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Two new bacterial strains, Marseille-P2698T (CSUR P2698 = DSM 103,121) and Marseille-P2260T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698T were C15:0 iso (63%), C15:0 anteiso (11%), and C17:0 3-OH iso (8%). Those found in Marseille-P2260T strain were C16:00 (39%), C18:1n9 (16%) and C18:1n7 (14%). Strains Marseille-P2698T and Marseille-P2260T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneusT, and of 90.98% and 95.07% with Odoribacter splanchnicusT and Eubacterium sulciT, respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicusT and E. sulciT respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698T and Marseille-P2260T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively. [ABSTRACT FROM AUTHOR]

Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive coccoid bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37 °C in anaerobic conditions. They also metabolize carbohydrates, such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains. The highest digital DNA–DNA hybridization (dDDH) values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. Strains Marseille-P3761 and Marseille-P3195 shared an OrthoANI value of 83.5% which was the highest value found with Peptoniphilus species studied here. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that Peptoniphilus coli sp. nov., and Peptoniphilus urinae sp. nov., are new species for which strains Marseille-P3761 (CSUR P3761 = CCUG 71,569) and Marseille-P3195 (CSUR P3195 = DSM 103,468) are their type strains, respectively of two new Peptoniphilus species, for which we propose the names Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., respectively. [ABSTRACT FROM AUTHOR]

Thanks to its ability to isolate previously uncultured bacterial species, culturomics has dynamized the study of the human microbiota. A new bacterial species, Gemella massiliensis Marseille-P3249T, was isolated from a sputum sample of a healthy French man. Strain Marseille-P3249T is a facultative anaerobe, catalase-negative, Gram positive, coccus, and unable to sporulate. The major fatty acids were C16:0 (34%), C18:1n9 (28%), C18:0 (15%) and C18:2n6 (13%). Its 16S rRNA sequence exhibits a 98.3% sequence similarity with Gemella bergeri strain 617-93T, its phylogenetically closest species with standing in nomenclature. Its digital DNA–DNA hybridization (dDDH) and OrthoANI values with G. bergeri of only 59.7 ± 5.6% and 94.8%, respectively. These values are lower than the thresholds for species delineation (> 70% and > 95%, respectively). This strain grows optimally at 37 °C and its genome is 1.80 Mbp long with a 30.5 mol% G + C content. Based on these results, we propose the creation of the new species Gemella massilienis sp. nov., strain Marseille-P3249T (= CSUR P3249 = DSMZ 103940). [ABSTRACT FROM AUTHOR]

The strain Marseille-P2133 is the type strain of a new bacterial species of the order Clostridiales that was isolated from a stool sample from a healthy volunteer. It is a strictly anaerobic Gram-negative coccobacillus. MALDI-TOF MS did not provide any identification. Strain Marseille-P2133T exhibits 97.4% similarity levels with the Fenollaria massiliensis strain 9401234T (NR_133038), a phylogenetically related species with standing in nomenclature. On the basis of these data, we propose the creation of Fenollaria timonensis sp. nov. [ABSTRACT FROM AUTHOR]

Biological control against malaria and its transmission is currently a considerable challenge. Plant-associated bacteria of the genus Asaia are frequently found in nectarivorous arthropods, they thought to have a natural indirect action on the development of plasmodium in mosquitoes. However, virtually nothing is known about its natural cycle. Here, we show the role of nectar-producing plants in the hosting and dissemination of Asaia. We isolated Asaia strains from wild mosquitoes and flowers in Senegal and demonstrated the transmission of the bacteria from infected mosquitoes to sterile flowers and then to 26.6% of noninfected mosquitoes through nectar feeding. Thus, nectar-producing plants may naturally acquire Asaia and then colonize Anopheles mosquitoes through food-borne contamination. Finally, Asaia may play an indirect role in the reduction in the vectorial capacity of Anopheles mosquitoes in a natural environment (due to Plasmodium-antagonistic capacities of Asaia) and be used in the development of tools for Asaia-based paratransgenetic malaria control. [ABSTRACT FROM AUTHOR]

Molecular methods have been considered to be the gold standard for the diagnosis of infectious lymphadenitis. However, culture remains critical in the case of low bacterial concentrations. We used molecular assays and culture to examine fresh lymph node biopsies from patients with suspected infectious lymphadenopathy. We analyzed 1762 lymph node biopsies of which 522 (30%) samples were found positive by real-time PCR; the most commonly amplified bacteria were Bartonella henselae (n = 438, 84%), Francisella tularensis (n = 46, 9%), and Mycobacterium spp. (n = 29, 6%). PCR amplification and sequencing of the 16S rDNA were positive for 359 (20%) lymph node specimens including mainly B. henselae (n = 167, 47%), Staphylococcus spp. (n = 77, 21%), and Streptococcus spp. (n = 41, 11%). In total, 351 lymph nodes were cultured on agar plates and 77 (22%) were positive. Significantly more lymph nodes infected by Gram-positive easy-growing agents were diagnosed by culture (n = 45) than by 16S rDNA PCR (p = 0.02). Culture remains critical for the diagnosis of easy-growing bacteria and mycobacteria; clinicians should be aware that a negative molecular result does not imply absence of infection. [ABSTRACT FROM AUTHOR]

Over the past decade, new culture methods coupled to genome and metagenome sequencing have enabled the number of isolated bacterial species with standing in nomenclature to rise to more than 15,000 whereas it was only 1791 in 1980. 'Culturomics', a new approach based on the diversification of culture conditions, has enabled the isolation of more than 1000 distinct human-associated bacterial species since 2012, including 247 new species. This strategy was demonstrated to be complementary to metagenome sequencing for the exhaustive study of the human microbiota and its roles in health and diseases. However, by identifying a large number of new bacterial species in a short time, culturomics has highlighted a need for taxonomic approaches adapted to clinical microbiology that would include the use of modern and reproducible tools, including high throughput genomic and proteomic analyses. Herein, we review the development of culturomics and genomics in the clinical microbiology field and their impact on bacterial taxonomy. [ABSTRACT FROM AUTHOR]

The identification of human-associated bacteria is very important to control infectious diseases. In recent years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial species and/or genera. Using this strategy, strain GM7, a strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese patient. It is a motile coccobacillus without catalase and oxidase activities. The genome of Gabonibacter massiliensis is 3,397,022 bp long with 2880 ORFs and a G+C content of 42.09 %. Of the predicted genes, 2,819 are protein-coding genes, and 61 are RNAs. Strain GM7 differs from the closest genera within the family Porphyromonadaceae both genotypically and in shape and motility. Thus, we propose that strain GM7 (=CSUR P2336 = DSM 101039) is the type strain of the new genus Gabonibacter gen. nov. and the new species G. massiliensis gen. nov., sp. nov. [ABSTRACT FROM AUTHOR]

The manipulation of the gut microbiota by diet, antibiotics, or probiotics could promote, prevent, or reverse the development of specific diseases, including obesity. A link has been proposed between obesity and the growth promoters (probiotics and antibiotics) that have been used in animals for more than 40 years to induce weight gain. Several species of the Lactobacillus genus that are frequently used as probiotics for human consumption merit particular attention because they are increased in the gut microbiota under high-fat diets, are more abundant in obese humans, and are selected by growth-promoter antibiotics; moreover, the administration of these bacteria in experimental models is linked to the development of obesity. However, other species or strains of the same genus are associated with an antiobesity effect. Newborns and infants are a particularly susceptible population in which the administration of antibiotics or probiotics could be related to the development of obesity in adulthood. [ABSTRACT FROM AUTHOR]