developmental biology métagénomique Bacteriological Techniques Bacteria 030306 microbiology bacteroidetes Bacteroidetes Bacteriology biology.organism_classification pyroséquençage Gastrointestinal Tract Metagenomics firmicute Pyrosequencing gram négatif bactérie gram positif immunodepression |
| Zdroj: | Journal of Clinical Microbiology Journal of Clinical Microbiology, 2013, 51 (10), pp.3286-3293. ⟨10.1128/JCM.00473-13⟩ Journal of Clinical Microbiology, American Society for Microbiology, 2013, 51 (10), pp.3286-3293. ⟨10.1128/JCM.00473-13⟩ Journal of Clinical Microbiology 10 (51), 3286-3293 . (2013) |
| ISSN: | 0095-1137 |
| DOI: | 10.1128/JCM.00473-13⟩ |
| Popis: | Studying the relationships between gut microbiota, human health, and diseases is a major challenge that generates contradictory results. Most studies draw conclusions about the gut repertoire using a single biased metagenomics approach. We analyzed 16 different stool samples collected from healthy subjects who were from different areas, had metabolic disorders, were immunocompromised, or were treated with antibiotics at the time of the stool collection. The analyses performed included Gram staining, flow cytometry, transmission electron microscopy (TEM), quantitative real-time PCR (qPCR) of the Bacteroidetes and Firmicutes phyla, and pyrosequencing of the 16S rRNA gene amplicons targeting the V6 region. We quantified 10 10 prokaryotes per gram of feces, which is less than was previously described. The Mann-Whitney test revealed that Gram-negative proportions of the prokaryotes obtained by Gram staining, TEM, and pyrosequencing differed according to the analysis used, with Gram-negative prokaryotes yielding median percentages of 70.6%, 31.0%, and 16.4%, respectively. A comparison of TEM and pyrosequencing analyses highlighted a difference of 14.6% in the identification of Gram-negative prokaryotes, and a Spearman test showed a tendency toward correlation, albeit not significant, in the Gram-negative/Gram-positive prokaryote ratio (ρ = 0.3282, P = 0.2146). In contrast, when comparing the qPCR and pyrosequencing results, a significant correlation was found for the Bacteroidetes / Firmicutes ratio (ρ = 0.6057, P = 0.0130). Our study showed that the entire diversity of the human gut microbiota remains unknown because different techniques generate extremely different results. We found that to assess the overall composition of bacterial communities, multiple techniques must be combined. The biases that exist for each technique may be useful in exploring the major discrepancies in molecular studies. |
| Databáze: | OpenAIRE |
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