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Using the taxono-genomics concept, we describe here a strictly anaerobic Gram-positive bacillus. This strain was isolated from the stool sample of a 50-year-old healthy Bedouin woman. The 16S rRNA gene sequence analysis and the whole-genome sequencing showed that this isolate belonged to the genus Gordonibacter in the family Eggerthellaceae. Based on these criteria, we propose the creation of Gordonibacter massiliensis sp. nov., strain Marseille-P2775T (= CSUR P2775).
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Strain SIT17T was isolated from the stool of a healthy 13-month-old Senegalese boy. It is a Gram-positive, anaerobic, rod-shaped, non-spore-forming and mobile bacterium. It exhibited 92.74% 16S rRNA gene sequence similarity with the Brassicibacter thermophilus strain Cel2f, the phylogenetically most closely related species. Its genome is about 2.87 Mb long with 27.39 mol% G + C content. We provide more details of Senegalia massiliensis strain SIT17T (= CSURP2130 = DSM 103071), the creation of which was previously announced.
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Strains Marseille-P4001 and Marseille-P3668 are new species from the order Bacteroidales isolated from healthy French volunteers. They are anaerobic Gram-negative rod-shaped bacteria. They exhibited 92.68% and 96.68% 16S rRNA sequence identities with Parabacteroides gordonii strain MS-1 and Parabacteroides chinchillae JCM 17104, respectively, the phylogenetically closest species. Their respective draft genomes measured 5.23 Mb and 3.73 Mb with 39.2 mol% and 40.8 mol% of G + C content. Using a taxonogenomics method, we propose here a brief description of Parabacteroides pacaensis sp. nov., strain Marseille-P4001T and Parabacteroides provencensis sp. nov., strain Marseille-P3668T as new bacterial species.
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OBJECTIVES: Methanogenic Archaea are considered as extremely oxygen-sensitive organisms, and their culture is fastidious, requiring specific equipment. We report here conditions allowing the cultivation of Methanobrevibacter smithii in an anaerobic chamber without the addition of hydrogen. METHODS: We first enriched the stool sample in an anaerobic liquid medium. To cultivate M. smithii with Bacteroides thetaiotaomicron and other hydrogen-producing bacteria on solid medium in an anaerobic chamber, we divided the agar plates into two compartments and seeded each strain on each compartment. Methane production was assessed by gas chromatography, and the growing colonies were authenticated by MALDI-TOF MS. RESULTS: We successfully cultured M. smithii from a liquid culture medium inoculated with stool collected from a healthy donor in an anaerobic chamber. The isolation in pure culture permitted successful culture on agar medium by our performing a co-culture with B. thetaiotaomicron. We also successfully tested the co-cultivation of M. smithii with other known hydrogen-producing bacteria. Gas chromatographic tests showed that these strains produced hydrogen in different amounts. Agar colonies of methanogens were obtained by co-culture with these bacteria, and methane production was detected. CONCLUSIONS: We propose a new approach to isolate and cultivate new strains of M. smithii by using a co-culture-based technique that can facilitate and make available the isolation of new methanogenic Archaea strains in clinical microbiology laboratories.
Assuntos
Bactérias/metabolismo , Hidrogênio/metabolismo , Methanobrevibacter/crescimento & desenvolvimento , Methanobrevibacter/isolamento & purificação , Adulto , Ágar , Anaerobiose , Bactérias/classificação , Bactérias/crescimento & desenvolvimento , Técnicas de Cocultura , Meios de Cultura , Fezes/microbiologia , Feminino , Voluntários Saudáveis , Humanos , Metano/análise , Metano/biossíntese , Methanobrevibacter/metabolismoRESUMO
The interest in studying gut microbiota has been rekindled with the advent of molecular techniques, in particular, metagenomics. Culturomics (high throughput microbial culture with identification of the colonies by Maldi-TOF) has demonstrated its complementarity with metagenomics for comprehensive study of the microbiota. The main metagenomic studies have revealed an increase in biodiversity, with in particular an increase of Spirochaetes and Prevotella in subjects of African origin compared with Western subjects. Studies on malnutrition have shown a reduction of all bacteria and in particular of anaerobic bacteria and methanogenic archaea. Of the 1,162 bacteria isolated by culturomics studies, 476 were isolated only from non-African samples, 445 were isolated in African and non-African groups, and 241 bacteria were isolated from samples of African origin including 68 new species. Further studies of African microbiota by culturomics and metagenomics will make it possible to assess whether some bacteria have particular specificities and if these might play a role in certain pathologies such as malnutrition.
Assuntos
Microbioma Gastrointestinal , Metagenômica/métodos , África , HumanosRESUMO
Bright-field transmission electron microscopy (TEM), TEM-negative staining technique, resin-embedding and ultramicrotomy, scanning TEM, scanning electron microscopy, atomic force microscopy and cryoelectron microscopy are imaging techniques used for describing giant viruses, their cycle and ultrastructure. Here we used the SECOM system, an integrated correlative light and electron microscopy using light and electronic imaging without sample transfer, to study cells infected with giant viruses, as shown by Tupanvirus, the ultrastructure of which was successfully observed. An improvement of the SECOM system with an eye to its use in fundamental and clinical research could be considered in the field of microbiology.
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We report here the main characteristics of 'Arabia massiliensis' strain Marseille-P3078T gen. nov., sp. nov., 'Gordonibacter massiliensis' Marseille-P2775T sp. nov. and 'Bacilliculturomica massiliensis' strain Marseille-P3303 gen. nov., sp. nov. The culturomics approach combined with taxonogenomics was used to characterize these strains, which were all isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman.
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We report here the main characteristics of 'Blautia phocaeensis' strain Marseille-P3441 sp. nov. and 'Lachnoclostridium edouardi' strain Marseille-P3397 sp. nov., that were isolated from a faecal specimen of a 42-year-old female Saudi Bedouin. We used a bacterial culturomics approach combined with taxono-genomics.
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We report here the main characteristics of 'Beduinibacterium massiliense' strain Marseille-P3337T gen. nov., sp. nov., 'Massilimaliae massiliensis' Marseille-P2963T gen. nov., sp. nov., 'Provencibacterium massiliense' Marseille-P2780T gen. nov., sp. nov. and 'Oscilibacter massiliensis' Marseille-P2778T sp. nov., all isolated from the stool of a Bedouin from Saudi Arabia. We used a bacterial culturomics approach combined with taxonogenomics.
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Mobilicoccus massiliensis strain SIT2 (= CSUR P1306 = DSM 29065) is a new type strain of Mobilicoccus sp. nov. isolated from the stool of a 2-year-old Nigerian boy with kwashiorkor. M. massiliensis is Gram positive, facultatively anaerobic, nonsporulating and motile. The 3 842 438 bp long genome contains 3362 protein-coding and 49 RNA genes, including one 5S rRNA gene, one 16S rRNA gene, one 23S rRNA gene and 46 tRNA genes.
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Microbial culturomics represents a completely new approach to investigate microbial diversity by using different optimized culture conditions, mass spectrometry, genome sequencing and annotation and phenotypic description that allow for an extensive characterization of new species and the study of the human microbiome. Here we present four new species within the genus Paenibacillus: 'Paenibacillus bouchesdurhonensis' strain Marseille-P3071T, 'Paenibacillus rubinfantis' strain MT18T, 'Paenibacillus senegalimassiliensis' strain SIT18T and 'Paenibacillus tuaregi' strain Marseille-P2472T, which are all facultatively aerobic and Gram-positive bacilli.
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We report here the main characteristics of "Lascolabacillus massiliensis" strain SIT8 (CSUR P1560) that was isolated from the stool of a healthy 28-month-old boy.
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We report the main characteristics of "Senegalia massiliensis" strain SIT17 (= CSUR P2130) that was isolated from the stool of a healthy 13-month-old Senegalese boy.
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Herein, we report the main characteristics of 'Flaviflexus massiliensis' strain SIT4(T) (CSURP1300), a new bacterium that was isolated from the stool specimen of a 2-year-old girl from Niger suffering from kwashiorkor.
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We report here the main characteristics of "Lagierella massiliensis" strain SIT14 (CSUR P2012), which was isolated from a stool specimen from a healthy 28-month-old Senegalese boy.
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Bacillus andreraoultii strain SIT1(T) (= CSUR P1162 = DSM 29078) is the type strain of B. andreraoultii sp. nov. This bacterium was isolated from the stool of a 2-year-old Nigerian boy with a severe form of kwashiorkor. Bacillus andreraoultii is an aerobic, Gram-positive rod. We describe here the features of this bacterium, together with the complete genome sequencing and annotation. The 4 092 130 bp long genome contains 3718 protein-coding and 116 RNA genes.
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Bacillus testis strain SIT10 (= CSUR P1492 = DSMZ 101190) is the new type strain collected from stool from a 2-year-old boy from Senegal during a culturomics study. This Gram-positive bacterium is a facultative anaerobic rod and a member of the Bacillaceae family. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 3 987 349 bp long genome (one chromosome but no plasmid) with 42.8% GC content contains 4005 protein-coding and 171 sRNA genes, including 19 5S rRNA gene, 15 16S rRNA genes and ten 23S rRNA genes.
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Taxonogenomics coupled with culturomics leads to descriptions of new bacteria. Thanks to this strategy, we report the main characteristics of "Peptoniphilus phoceensis" strain SIT15, a new bacterium isolated from a stool sample of a 1-year-old healthy Senegalese boy.
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A new Actinobacterium, designated Tessaracoccus massiliensis type strain SIT-7(T) (= CSUR P1301 = DSM 29060), have been isolated from a Nigerian child with kwashiorkor. It is a facultative aerobic, Gram positive, rod shaped, non spore-forming, and non motile bacterium. Here, we describe the genomic and phenotypic characteristics of this isolate. Its 3,212,234 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 67.81% and contains 3,058 protein-coding genes and 49 RNA genes.
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We report here the main characteristics of a new bacterium named 'Beduinella massiliensis' strain Marseille-P2846(T) (CSURP2846P) that was isolated from a faecal specimen of a 50-year-old Saudi Bedouin female and propose the creation of a new family 'Beduinellaceae'.