Article
Immunology
Mudra Khare, Dhiraj Sinha, Rita Zgheib, Sory Ibrahima Traore, Jean-Christophe Lagier, Didier Raoult, Pierre-Edouard Fournier
Summary: Strain Marseille-P1302, isolated from a 2-year-old Nigerian boy suffering from Kwash-iorkor, exhibits similarity with Brevilactibacter species, but is phylogenetically closest to Brevilactibacter sinopodophylli. Based on genomic data, a new genus Nigeribacterium is proposed, with strain Marseille-P1302 as the type strain of the new species Nigeribacterium massiliense gen. nov., sp. nov.
MICROBES AND INFECTION
(2021)
Article
Microbiology
Mariem Ben Khedher, Fatou Samba Diouf, Cheikh Ibrahima Lo, Stephane Alibar, Guillaume Durand, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar
Summary: Strain GD8 is a new species isolated from fresh stool of a French volunteer, belonging to the order Coriobacteriales. It is an anaerobic Gram-positive bacterium isolated from human gut microbiota, with a genome size of 2,836,446 bp and a G + C content of 64.1%. The analysis of the 16S rRNA gene showed that GD8 has 96.2% similarity with Collinsella massiliensis strain An5, which is the phylogenetically related species.
ARCHIVES OF MICROBIOLOGY
(2021)
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)
Article
Microbiology
Camille Valles, Morgane Mailhe, Davide Ricaboni, Nicholas Armstrong, Stephane Alibar, Veronique Vitton, Jean-Christophe Lagier, Didier Raoult, Maryam Tidjani Alou
Summary: This study describes the isolation of a new genus, Negativibacillus massiliensis, from the left colon of a healthy woman, with details on its characteristics and genomic information. The proposed creation of Negativibacillus massiliensis as the 43rd genus within the Ruminococcaceae family is based on the strain's genetic and phenotypic characteristics.
MICROBIOLOGY RESEARCH
(2021)
Article
Microbiology
He Qi, Defeng Liu, Yang Zou, Nan Wang, Han Tian, Chunling Xiao
Summary: C17(T) is a novel species of Streptococcus, isolated from a healthy child in Shenyang, China, with specific phenotypic and genomic characteristics, showing high susceptibility to several antibiotics.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2021)
Article
Microbiology
Hoang Thong Kieu, Thi Phuong Thao Pham, Cheikh Ibrahima Lo, Stephane Alibar, Ludivine Brechard, Nicholas Armstrong, Philippe Decloquement, Aldiouma Diallo, Cheikh Sokhna, Matthieu Million, Jean-Christophe Lagier, Didier Raoult, Maryam Tidjani Alou
Summary: Using the culturomics approach, a previously unknown strain named Weizmannia faecalis was isolated and identified within the Weizmannia genus. The strain was isolated from a healthy subject's feces and showed similar characteristics to Weizmannia coagulans. However, there were some genomic differences between the two strains.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Mossaab Maaloum, Pamela Afouda, Cheikh Ibrahima Lo, Gregory Dubourg, Thi Tien Nguyen, Anthony Levasseur, Rachid Saile, Didier Raoult, Pierre-Edouard Fournier
Summary: In this study, a new Prevotella species, Prevotella merdaesp. nov., isolated from humans was described. The bacterium was isolated from a fecal sample of a healthy fecal transplant donor. It displayed distinct phenotypic characteristics and had a unique genome composition.
FEMS MICROBIOLOGY LETTERS
(2022)
Article
Microbiology
Mossaab Maaloum, Cheikh Ibrahima Lo, Sokhna Ndongo, Marine Makoa Meng, Rachid Saile, Stephane Alibar, Didier Raoult, Pierre-Edouard Fournier
Summary: The culturomics method was used to isolate a new member of the Ottowia genus from a stool sample of a healthy volunteer. The isolated strain Marseille-P4747(T) showed a 96.18% 16S rRNA sequence identity with Ottowia beijingensis strain GCS-AN-3 (NR_133803.1), the closest named species. Based on various analysis, we concluded that Ottowia massiliensis sp. nov. is a new species represented by Marseille-P4747(T) ( = CSUR P4747 = CECT 30348), with a taxonogenomic description provided.
FEMS MICROBIOLOGY LETTERS
(2022)
Article
Microbiology
Luis Johnson Kangale, Didier Raoult, Fournier Pierre-Edouard
Summary: A new bacterial strain, Marseille-Q2390, from the planarian S. mediterranea was isolated and characterized, leading to the proposal of a new species, Pedobacter ghigonii sp. nov. This white-pigmented, Gram-negative, rod-shaped bacterium grows in aerobic conditions and belongs to the family Sphingobacteriaceae. Genomic analysis confirmed its distinctiveness from closely related strains and its classification as a new species.
MICROBIOLOGY RESEARCH
(2021)
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
Biochemistry & Molecular Biology
Samantha L. Goldman, Jon G. Sanders, Weiwei Yan, Anthony Denice, Margaret Cornwall, Kathleen N. Ivey, Emily N. Taylor, Alex R. Gunderson, Michael J. Sheehan, Deus Mjungu, Elizabeth V. Lonsdorf, Anne E. Pusey, Beatrice H. Hahn, Andrew H. Moeller
Summary: The study shows that culturing methods can recover a high number of bacterial genera from vertebrate gut microbiotas, including rare ones missed by culture-independent sequencing. Culturing not only improves inventories but also enables the discovery of novel species related to human pathogens.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Microbiology
Maxime Descartes Mbogning Fonkou, Cheikh Ibrahima Lo, Zouina Mekhalif, Melhem Bilen, Enora Tomei, Edmond Kuete Yimagou, Gregory Dubourg, Didier Raoult, Florence Fenollar, Pierre-Edouard Fournier
Summary: Culturomics has enhanced research on human microbiota by isolating previously uncultured bacterial species. A new bacterial species, Gemella massiliensis, was successfully isolated from a sputum sample of a healthy French man. This strain exhibits unique characteristics and genetic differences compared to its closest known species, Gemella bergeri.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Aurelie Morand, Mamadou Lamine Tall, Edmond Kuete Yimagou, Issa Isaac Ngom, Cheikh Ibrahima Lo, Florent Cornu, Michel Tsimaratos, Jean-Christophe Lagier, Anthony Levasseur, Didier Raoult, Pierre-Edouard Fournier
Summary: This study describes a new species Anaerococcus urinomassiliensis, isolated from the urine of a 17-year-old boy with autoimmune hepatitis and membranoproliferative glomerulonephritis. The strain exhibits specific genetic characteristics, is primarily of human origin, and belongs to the genus of anaerobic bacteria.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Noa Zecharia, Helena Krasnov, Miri Vanunu, Andreina Castillo Siri, Ami Haberman, Orit Dror, Lera Vakal, Rodrigo P. P. Almeida, Lior Blank, Dani Shtienberg, Ofir Bahar
Summary: This study investigated the causal agent, genetic diversity, and host range of almond leaf scorch (ALS) in Israel. It confirmed that Xylella fastidiosa is the causal agent of ALS in Israel and described its genetic and host range characteristics. The study also revealed that ALS spread continues to threaten the almond and grapevine industries in Israel.
Article
Biotechnology & Applied Microbiology
Rakshak Kumar, Shruti Sinai Borker, Aman Thakur, Pooja Thapa, Sanjeet Kumar, Srijana Mukhia, Kumari Anu, Amita Bhattacharya, Sanjay Kumar
Summary: Picrorhiza kurroa Royle ex Benth is an endangered medicinal herb due to overharvesting, and biopriming with plant growth-promoting rhizobacteria, such as Serratia quinivorans PKL:12, has been shown to effectively enhance the vegetative growth and survival of micropropagated plantlets. Genomic evidence suggests that PKL:12 has genes encoding proteins for cold adaptation and plant growth-promoting traits, making it a potential biocontrol agent for bio-hardening micropropagated P. kurroa in cold regions.
Article
Virology
Philippe Colson, Philippe Gautret, Jeremy Delerce, Herve Chaudet, Pierre Pontarotti, Patrick Forterre, Raphael Tola, Marielle Bedotto, Lea Delorme, Wahiba Bader, Anthony Levasseur, Jean-Christophe Lagier, Matthieu Million, Nouara Yahi, Jacques Fantini, Bernard La Scola, Pierre-Edouard Fournier, Didier Raoult
Summary: This study investigated the dynamics of the French variant Marseille-4 of SARS-CoV-2 over a 10-month period, identifying two subvariants and analyzing their mutations and lifetimes. The findings suggest that beneficial mutations can initiate new outbreaks, while the accumulation of other mutations can result in the disappearance of lineages.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Microbiology
Malak Zoaiter, Reham Magdy Wasfy, Aurelia Caputo, Florence Fenollar, Zaher Zeaiter, Pierre-Edouard Fournier, Linda Houhamdi
Summary: Strain Marseille-Q6994 was isolated from a 72-year-old patient with pneumonia in France. Through bacterial morphology, gene sequence comparison, and genomic analysis, the study confirmed that the strain belongs to a new species, named Streptococcus bouchesdurhonensis.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Immunology
Alissa Hammoud, Meriem Louni, Florence Fenollar, Hubert Bassene, Masse Sambou, Nathalie Duclos, Georges Diatta, Cheikh Sokhna, Anthony Levasseur, Didier Raoult, Oleg Mediannikov
Summary: The current paradigm of trench fever transmission by body lice is challenged by the isolation of identical strains of Bartonella quintana from patients and head lice. Confirmation of head lice as a vector will have implications for the treatment and prevention of louse-borne diseases. This study provides evidence of head lice vectorial capacity by detecting live B. quintana in head lice and finding genetic identity between strains from patients' blood and head lice during an outbreak.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Imene Ikram Hassani, Ines Quadri, Archana Yadav, Sonia Bouchard, Didier Raoult, Hocine Hacene, Christelle Desnues
Summary: This study analyzed and compared the diversity of halophilic archaea in Zehrez-Chergui (Saharian chott), Algeria, using both PCR amplification and cultivation approaches. A total of 45 distinct strains were characterized, indicating their membership in the class Halobacteria. Phylogenetic analysis revealed that 23 strains were related to 6 genera of halophilic archaea, including Halopiger which was dominant in this hypersaline environment. The molecular analysis identified a diverse range of archaeological species, highlighting the importance of combining both methods to obtain comprehensive information.
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
Microbiology
David R. Arahal, Carolee T. Bull, Hans-Juergen Busse, Henrik Christensen, Maria Chuvochina, Svetlana N. Dedysh, Pierre -Edouard Fournier, Konstantinos T. Konstantinidis, Charles T. Parker, Ramon Rossello-Mora, Antonio Ventosa, Markus Goeker
Summary: In this paper, the Judicial Commission offers guidance and assistance to authors, reviewers, and editors in interpreting the International Code of Nomenclature of Prokaryotes (ICNP) and in submitting Requests for an Opinion or other suggestions related to the ICNP. The paper also discusses the role of the Judicial Commission and addresses various types of nomenclature-related proposals that may not be suitable for a Request. The study is based on a comprehensive review of all Judicial Opinions issued since 1980.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
David R. Arahal, Carolee T. Bull, Henrik Christensen, Maria Chuvochina, Svetlana N. Dedysh, Pierre- Edouard Fournier, Konstantinos T. Konstantinidis, Charles T. Parker, Ramon Rossello-Mora, Antonio Ventosa, Markus Goeker
Summary: Judicial Opinion 128 addresses nomenclatural issues regarding class names in the International Code of Nomenclature of Prokaryotes. It confirms that the suffix -proteobacteria does not indicate a joint taxonomic or phylogenetic placement. It also clarifies the nomenclatural type of Mollicutes and explains that the rejection of a name does not automatically include other names with similar spelling but different ranks. Additionally, it corrects the orthography of several class names.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Infectious Diseases
Estelle Sabourin, Isabelle Podglajen, Pierre-Edouard Fournier, Jean-Luc Mainardi
Summary: This study evaluated the effectiveness of the recommended treatment for endovascular infections caused by C. burnetii. The results showed that the treatment regimen with doxycycline and hydroxychloroquine achieved good clinical and biological outcomes in patients with endovascular infections.
JOURNAL OF INFECTION AND CHEMOTHERAPY
(2023)
Article
Virology
Philippe Colson, Gwilherm Penant, Jeremy Delerce, Celine Boschi, Nathalie Wurtz, Marielle Bedotto, Stephanie Branger, Philippe Brouqui, Philippe Parola, Jean-Christophe Lagier, Nadim Cassir, Herve Tissot-Dupont, Matthieu Million, Sarah Aherfi, Bernard La Scola
Summary: A large outbreak of Monkeypox virus (MPXV) infections occurred in nonendemic countries in May 2022. DNA metagenomics using next-generation sequencing was performed on clinical samples from MPXV-infected patients diagnosed between June and July 2022. The study identified 18 MPXV genomes classified in clade IIb, lineage B.1, with four B.1 sublineages. The genomes showed a high number of mutations compared to previous genomes, including nonsynonymous mutations in genes encoding central proteins and the presence of bacterial superinfection in some patients.
JOURNAL OF MEDICAL VIROLOGY
(2023)
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)
Article
Infectious Diseases
Bekir Celebi, Derya Karatas Yeni, Yusuf Yilmaz, Ferhat Matur, Cahit Babur, Mehmet Ali Oktem, Mustafa Sozen, Ahmet Karatas, Didier Raoult, Oleg Mediannikov, Pierre Edouard Fournier
Summary: This study examined Borrelia species in rodents captured from rural areas of Turkey. Borrelia miyamotoi was discovered in 1.7% of the blood samples collected from wild rodents. This is the first report of B. miyamotoi presence in rodents in Turkey.
TICKS AND TICK-BORNE DISEASES
(2023)
Article
Virology
Coline Mortier, Herve Tissot-Dupont, Florian Cardona, Christiane Bruel, Salima Lahouel, Hanane Lasri, Karim Bendamardji, Celine Boschi, Philippe Parola, Matthieu Million, Philippe Colson, Philippe Brouqui, Bernard La Scola, Jean-Christophe Lagier, Nadim Cassir
Summary: In the current global outbreak of mpox, the clinical presentation is poorly specific and reinforces the importance of microbiological confirmation. Symptomatic patients who test negative for the virus should undergo a broad differential diagnosis.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Microbiology
Fatou Samba Diouf, Mamadou Beye, Mapenda Gaye, Babacar Mbaye, Stephane Alibar, Mariema Sarr, Gregory Dubourg, Jean-Christophe Lagier, Cheikh Sokhna, Florence Fenollar, Pierre-Edouard Fournier, Cheikh Ibrahima Lo
Summary: Blood is normally sterile, but bacteria in the bloodstream indicate an anomaly. By performing a blood culture on a patient with thalassemia major, a new strain of Streptococcus was isolated and identified through phenotypic, phylogenetic, and genomic characteristics analysis. Named Streptococcus thalassemiae sp. nov., this strain showed similarity to Streptococcus mitis but had significant differences based on DNA-DNA hybridization and average nucleotide identity analysis. This research demonstrates the importance of studying bacterial strains in blood cultures for accurate diagnosis.
INTERNATIONAL JOURNAL OF MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Omar Zmerli, Sara Bellali, Gabriel Haddad, Akiko Hisada, Yusuke Ominami, Didier Raoult, Jacques Bou Khalil
Summary: Phosphotungstic acid (PTA) staining is a commonly used negative staining method in scanning electron microscopy (SEM) for assessing the viability of microorganisms. This study demonstrates that PTA staining can effectively differentiate between live and dead bacteria, providing a rapid, cost-effective, and efficient viability assay for microbiome investigations and antimicrobial susceptibility testing.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Correction
Microbiology
Cheikh Ibrahima Lo, Niokhor Dione, Aminata Mbaye, Patricia Fernandez-Mellado Gomez, Issa Isaac Ngom, Camille Valles, Stephane Alibar, Jean-Christophe Lagier, Florence Fenollar, Pierre-Edouard Fournier, Didier Raoult, Seydina M. Diene
FEMS MICROBIOLOGY LETTERS
(2023)
