Massilistercora timonensis gen. nov., sp. nov., a new bacterium isolated from the human microbiota

Massilistercora timonensis gen. nov., sp. nov. strain Marseille-P3756T is a new species of the phylum Firmicutes; it was isolated from the human gut microbiota and has a genome of 2 769 591 bp (51.2% G + C). The closest species based on 16S rRNA sequence was Merdimonas faecis strain BR31 with 95.2 % sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P3756T as the type strain of Massilistercora timonensis sp. nov., a new species within the genus Massilistercora.

Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology

Microbiology has been largely developed thanks to the discovery and optimization of culture media. The first liquid artificial culture medium was created by Louis Pasteur in 1860. Previously, bacterial growth on daily materials such as some foods had been observed. These observations highlighted the importance of the bacteria's natural environment and their nutritional needs in the development of culture media for their isolation. A culture medium is essentially composed of basic elements (water, nutrients), to which must be added different growth factors that will be specific to each bacterium and necessary for their growth. The evolution of bacterial culture through the media used for their culture began with the development of the first solid culture medium by Koch, allowing not only the production of bacterial colonies, but also the possibility of purifying a bacterial clone. The main gelling agent used in solid culture media is agar. However, some limits have been observed in the use of agar because of some extremely oxygen-sensitive bacteria that do not grow on agar media, and other alternatives were proposed and tested. Then, the discovery of antimicrobial agents and their specific targets prompted the emergence of selective media. These inhibiting agents make it possible to eliminate undesirable bacteria from the microbiota and select the bacteria desired. Thanks to a better knowledge of the bacterial environment, it will be possible to develop new culture media and new culture conditions, better adapted to certain fastidious bacteria that are difficult to isolate.

Neoactinobaculum massilliense gen. nov., a new genesis and Pseudopropionibacterium massiliense sp. nov., a new bacterium isolated from the human oral microbiota

Neoactinobaculum massilliense gen. nov., strain Marseille-P6182^T (= CSUR P6182) and Pseudopropionibacterium massiliense sp. nov., strain Marseille-P6184^T (= CSUR P6184) are a new bacterial genus and new bacterial species belonging to the Actinobacteria phylum that have been isolated from the human oral microbiota.

Massilicoli timonensis sp. nov., a new bacterium isolated from the human microbiota

Massilicoli timonensis sp. nov., strain Marseille-P3755^T (= CSUR P3755 = DSM 103513) is a new bacterial species from the phylum Firmicutes and the family Clostridiales which was isolated from the human gut microbiota.

Genome sequence and description of Bacteroides bouchesdurhonensis sp. nov., a new anaerobic bacterium isolated from the human gut

Bacteroides bouchesdurhonensis sp. nov., strain Marseille-P2653^T (= CSUR; P2653=DSM103120) is a new bacterial species belonging to the Firmicutes phylum in the family Bacteroidaceae that was isolated from the human gut microbiota.

Massilimicrobiota timonensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota

Massilimicrobiota timonensis gen. nov., sp. nov. strain Marseille-P2264 is a new species from Firmicutes phylum isolated from the human gut. Its genome was 2,849,574 bp-long with a 31.8% G+C content. The closest species based on 16S rRNA sequence was Longibaculum muris with 95.6% sequence similarity. Considering phenotypic features, 16S rRNA sequence and comparative genome studies, we proposed Marseille-P2264 as the type strain of Massilimicrobiota timonensis gen. nov., sp. nov.

Isolation and culture of Methanobrevibacter smithii by co-culture with hydrogen-producing bacteria on agar plates

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.

Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum

Enterococcus timonensis sp. nov., strain Marseille-P2817^T, is a facultatively anaerobic, motile and non-spore-forming Gram-positive coccus which was isolated from the sputum of a healthy adult man in Marseilles. We present herein its phenotypic description together with MALDI-TOF (matrix-assisted laser-desorption/ionization time-of-flight) mass spectrometry analysis and genome sequencing and comparison. The genome of Enterococcus timonensis is 2 123 933 bp long with 38.46 mol% of G+C content, and it contains 1983 protein-coding genes and 65 RNA genes (including nine rRNA genes).

Corrigendum to "'Bacteroides mediterraneensis' sp. nov., a new human-associated bacterium isolated from ileum specimen"

[This corrects the article DOI: 10.1016/j.nmni.2016.06.003.].

Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery

A new bacterium, strain AT3^T, was isolated by microbial culturomics from a faecal sample from a Frenchman after bariatric surgery. The isolate exhibited 96.6% 16S ribosomal RNA gene nucleotide sequence similarity with Anaerotruncus colihominis strain WAL 14565^T = CCUG 45055^T = CIP 107754^T. Phenotypic and genomic characteristics showed that the new strain represents a novel species, for which the name Anaerotruncus massiliensis sp. nov. is proposed. The type strain is strain AT3^T = CSUR P2007^T = DSM 100567^T.

Genome sequence and description of Clostridium niameyense sp. nov., isolated from a human with marasmus in Nigeria

Clostridium niameyense sp. nov. strain MT5 is the type strain of C. niameyense sp. nov., a new species within the genus Clostridia. C. niameyense is a Gram-positive, anaerobic bacillus. The strain MT5 (= CSUR P1468 = DSMZ 100441), whose genome is described here, was isolated from a faecal sample collected from a patient with anorexia and marasmus living in Nigeria. The genome is 2 542 841 bp long with 27.44% G + C content and consists of six scaffolds.

Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov

Bacillus salis strain ES3^T (= CSUR P1478 = DSM 100598) is the type strain of B. salis sp. nov. It is an aerobic, Gram-positive, moderately halophilic, motile and spore-forming bacterium. It was isolated from commercial table salt as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of halophilic bacteria in salty food. Here we describe the phenotypic characteristics of this isolate, its complete genome sequence and annotation, together with a comparison with closely related bacteria. Phylogenetic analysis based on 16S rRNA gene sequences indicated 97.5% similarity with Bacillus aquimaris, the closest species. The 8 329 771 bp long genome (one chromosome, no plasmids) exhibits a G+C content of 39.19%. It is composed of 18 scaffolds with 29 contigs. Of the 8303 predicted genes, 8109 were protein-coding genes and 194 were RNAs. A total of 5778 genes (71.25%) were assigned a putative function.

Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon

Strain Marseille-P2645^T was isolated in a colon sample from a Frenchwoman who underwent a colonoscopy. Bacterial cells were Gram negative, non–spore forming, mobile and strictly anaerobic. The genome of strain Marseille-P2645^T is 3 950 441 bp long and contains 3374 protein-coding genes. The DNA G+C content is of 51.66 mol%. Strain Marseille-P2645^T exhibited a 92.9% sequence similarity with Bacteroides helcogenes strain P36-108^T (GenBank accession no. CP002352), the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2645^T (= CSUR P2645 = DSM 103034) is therefore a candidate as a type species of a new genus belonging to the Bacteroidaceae family, for which the name of Mediterranea massiliensis gen. nov., sp. nov., is proposed.

'Gracilibacillus phocaeensis' sp. nov., 'Sediminibacillus massiliensis' sp. nov. and 'Virgibacillus ndiopensis' sp. nov., three halophilic species isolated from salty human stools by culturomics

We report the isolation of three bacterial strains that could not be identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry screening. ‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov. are halophilic species isolated from salty human stools by culturomics.

Genome sequence and description of Mobilicoccus massiliensis sp. nov. isolated from the stool of a Nigerian boy with kwashiorkor

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.

Dakarella massiliensis gen. nov., sp. nov., strain ND3T: a new bacterial genus isolated from the female genital tract

Strain ND3^T was isolated from the genital tract of a 28-year-old woman with bacterial vaginosis. This strain exhibited a 16S rRNA gene sequence similarity of 92.4% with Sutterella wadsworthensis, the phylogenetically closest species with standing in nomenclature. Strain ND3^T was a strictly anaerobic Gram-negative rod and member of the family Sutterellaceae. It exhibited a genome of 2 476 884 bp containing 2175 protein-coding and 62 RNA genes. On the basis of these data, we propose the creation of ‘Dakarella massiliensis’ sp. nov. with strain ND3^T (= CSUR P1938 = DSM 100447) as the type strain.

'Prevotella ihumii' sp. nov. and 'Varibaculum timonense' sp. nov., two new bacterial species isolated from a fresh human stool specimen

Here we report the main characteristics of ‘Prevotella ihumii’ sp. nov., CSUR-P3385^T and ‘Varibaculum timonense’ sp. nov., CSUR-P3369^T isolated in September 2016 from a fresh stool sample of healthy French volunteer woman.

Description of 'Bacillus dakarensis' sp. nov., 'Bacillus sinesaloumensis' sp. nov., 'Gracilibacillus timonensis' sp. nov., 'Halobacillus massiliensis' sp. nov., 'Lentibacillus massiliensis' sp. nov., 'Oceanobacillus senegalensis' sp. nov., 'Oceanobacillus timonensis' sp. nov., 'Virgibacillus dakarensis' sp. nov. and 'Virgibacillus marseillensis' sp. nov., nine halophilic new species isolated from human stool

We report the main characteristics of 'Bacillus dakarensis' P3515^T sp. nov., 'Bacillus sinesaloumensis' P3516^T sp. nov., 'Gracilibacillus timonensis' P2481^T sp. nov., 'Halobacillus massiliensis' P3554^T sp. nov., 'Lentibacillus massiliensis' P3089^T sp. nov., 'Oceanobacillus senegalensis' P3587^T sp. nov., 'Oceanobacillus timonensis' P3532^T sp. nov., 'Virgibacillus dakarensis' P3469^T sp. nov. and 'Virgibacillus marseillensis' P3610^T sp. nov., that were isolated in 2016 from salty stool samples (≥1.7% NaCl) from healthy Senegalese living at Dielmo and N'diop, two villages in Senegal.

Genome sequence and description of Anaeromassilibacillus senegalensis gen. nov., sp. nov., isolated from the gut of patient with kwashiorkor

Using the culturomics strategy, a wide range of anaerobic bacteria was discovered including Anaeromassilibacillus senegalensis strain mt9^T (= CSUR P1511 = DSM 102954), isolated from the gut microbiota of a 1-year-old Senegalese patient with kwashiorkor. This Gram-negative strain is a strictly anaerobic, spore-forming rod motile by a polar flagellum. The 3 511 289 bp long genome of this strain contains 3046 protein-coding and 49 RNA genes, including 45 tRNA and four rRNA genes, and exhibits a G+C content of 52.94%. Here we describe the features of this organism, together with the complete genome sequence and annotation.

Noncontiguous finished genome sequence and description of Prevotella phocaeensis sp. nov., a new anaerobic species isolated from human gut infected by Clostridium difficile

Prevotella phocaeensis sp. nov. strain SN19^T (= DSM 103364) is a new species isolated from the gut microbiota of patient with colitis due to Clostridium difficile. Strain SN19^T is Gram-negative rod-shaped bacteria, strictly anaerobic, nonmotile and non-endospore forming. The predominance fatty acid is hexadecanoic acid. Its 16S rRNA showed a 97.70% sequence identity with its phylogenetically closest species, Prevotella oralis. The genome is 2 922 117 bp long and contains 2486 predicted genes including 56 RNA genes.

Draft genome sequence of a human-associated isolate of Haloferax alexandrinus strain Arc-hr, an extremely halophilic archaea

We report the draft genome sequence of Haloferax alexandrinus strain Arc-hr (CSUR P798), isolated from the human gut of a 10-year-old Amazonian individual. Its 3 893 626 bp genome exhibits a 66.00% GC content. The genome of the strain Arc-hr contains 37 genes identified as ORFans, seven genes associated to halocin and 11 genes associated with polyketide synthases or nonribosomal peptide synthetases.

Rubeoparvulum massiliense gen. nov., sp. nov., a new bacterial genus isolated from the human gut of a Senegalese infant with severe acute malnutrition

Rubeoparvulum massiliense strain mt6^T was isolated from the gut microbiota of a severely malnourished boy from Senegal and consisted of facultative anaerobic, spore-forming, nonmotile and Gram-negative rods. R. massiliense showed a 92% similarity with the 16S rRNA of Bacillus mannanilyticus. The genome of strain mt6^T is 2 843 796 bp long with a 43.75% G+C content. It contains 2735 protein-coding genes and 76 RNA genes, among which are nine rRNA genes.

“Ihuprevotella massiliensis” gen. nov., sp. nov., isolated from human gut

We report here the main characteristics of “Ihuprevotella massiliensis” strain Marseille-P2826^T (CSURP 2826) that was isolated from a human right colon lavage sample.

Corynebacterium phoceense sp. nov., strain MC1T a new bacterial species isolated from human urine

Corynebacterium phoceense strain MC1 (= CSUR P1905 = DSM 100570) is a novel Corynebacterium species isolated from the urine of a kidney transplant recipient as a part of a culturomics study. Corynebacterium phoceense is a Gram-positive, sporogenous, strictly aerobic, and nonmotile coccobacillus. Here we describe strain MC1 and provide its complete annotated genome sequence according to the taxonogenomics concept. Its genome is 2 793 568 bp long and contains 2575 protein-coding genes and 67 RNA genes, including eight rRNA genes.

‘ Marseilla massiliensis ’ gen. nov., sp. nov., isolated from human right colon

We report here the main characteristics of ‘Marseilla massiliensis’ strain Marseille-P2475^T (CSURP2475) isolated from the human right colon.

"Varibaculum massiliense" sp. nov., a new bacterial species isolated from human urine

We report the main characteristics of “Varibaculum massiliense” strain Marseille-P2802^T (=CSUR P2802), which was isolated from urine sample of a 59-year-old man with end-stage renal disease.

"Lagierella massiliensis," a new bacterium detected in human feces

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.

'Halomonas massiliensis' sp. nov., a new halotolerant bacterium isolated from the human gut

We report here the main characteristics of ‘Halomonas massiliensis’ strain Marseille-P2426^T (CSUR P2426), a new species of the Halomonas genus that was isolated from the stool sample of a healthy 24-year-old Senegalese man.

"Lachnoclostridium touaregense," a new bacterial species isolated from the human gut microbiota

We report the main characteristics of “Lachnoclostridium touaregense” strain Marseille-P2415^T (= CSUR P2415 = DSM 102219), a new bacterial species isolated from the gut microbiota of a healthy young girl from Niger.

'Flaviflexus massiliensis', a new bacterial species isolated from the human gut

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.

'Bacteroides mediterraneensis' sp. nov., a new human-associated bacterium isolated from ileum specimen

We report here the main characteristics of ‘Bacteroides mediterraneensis’ strain Marseille-P2644^T (CSURP2644) that was isolated from the stored samples of gut.

"Prevotellamassilia timonensis," a new bacterial species isolated from the human gut

We describe here the main characteristics of "Prevotellamassilia timonensis" gen. nov., sp. nov., strain Marseille-P2831(T) (CSUR P2831), a new member of the Prevotellaceae family that was isolated from stool samples from a 45-year-old patient.

Actinomyces urinae sp. nov., isolated from 13-year-old girl affected by nephritic syndrome

Here, we report the main characteristics of Actinomyces urinae strain Marseille-P2225^T (CSURP2225) isolated from a human urine sample.

"Massiliomicrobiota timonensis," a new bacterial species isolated from the human gut

We report the main characteristics of a new bacterium, “Massiliomicrobiota timonensis” strain SN16 (= CSUR P2264), which was isolated from the stool of a 87-year-old patient.

'Culturomica massiliensis', a new bacterium isolated from the human gut

We report here the main characteristics of ‘Culturomica massiliensis’, strain Marseille-P2698^T (CSUR P2698) a new genus isolated from the stool specimen in a 66-year-old man.

'Phocea massiliensis' a new bacterial species isolated from the human gut

We present here the main characteristics of ‘Phocea massiliensis’ strain Marseille-P2769^T (CSUR P2769), which is a new genus isolated from the stool of a 45-year-old patient.

'Negativicoccus massiliensis', a new species identified from human stool from an obese patient after bariatric surgery

We report here the main characteristics of ‘Negativicoccus massiliensis’ strain AT7 (CSURP = P2082, DSM = 100853) isolated from a stool sample collected from a 47-year-old obese French man before bariatric surgery.

'Eisenbergiella massiliensis', a new species isolated from human stool collected after bariatric surgery

We report the principal characteristics of ‘Eisenbergiella massiliensis’ sp. nov. strain AT11 (CSURP = P2120, DSM = 101499) that was isolated from a stool sample collected after bariatric surgery of a 56-year-old obese French woman.

Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut

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.

Christensenella timonensis, a new bacterial species isolated from the human gut

We propose a new species, Christensenella timonensis, strain Marseille-P2437(T) (CSUR P2437(T)), which was isolated from gut microbiota of a 66-year-old patient as a part of culturomics study. C. timonensis represents the second species isolated within the Christensenella genus.

Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut

Numidum massiliense gen. nov., sp. nov., strain mt3(T) is the type strain of Numidum gen. nov., a new genus within the family Bacillaceae. This strain was isolated from the faecal flora of a Tuareg boy from Algeria. We describe this Gram-positive facultative anaerobic rod and provide its complete annotated genome sequence according to the taxonogenomics concept. Its genome is 3 755 739 bp long and contains 3453 protein-coding genes and 64 RNA genes, including eight rRNA genes.

Noncontiguous finished genome sequence and description of Enterococcus massiliensis sp. nov

Enterococcus massiliensis strain sp. nov. (= CSUR P1927 = DSM 100308) is a new species within the genus Enterococcus. This strain was first isolated from a fresh stool sample of a man during culturomics study of intestinal microflora. Enterococcus massiliensis is a Gram-positive cocci, facultative anaerobic and motile. E. massiliensis is negative for mannitol and positive for β-galactosidase, contrary to E. gallinarum. The complete genome sequence is 2 712 841 bp in length with a GC content of 39.6% and contains 2617 protein-coding genes and 70 RNA genes, including nine rRNA genes.

Anaeromassilibacillus senegalensis gen. nov., sp. nov., isolated from the gut of a child with kwashiorkor

We report the main characteristics of Anaeromassilibacillus senegalensis strain mt9(T) (= CSUR P1511) isolated from the stool of a 1-year-old kwashiorkor patient from Senegal.

Romboutsia timonensis, a new species isolated from human gut

The exploration of the human microbiome was recently revolutionized by microbial culturomics and taxonogenomics. Thanks to this approach, we report here the main characteristics of Romboutsia timonensis strain Marseille-P326, a new bacterium isolated from the right human colon by colonoscopy in a 63-year-old French man with severe anaemia with melaena.

Isolation of new species "Peptoniphilus phoceensis" from human gut

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.

Genome sequence and description of Anaerosalibacter massiliensis sp. nov

Anaerosalibacter massiliensis sp. nov. strain ND1(T) (= CSUR P762 = DSM 27308) is the type strain of A. massiliensis sp. nov., a new species within the genus Anaerosalibacter. This strain, the genome of which is described here, was isolated from the faecal flora of a 49-year-old healthy Brazilian man. Anaerosalibacter massiliensis is a Gram-positive, obligate anaerobic rod and member of the family Clostridiaceae. With the complete genome sequence and annotation, we describe here the features of this organism. The 3 197 911 bp long genome (one chromosome but no plasmid) contains 3271 protein-coding and 62 RNA genes, including six rRNA genes.

Drancourtella massiliensis gen. nov., sp. nov. isolated from fresh healthy human faecal sample from South France

Strain GD1(T) gen. nov., sp. nov., is the type strain of the newly proposed genus and species Drancourtella massiliensis, belonging to the Clostridiales order. This strain, isolated from the stool of a healthy person, is a Gram-positive rod, oxygen intolerant and nonmotile, with spore-forming activity. The features of this organism and its genome sequence are described. The draft genome is 3 057 334 bp long with 45.24% G + C content; it contains 2861 protein-coding genes and 64 RNA genes.

Massilibacterium senegalense gen. nov., sp. nov., a new bacterial genus isolated from the human gut

Massilibacterium senegalense gen. nov., sp. nov., strain mt8^T, is the type strain of Massilibacterium gen. nov., a new genus within the Bacillaceae family. This Gram-negative facultative anaerobic rod was isolated from the gut microbiota of a severely malnourished boy. Its phenotypic description is hereby presented with a complete annotation of its genome sequence. This genome is 5 697 950 bp long and contains 5615 protein-coding genes and 178 RNA genes, among which are 40 rRNA genes.