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176 results on '"Raoult, Didier"'

1. Retraction Note: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition

Author

Million, Matthieu, Alou, Maryam Tidjani, Khelaifia, Saber, Bachar, Dipankar, Lagier, Jean-Christophe, Dione, Niokhor, Brah, Souleymane, Hugon, Perrine, Lombard, Vincent, Armougom, Fabrice, Fromonot, Julien, Robert, Catherine, Michelle, Caroline, Diallo, Aldiouma, Fabre, Alexandre, Guieu, Régis, Sokhna, Cheikh, Henrissat, Bernard, Parola, Philippe, and Raoult, Didier

Published
2023
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22. Major discrepancy between factual antibiotic resistance and consumption in South of France: analysis of 539,037 bacterial strains

Author

Diallo, Ousmane Oumou, Baron, Sophie Alexandra, Dubourg, Gregory, Chaudet, Hervé, Halfon, Philippe, Camiade, Sabine, Comte, Béatrice, Joubert, Stéphanie, François, Arnaud, Seyral, Philippe, Parisot, François, Casalta, Jean-Paul, Ruimy, Raymond, Maruejouls, Christophe, Achiardy, Jean-Christophe, Burignat, Sophie, Carvajal, Joseph, Delaunay, Edouard, Meyer, Sandra, Levy, Pierre-Yves, Roussellier, Patricia, Brunet, Patrick, Bosi, Claude, Stolidi, Philippe, Arzouni, Jean-Pierre, Gay, Gisele, Hance, Pierre, Colson, Philippe, Raoult, Didier, and Rolain, Jean-Marc

Published
2020
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38. Full-length title: Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection

Author

Colson, Philippe, Dhiver, Catherine, Tamalet, Catherine, Delerce, Jeremy, Glazunova, Olga O., Gaudin, Maxime, Levasseur, Anthony, and Raoult, Didier

Subjects
Retrovirus, lcsh:R, Tryptophan, virus diseases, lcsh:Medicine, HIV Infections, Genome, Viral, Virus Replication, Publisher Correction, Article, Gastrointestinal Microbiome, Cytidine Deaminase, DNA, Viral, HIV Seropositivity, Mutation, Codon, Terminator, HIV-1, Humans, Female, lcsh:Q, APOBEC Deaminases, Infection, lcsh:Science
Abstract

Strategies to cure HIV-infected patients by virus-targeting drugs have failed to date. We identified a HIV-1-seropositive woman who spontaneously suppressed HIV replication and had normal CD4-cell counts, no HIV-disease, no replication-competent virus and no cell HIV DNA detected with a routine assay. We suspected that dramatic HIV DNA degradation occurred post-infection. We performed multiple nested-PCRs followed by Sanger sequencing and applied a multiplex-PCR approach. Furthermore, we implemented a new technique based on two hybridization steps on beads prior to next-generation sequencing that removed human DNA then retrieved integrated HIV sequences with HIV-specific probes. We assembled ≈45% of the HIV genome and further analyzed the G-to-A mutations putatively generated by cellular APOBEC3 enzymes that can change tryptophan codons into stop codons. We found more G-to-A mutations in the HIV DNA from the woman than in that of her transmitting partner. Moreover, 74% of the tryptophan codons were changed to stop codons (25%) or were deleted as a possible consequence of gene inactivation. Finally, we found that this woman’s cells remained HIV-susceptible in vitro. Our findings show that she does not exhibit innate HIV-resistance but may have been cured of it by extrinsic factors, a plausible candidate for which is the gut microbiota.

Published
2020

40. RETRACTED ARTICLE: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition

Author

Million, Matthieu, Tidjani Alou, Maryam, Khelaifia, Saber, Bachar, Dipankar, Lagier, Jean-Christophe, Dione, Niokhor, Brah, Souleymane, Hugon, Perrine, Lombard, Vincent, Armougom, Fabrice, Fromonot, Julien, Robert, Catherine, Michelle, Caroline, Diallo, Aldiouma, Fabre, Alexandre, Guieu, Régis, Sokhna, Cheikh, Henrissat, Bernard, Parola, Philippe, and Raoult, Didier

Published
2016
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41. Optimization and standardization of the culturomics technique for human microbiome exploration.

Author

Diakite, Ami, Dubourg, Grégory, Dione, Niokhor, Afouda, Pamela, Bellali, Sara, Ngom, Issa Isaac, Valles, Camille, Tall, Mamadou lamine, Lagier, Jean-Christophe, and Raoult, Didier

Subjects
HUMAN microbiota, METAGENOMICS, BACTERIAL cultures, BACTERIAL diversity, BACTERIA classification
Abstract

Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the discovery and the description of hundreds of new taxa. While this approach relies on the variation of culture conditions and media, we have tested so far more than 300 conditions since the beginning of culturomics studies. In this context, we aimed herein to identify the most profitable conditions for optimizing culturomics approach. For this purpose, we have analysed a set of 58 culturomics conditions that were previously applied to 8 faecal specimens, enabling the isolation of 497 bacterial species. As a result, we were able to reduce the number of conditions used to isolate these 497 of more than a half (i.e. to 25 culture conditions). We have also established a list of the 16 conditions that allowed to capture 98% of the total number of species previously isolated. These data constitute a methodological starting point for culture-based microbiota studies by improving the culturomics workflow without any loss of captured bacterial diversity. [ABSTRACT FROM AUTHOR]

Published
2020
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42. Gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools.

Author

Bittar, Fadi, Keita, Mamadou B., Lagier, Jean-Christophe, Peeters, Martine, Delaporte, Eric, and Raoult, Didier

Subjects
WESTERN lowland gorilla, PATHOGENIC bacteria, ZOONOSES, ACINETOBACTER baumannii, KLEBSIELLA pneumoniae, ESCHERICHIA coli, SERRATIA marcescens, CLOSTRIDIUM botulinum
Abstract

Wild apes are considered to be the most serious reservoir and source of zoonoses. However, little data are available about the gut microbiota and pathogenic bacteria in gorillas. For this propose, a total of 48 fecal samples obtained from 21 Gorilla gorilla gorilla individuals (as revealed via microsatellite analysis) were screened for human bacterial pathogens using culturomics and molecular techniques. By applying culturomics to one index gorilla and using specific media supplemented by plants, we tested 12,800 colonies and identified 147 different bacterial species, including 5 new species. Many opportunistic pathogens were isolated, including 8 frequently associated with human diseases; Mycobacterium bolletii, Proteus mirabilis, Acinetobacter baumannii, Klebsiella pneumoniae, Serratia marcescens, Escherichia coli, Staphylococcus aureus and Clostridium botulinum. The genus Treponema accounted for 27.4% of the total reads identified at the genus level via 454 pyrosequencing. Using specific real-time PCR on 48 gorilla fecal samples, in addition to classical human pathogens, we also observed the fastidious bacteria Bartonella spp. Borrelia spp., Coxiella burnetii and Tropheryma whipplei in the gorilla population. We estimated that the prevalence of these pathogens vary between 4.76% and 85.7%. Therefore, gorillas share many bacterial pathogens with humans suggesting that they could be a reservoir for their emergence. [ABSTRACT FROM AUTHOR]

Published
2014
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43. Pathogenic Eukaryotes in Gut Microbiota of Western Lowland Gorillas as Revealed by Molecular Survey.

Author

Hamad, Ibrahim, Keita, Mamadou B., Peeters, Martine, Delaporte, Eric, Raoult, Didier, and Bittar, Fadi

Subjects
EUKARYOTES, WESTERN lowland gorilla, PRIMATES, RIBOSOMAL RNA, CANDIDA tropicalis, NECATOR americanus
Abstract

Although gorillas regarded as the largest extant species of primates and have a close phylogenetic relationship with humans, eukaryotic communities have not been previously studied in these populations. Herein, 35 eukaryotic primer sets targeting the 18S rRNA gene, internal transcribed spacer gene and other specific genes were used firstly to explore the eukaryotes in a fecal sample from a wild western lowland gorilla (Gorilla gorilla gorilla). Then specific real-time PCRs were achieved in additional 48 fecal samples from 21 individual gorillas to investigate the presence of human eukaryotic pathogens. In total, 1,572 clones were obtained and sequenced from the 15 cloning libraries, resulting in the retrieval of 87 eukaryotic species, including 52 fungi, 10 protozoa, 4 nematodes and 21 plant species, of which 52, 5, 2 and 21 species, respectively, have never before been described in gorillas. We also reported the occurrence of pathogenic fungi and parasites (i.e. Oesophagostomum bifurcum (86%), Necator americanus (43%), Candida tropicalis (81%) and other pathogenic fungi were identified). In conclusion, molecular techniques using multiple primer sets may offer an effective tool to study complex eukaryotic communities and to identify potential pathogens in the gastrointestinal tracts of primates. [ABSTRACT FROM AUTHOR]

Published
2014
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44. Detection of Termites and Other Insects Consumed by African Great Apes using Molecular Fecal Analysis.

Author

Hamad, Ibrahim, Delaporte, Eric, Raoult, Didier, and Bittar, Fadi

Subjects
EDIBLE insects, TERMITES, FECAL analysis, GORILLA (Genus), CHIMPANZEES, BONOBO, GENE libraries
Abstract

The consumption of insects by apes has previously been reported based on direct observations and/or trail signs in feces. However, DNA-based diet analyses may have the potential to reveal trophic links for these wild species. Herein, we analyzed the insect-diet diversity of 9 feces obtained from three species of African great apes, gorilla (Gorilla gorilla gorilla), chimpanzee (Pan troglodytes) and bonobo (Pan paniscus), using two mitochondrial amplifications for arthropods. A total of 1056 clones were sequenced for Cyt-b and COI gene libraries, which contained 50 and 56 operational taxonomic units (OTUs), respectively. BLAST research revealed that the OTUs belonged to 32 families from 5 orders (Diptera, Isoptera, Lepidoptera, Coleoptera, and Orthoptera). While ants were not detected by this method, the consumption of flies, beetles, moths, mosquitoes and termites was evident in these samples. Our findings indicate that molecular techniques can be used to analyze insect food items in wild animals. [ABSTRACT FROM AUTHOR]

Published
2014
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45. Dramatic reduction of culture time of Mycobacterium tuberculosis.

Author

Ghodbane, Ramzi, Raoult, Didier, and Drancourt, Michel

Subjects
*MYCOBACTERIUM tuberculosis, *BACTERIAL cultures, *TUBERCULOSIS diagnosis, *MEDICAL protocols, *BIOFLUORESCENCE, *DISEASE susceptibility, *RIFAMPIN
Abstract

Mycobacterium tuberculosis culture, a critical technique for routine diagnosis of tuberculosis, takes more than two weeks. Here, step-by-step improvements in the protocol including a new medium, microaerophlic atmosphere or ascorbic-acid supplement and autofluorescence detection dramatically shortened this delay. In the best case, primary culture and rifampicin susceptibility testing were achieved in 72 hours when specimens were inoculated directly on the medium supplemented by antibiotic at the beginning of the culture. [ABSTRACT FROM AUTHOR]

Published
2014
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46. Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon.

Author

Anani, Hussein, Abdallah, Rita Abou, Khoder, May, Fontanini, Anthony, Mailhe, Morgane, Ricaboni, Davide, Raoult, Didier, and Fournier, Pierre-Edouard

Subjects
GUT microbiome, RIBOSOMAL RNA, RNA sequencing, ANEMIA, PHYLOGENY
Abstract

The gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov. [ABSTRACT FROM AUTHOR]

Published
2019
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47. Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus.

Author

Pham, Thi-Phuong-Thao, Tidjani Alou, Maryam, Bachar, Dipankar, Levasseur, Anthony, Brah, Souleymane, Alhousseini, Daouda, Sokhna, Cheikh, Diallo, Aldiouma, Wieringa, Frank, Million, Matthieu, and Raoult, Didier

Abstract

Kwashiorkor and marasmus are considered to be two different clinical diseases resulting from severe malnutrition, but this distinction has been questioned. In a previous study comparing children with kwashiorkor and healthy children from Niger and Senegal, we found a dramatic gut microbiota alteration with a predominant depletion of anaerobes and enrichment in Proteobacteria and Fusobacteria in kwashiorkor. However, it remained unknown whether this association was related to malnutrition or was a specific feature of kwashiorkor. In this continuation study, we added 7 new marasmus subjects and 71,162 new colonies from the same countries. Our results showed that, compared to marasmus, the kwashiorkor gut microbiota was characterized by an increased proportion of Proteobacteria (culturomics, Marasmus 5.0%, Kwashiorkor 16.7%, p < 0.0001; metagenomics, Marasmus 14.7%, Kwashiorkor 22.0%, p = 0.001), but there was a decreased proportion of Bacteroidetes in marasmus (culturomics, Marasmus 0.8%, Kwashiorkor 6.5%, p = 0.001; metagenomics, Marasmus 5.4%, Kwashiorkor 7.0%, p = 0.03). Fusobacterium was more frequently cultured from kwashiorkor. All detected potential pathogenic species were enriched in the kwashiorkor gut microbiota. These results provide a biological basis to support the usage of an antibiotic therapy more effective in suppressing the overgrowth of bacterial communities resistant to penicillin, combined with antioxidants and probiotics for nutritional recovery therapies, particularly for kwashiorkor. [ABSTRACT FROM AUTHOR]

Published
2019
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49. Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition.

Author

Million, Matthieu, Tidjani Alou, Maryam, Khelaifia, Saber, Bachar, Dipankar, Lagier, Jean-Christophe, Dione, Niokhor, Brah, Souleymane, Hugon, Perrine, Lombard, Vincent, Armougom, Fabrice, Fromonot, Julien, Robert, Catherine, Michelle, Caroline, Diallo, Aldiouma, Fabre, Alexandre, Guieu, Régis, Sokhna, Cheikh, Henrissat, Bernard, Parola, Philippe, and Raoult, Didier

Published
2016
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