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
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.
Review
Plant Sciences
Sariel Huebner
Summary: Graph-based pangenomes can provide a comprehensive platform to study diversity in populations or species, but still face challenges in species with large complex genomes. However, with advancing technology, the graph-pangenome is expected to become a central platform in genomics studies and applications.
CURRENT OPINION IN PLANT BIOLOGY
(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
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
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
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)
Correction
Genetics & Heredity
Sahare Kokcha, Ajay Kumar Mishra, Jean-Christophe Lagier, Matthieu Million, Quentin Leroy, Didier Raoult, Pierre-Edouard Fournier
ENVIRONMENTAL MICROBIOME
(2023)
Article
Infectious Diseases
Anna Barbiero, Tommaso Manciulli, Michele Spinicci, Iacopo Vellere, Maria Grazia Colao, Gian Maria Rossolini, Alessandro Bartoloni, Didier Raoult, Lorenzo Zammarchi
Summary: This study reports ten cases of SENLAT in Tuscany, Italy, with symptoms including scalp eschar and cervical lymphadenopathy. The difficulty of microbiological diagnosis and previous antibiotic treatment administration hindered the identification of the causative agent.
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
Infectious Diseases
Bo Bodker Jensen, Nanna Skaarup Andersen, Silke Woelfel, Ming Chen, Helene M. Paarup, Carsten Riis Olesen, Pierre Edouard Fournier, Per Moestrup Jensen, Sigurdur Skarphedinsson
Summary: Rickettsia helvetica infection rate in ticks in Denmark is 4.9%, with higher rates in adult ticks. The prevalence of anti-R. helvetica antibodies in roe deer is 2.8% and 6% in Lyme neuroborreliosis patients.
TICKS AND TICK-BORNE DISEASES
(2023)
Correction
Public, Environmental & Occupational Health
Thi Loi Dao, Van Thuan Hoang, Amal Magmoun, Tran Duc Anh Ly, Sophie Alexandra Baron, Linda Hadjadj, Naomie Canard, Tassadit Drali, Frederique Gouriet, Didier Raoult, Philippe Parola, Pierre Marty, Jean-Marc Rolain, Philippe Gautret
TRAVEL MEDICINE AND INFECTIOUS DISEASE
(2023)
Article
Immunology
Sabrina Naud, Camille Valles, Abdourahim Abdillah, Linda Abou Chacra, Fatima Zouina Mekhalif, Ahmad Ibrahim, Aurelia Caputo, Jean-Pierre Baudoin, Frederique Gouriet, Fadi Bittar, Jean-Christophe Lagier, Stephane Ranque, Florence Fenollar, Maryam Tidjani Alou, Didier Raoult
Summary: In this study, TM7 were found to be ubiquitous members of the human oral microbiota and were also detected in other human samples, including fecal, breast milk, vaginal, and urine samples. TM7 were also detected in infectious samples, such as blood cultures and cardiac valves, at a low prevalence. The findings suggest that TM7 are human commensals and may have a role in a pathological setting, warranting further investigation.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Cell Biology
Seydina M. Diene, Pierre Pontarotti, Said Azza, Nicholas Armstrong, Lucile Pinault, Eric Chabriere, Philippe Colson, Jean-Marc Rolain, Didier Raoult
Summary: Beta-lactamase enzymes are capable of conferring resistance to widely used antibiotics in human medicine, making them a topic of significant interest. Among these enzymes, the class B beta-lactamases are a type of metallo-beta-lactamase fold protein found not only in bacteria but also in other organisms. Previously unexplored in other organisms due to various barriers, modern search approaches have now uncovered their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These multifunctional enzymes exhibit diverse enzymatic or non-enzymatic activities, with at least thirteen reported activities such as beta-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. This review discusses the existence of M beta L fold enzymes in different domains of life, presents suitable approaches for studying their homologous sequences in unexpected sources, and presents described M beta L fold enzymes with demonstrated enzymatic or non-enzymatic activities.
Article
Immunology
Marie Jumpertz, Jacques Sevestre, Lea Luciani, Linda Houhamdi, Pierre-Edouard Fournier, Philippe Parola
Summary: Monitoring and analyzing ticks removed from patients in Marseille, France, revealed the presence of various tick species and bacterial pathogens. Identification of the ticks and detection of bacterial DNA in the ticks can aid in clinical diagnosis, treatment, and surveillance of tickborne diseases. The most common bacterial pathogens found were Rickettsia raoultii, R. slovaca, Borrelia spp., and R. massiliae.
EMERGING INFECTIOUS DISEASES
(2023)
