Article
Microbiology
Manon Boxberger, Sibylle Magnien, Angeline Antezack, Clara Rolland, Marine Makoa Meng, Cheikh Ibrahima Lo, Bernard La Scola, Nadim Cassir
Summary: By studying the human skin microbiota, we isolated a new bacterium called Leucobacter manosquensis sp. nov. Marseille-Q4368 strain from the forehead of a healthy woman. This bacterium showed phenotypical and genomic differences from its closely related species.
Article
Multidisciplinary Sciences
Afaf Hamame, Reham Magdy Wasfy, Cheikh Ibrahima Lo, Florence Fenollar, Didier Raoult, Pierre-Edouard Fournier, Linda Houhamdi
Summary: Two new bacterial strains, Marseille-P2698(T) and Marseille-P2260(T), were isolated from human stools using the culturomic method. These two strains were fully described using the taxonogenomic approach. Marseille-P2698(T) was identified as a Gram-negative, motile, non-spore-forming, rod-shaped bacterium, while Marseille-P2260(T) was identified as a Gram-positive, motile, spore-forming rod-shaped bacterium.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Samuel Bellais, Melanie Nehlich, Maryne Ania, Aurore Duquenoy, Wilfrid Mazier, Ger van den Engh, Jan Baijer, Nicole Simone Treichel, Thomas Clavel, Ilia Belotserkovsky, Vincent Thomas
Summary: Flow cytometry and cell sorting under anaerobic conditions can be used to detect, separate, and cultivate gut commensal bacteria. This study successfully isolated the extremely oxygen sensitive species Faecalibacterium prausnitzii and the under-represented keystone species Christensenella minuta, demonstrating the specificity of the antibodies and the effectiveness of the sorting strategies.
Article
Gastroenterology & Hepatology
Kaisa Hiippala, Imran Khan, Aki Ronkainen, Fredrik Boulund, Helena Vaha-Makila, Maiju Suutarinen, Maike Seifert, Lars Engstrand, Reetta Satokari
Summary: We isolated a novel strain E10-96H of Pseudoruminococcus massiliensis, a strictly anaerobic species, from a healthy fecal donor. The whole genome sequence of E10-96H showed high similarity with the type strain and revealed its potential role in fiber degradation, cross-feeding of other species, and butyrate production in the intestinal ecosystem. E10-96H exhibited commensal behavior with the host epithelium, adhered to enterocytes without provoking a proinflammatory response. Further studies are needed to explore the role of P. massiliensis in intestinal ecology.
Article
Microbiology
Katharine M. Ng, Sagar Pannu, Sijie Liu, Juan C. Burckhardt, Thad Hughes, Will Van Treuren, Jen Nguyen, Kisa Naqvi, Bachviet Nguyen, Charlotte A. Clayton, Deanna M. Pepin, Samuel R. Collins, Carolina Tropini
Summary: Changes in gut environmental factors such as pH and osmolality can significantly impact the composition of the gut microbiome. In this study, we examined the growth of 92 human gut bacterial strains under varying pH and osmolality conditions and identified stress response genes that contribute to bacterial tolerance. Machine learning analysis revealed genes that predict differential tolerance to acid or osmotic stress. Our findings also demonstrate the generalizability of in vitro stress tolerance results and the importance of physical parameters in determining microbial abundance in complex communities.
Article
Multidisciplinary Sciences
Fatima Mekhalif, Rita Zgheib, Jean Akiana, Melhem Bilen, Geor Mongo Ndombe, Florence Fenollar, Pierre-Edouard Fournier, Didier Raoult, Stephane Alibar, Oleg Mediannikov, Cheikh Ibrahima Lo
Summary: The Microbial Culturomics Project discovered a new bacterial species, Peptostreptococcus faecalis sp. nov., isolated from a stool sample of a healthy indigenous Congolese volunteer. The strain Marseille-P4308(T) is a Gram-positive coccus shaped bacterium that grows optimally at 37 degrees C.
Article
Microbiology
Sory Ibrahima Traore, Cheikh Ibrahima Lo, Melhem Bilen, Didier Raoult, Florence Fenollar, Pierre-Edouard Fournier
Summary: Strain Marseille-P2012(T) has been identified as a new bacterial genus within the phylum Firmicutes, isolated from stool samples of a healthy 2-year-old Senegalese boy. This Gram-positive, anaerobic, non-motile coccus-shaped bacterium shows genetic similarity to Finegoldia magna strain ATCC 29328. Its genome is characterized by a length of 1,832,315 bp and a G + C content of 32.46 mol%.
CURRENT MICROBIOLOGY
(2021)
Article
Medical Laboratory Technology
Sanjam S. Sawhney, Caitlin Johnson, Angela Shupe, Jeremy Fine, Gautam Dantas, Carey-Ann D. Burnham, Melanie L. Yarbrough
Summary: The composition of urinary microbiota in men who have sex with men (MSM) was investigated in this study. The microbial composition in MSM urine specimens was found to be significantly different from that in clinical urine specimens. The recovery of microbial species was enhanced using specific culture methods. The findings provide insights into urologic disease in MSM and may improve the detection of genitourinary infections.
CLINICAL CHEMISTRY
(2022)
Article
Infectious Diseases
S. Naud, S. Bellali, H. Anani, C. Lo, A. Yacouba, M. Tidjani Alou, N. Armstrong, M. Bonvalet, L. Zitvogel, D. Raoult, J-C Lagier
Summary: An anaerobic, facultative Gram-stain positive bacterium was isolated from human gut microbiota, considered to be a new genus within the phylum Firmicutes. The draft genome size of the strain is 4,142,938 bp with 44.4% of G + C content. The newly proposed bacterial genus is named Luxibacter massiliensis gen. nov., sp. nov.
NEW MICROBES AND NEW INFECTIONS
(2021)
Article
Microbiology
Angeline Antezack, Manon Boxberger, Bernard La Scola, Virginie Monnet-Corti
Summary: This study described a novel species of Catonella, named Catonella massiliensis sp. nov., isolated from the saliva of a clinically healthy individual following successful treatment of periodontitis. The bacterium exhibited specific growth conditions and fatty acid profiles, showing genetic similarity to C. morbi but distinct enough to be classified as a new species within the genus.
Article
Gastroenterology & Hepatology
Sara Bellali, Jean-Christophe Lagier, Matthieu Million, Hussein Anani, Gabriel Haddad, Rania Francis, Edmond Kuete Yimagou, Saber Khelaifia, Anthony Levasseur, Didier Raoult, Jacques Bou Khalil
Summary: This study investigated whether some microbial species in the human gut microbiota remain uncultured because they are dead before reaching the end of the gastrointestinal tract. By combining flow cytometry and 16S metagenomics analysis with microbial culturomics, it was revealed that only a portion of bacteria were alive, while the rest of the uncultured bacteria were rare, dead, or injured. This highlights the importance of both metagenomics and culturomics approaches for a comprehensive understanding of the diversity in the human gut microbiota.
Article
Microbiology
Reham Magdy Wasfy, Babacar Mbaye, Patrick Borentain, Maryam Tidjani Alou, Maria Leticia Murillo Ruiz, Aurelia Caputo, Claudia Andrieu, Nicholas Armstrong, Matthieu Million, Rene Gerolami, Mao Hagihara, Hideo Kato
Summary: This study identified Enterocloster species, specifically E. bolteae, enriched in the gut microbiota of patients with chronic HBV infection. Ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future.
Article
Microbiology
Myriam Benlaifaoui, Corentin Richard, Awa Diop, Sabrine Naimi, Wiam Belkaid, Eve Bernet, Frederic Veyrier, Arielle Elkrief, Louis-Marie Bobay, Bertrand Routy, Khoudia Diop
Summary: We describe a new member of human gut microbiota, Tractidigestivibacter montrealensis sp. nov., through a polyphasic taxonomic analysis. Strain KD21(T) was isolated from a healthy female volunteer's fecal sample and is an anaerobic, non-motile, Gram-positive, saccharolytic bacterium. It can grow at temperatures between 28°C to 37°C, pH range of 6.0 to 8.0, and with 0 to 5.0 g/l NaCl. Phylogenetic analysis revealed its distinctness from other species, with a 98.48% similarity to T. scatoligenes SK9K4(T). The strain represents a novel species within the genus Tractidigestivibacter, named T. montrealensis sp. nov., with KD21(T) as the type strain.
FEMS MICROBIOLOGY LETTERS
(2023)
Review
Medicine, General & Internal
Wit Thun Kwa, Saishreyas Sundarajoo, Kai Yee Toh, Jonathan Lee
Summary: The microbiome is associated with a variety of diseases, and the gut microbiome reflects the dynamic health status and can be modified, showing great potential for understanding human physiology. Recent advances in high-throughput sequencing methods have enabled extensive studies on the gut microbiome. Emerging technologies such as metatranscriptomics, metabolomics, culturomics, and synthetic biology have shifted microbiome research towards mechanistic analyses. This review aims to highlight different approaches to studying the microbiome, discuss current limitations and future prospects of these techniques, and promote their adoption in clinical practice.
SINGAPORE MEDICAL JOURNAL
(2023)
Article
Microbiology
Sara Bellali, Gabriel Haddad, Thi-Phuong-Thao Pham, Rim Iwaza, Ahmad Ibrahim, Nicholas Armstrong, Amael Fadlane, Carine Couderc, Aldiouma Diallo, Cheikh Sokhna, Matthieu Million, Didier Raoult, Maryam Tidjani Alou
Summary: Two new bacterial strains were isolated from a 14-week-old Senegalese girl, classified into different families and orders, with genomes containing a high percentage of genes encoding enzymes related to genetic information processing, indicating a high growth rate and adaptability. These new taxa were extensively described and characterized using taxono-genomic description concept in this paper.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Article
Microbiology
Reham Magdy Wasfy, Malak Zoaiter, Melhem Bilen, Maryam Tidjani Alou, Cheikh Ibrahima Lo, Sara Bellali, Aurelia Caputo, Stephane Alibar, Claudia Andrieu, Didier Raoult, Pierre Edouard Fournier, Matthieu Million
Summary: This article reports a novel bacterial strain Marseille-P4005(T) isolated from a stool sample of a healthy donor. It is a Gram-stain negative, non-motile, non-spore-forming rod that grows optimally at 37 degrees C and at pH 7.0. Genomic analysis revealed it as a new species within the genus Agathobaculum, named Agathobaculum massiliense sp. nov. The strain showed resistance to several antibiotics and exhibited specific metabolic capabilities.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2023)
Review
Infectious Diseases
Myrto Koutantou, Konstantinos Kambas, Sofia Makka, Pierre-Edouard Fournier, Didier Raoult, Emmanouil Angelakis
Summary: Cat scratch disease (CSD) is difficult to diagnose, and serological assays have limitations in terms of sensitivity and specificity. Molecular assays should be considered as the gold standard for confirming CSD, and lymph node biopsy may be necessary in suspicious cases.
CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY
(2023)
Article
Microbiology
Sory Ibrahima Traore, Cheikh Ibrahima Lo, Maaloum Mossaab, Guillaume Durand, Jean Christophe Lagier, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar
Summary: Bacterial strain Marseille-P3954 was isolated from a stool sample of a 35-year-old male patient living in France. It belongs to a new bacterial genus, classified in a new family, based on its genomic, phenotypic, and phylogenetic evidences. The proposed classification is Maliibacterium massiliense gen. nov., sp. nov. with the type strain Marseille-P3954 (CSUR P3954 = CECT 9568).
CURRENT MICROBIOLOGY
(2023)
Article
Infectious Diseases
Gwenola Picard, Lucie Fournier, Anna Maisa, Claire Grolhier, Souhaila Chent, Caroline Huchet-Kervalla, Jeanne Sudour, Mael Pretet, Laurence Josset, Sylvie Behillil, Justine Schaeffer
Summary: The detection of emerging variant B.1.640 in France was achieved through genomic surveillance, and investigations were performed to inform public health decisions. B.1.640 was initially found in a school cluster and later spread throughout France. Although it did not outcompete the Delta variant, the importation and continuous low-level spread of B.1.640 raised concerns about its public health impact.
Article
Anatomy & Morphology
Abdourahamane Yacouba, Sara Bellali, Gabriel Haddad, Noelle Mavros, Anthony Fontanini, Gregory Dubourg, Jean-Christophe Lagier, Didier Raoult, Jacques Bou Khalil
Summary: SEM and EDX were used to detect and identify microorganisms and crystals in urine samples, showing promising results for their application in urine sediment analysis.
MICROSCOPY RESEARCH AND TECHNIQUE
(2023)
Review
Microbiology
Saber Khelaifia, Pilliol Virginie, Souad Belkacemi, Herve Tassery, Elodie Terrer, Gerard Aboudharam
Summary: Recent years have seen a shift towards culture-dependent approaches in the study of the human microbiota. However, studies on the oral microbiota have been limited. This article presents various methodologies and culture media for studying the oral microbiota through culture, focusing on eukaryota, bacteria, and archaea. The review aims to provide a comprehensive understanding of the oral microbiota's role in oral health and diseases.
Article
Infectious Diseases
Juan Ambrosioni, Marta Hernandez-Meneses, Emanuele Durante-Mangoni, Pierre Tattevin, Lars Olaison, Tomas Freiberger, John Hurley, Margaret M. Hannan, Vivian Chu, Bruno Hoen, Asuncion Moreno, Guillermo Cuervo, Jaume Llopis, Jose M. Miro
Summary: This study compared the epidemiological features and outcomes of infective endocarditis (IE) in different European regions and time periods in the 21st century. The results showed that despite an increase in the complexity of IE cases, prognosis has improved in recent years with a significant decrease in 6-month mortality. The source of infection differed between regions, but the outcomes were not different.
INFECTIOUS DISEASES AND THERAPY
(2023)
Correction
Genetics & Heredity
Sahare Kokcha, Ajay Kumar Mishra, Jean-Christophe Lagier, Matthieu Million, Quentin Leroy, Didier Raoult, Pierre-Edouard Fournier
ENVIRONMENTAL MICROBIOME
(2023)
Article
Microbiology
Malak Zoaiter, Pierre-Edouard Fournier, Linda Houhamdi
Summary: Here, we present two draft genomes of Fusobacterium simiae strains DSM 19848 and Marseille-Q7035, isolated from monkey dental plaque and human intra-abdominal abscess puncture fluid, respectively. The genome sizes of these strains are 2.4 Mb and 2.5 Mb, with G+C contents of 27.1% and 27.2%, respectively.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Correction
Infectious Diseases
Thi Loi Dao, Naomie Canard, Van Thuan Hoang, Tran Duc Anh Ly, Tassadit Drali, Laetitia Ninove, Florence Fenollar, Didier Raoult, Philippe Parola, Pierre Marty, Philippe Gautret
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2023)
Expression of Concern
Microbiology
T. Adekambi, M. Reynaud-Gaubert, G. Greub, M-J Gevaudan, B. La Scola, D. Raoult, D. Drancourt
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Expression of Concern
Microbiology
W. Xu, D. Raoult
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Immunology
Babacar Mbaye, Reham Magdy Wasfy, Maryam Tidjani Alou, Patrick Borentain, Claudia Andrieu, Aurelia Caputo, Didier Raoult, Rene Gerolami, Matthieu Million
Summary: This study analyzed the microbial composition of NASH patients and controls using 16S rRNA sequencing and qPCR. The results showed an association between Lactobacillus and Lactoccocus with NASH, and an association between Methanobrevibacter, Faecalibacterium, and Romboutsia with controls. At the species level, ethanol-producing species of Lactobacillus and an already associated species of dysbiosis were associated with NASH. This study highlights the potential role of ethanol-producing gut microbes in NASH.
MICROBIAL PATHOGENESIS
(2023)
Article
Microbiology
Farah Azouzi, Louis Olagne, Sophie Edouard, Serge Cammilleri, Pierre-Edouard Magnan, Pierre-Edouard Fournier, Matthieu Million
Summary: Cardiovascular infections caused by Coxiella burnetii are the most severe and potentially lethal among persistent localized infections. The use of 18-FDG PET scans has allowed for the detection of non-aortic vascular infections, expanding clinicians' understanding of these infections beyond the heart and aorta.
Article
Medicine, General & Internal
Jaishriram Rathored, Surendra Kumar Sharma, Aarti Chauhan, Bhagteshwar Singh, Jayant Nagesh Banavaliker, V. Sreenivas, Abhay Krishna Srivastava
Summary: This study found a significant association between serum vitamin D concentration and dietary intake as well as sunlight exposure in MDR-TB, DS-PTB patients and healthy controls. Dietary intake may be more important than sun exposure in determining serum vitamin D levels.
ANNALS OF MEDICINE
(2023)
