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Google Books Team introduces “culturomics” in Science Magazine | Francis' world inside out
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Citations Publications citing this paper. Therefore we propose the creation of the new genus "Gorbachella" Gor. NL gen. GD7 is the type strain of the species Gorbachella massiliensis ma. The colonies appeared to be translucent, rough, non-hemolytic, motile, non-spore forming, with 1 mm size. The cells were rod-shaped with Gram-negative staining. Oxidase and catalase activities were negative.
The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species
Strain GD5T showed So we propose to classify GD5T as a new species within the genus Fenollaria in the phylum Firmicutes 4. GD5 is the type strain of the species "Fenollaria timonensis" ti. The colonies appeared translucent, rough, non-hemolytic, motile, non-spore forming, with 1 mm size.
The cells were Gram-negative. Catalase and oxidase activities were negative.
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Strain GD4 presented a sequence identity of We propose to putatively classify GD4 as a new member of the genus Intestinimonas in the phylum Firmicutes 4. GD4 is the type strain of the species "Intestinimonas timonensis" ti. The cells were rod-shaped with Gram-positive staining. Then we propose the creation of the new species "Collinsella ihuae " within the phylum Actinobacteria 4. GD8 is the type strain of the species "Collinsella ihuae" i. Deposit in a culture collection. Abstract of research paper on Biological sciences, author of scientific article — G.
Durand, F. We used two African stools, both from healthy young males living in rural Senegal, and a stool from a French obese individual with a body mass index of Moreover, with the aim of selecting a minority population, we used antibiotics, both active and passive filtration, and bacteriophages. When the strains remained unrecognized, the 16S rRNA gene was sequenced. We studied stool samples from two young lean Africans from a rural environment in Senegal Fig. This analysis resulted in the identification of 99 bacterial species, 42 of which had never been found in the human gut Fig.
Phylogenetic tree representing the new bacterial species and genera obtained by culturomics. Red labels indicate the new species found in the Senegalese patients and obese patient. Tree branches in red, dark green, purple and blue represent the phyla Bacteroidetes , Proteobacteria , Actinobacteria , and Firmicutes , respectively. Green squares denote new species found in the obese patient. Dark circles indicate that the genome sequence is available for the closest neighbour species. In addition to the better training of the operators, as and when necessary, each previously unknown bacterial spectrum was added to our data bank, facilitating the screening for further studies.
Indeed, with the third stool sample, we tested, under eight different culture conditions, 50— colonies that were indistinguishable in appearance. This experiment allowed us to identify several species, notably those from the genus Enterococcus , for which identification in routine bacteriology is mainly based on colony morphology. Therefore, we used antibiotics in culture media to eliminate sensitive organisms and thus facilitate the identification of resistant ones. First, to identify new proteobacteria, we had to develop alternative strategies, because Escherichia coli is the overwhelmingly dominant bacterial species in the human gut under aerobic conditions.
We used a cocktail of E. Otherwise, an effective method to remove the major bacterial population was active filtration with successive membranes from 5 to 0. Incubation of clinical samples in blood culture bottles is known to promote the growth of Kingella kingae in osteoarticular infections.
This approach yielded three new genera and three new species. Addition of sheep blood to the blood culture bottle allowed us to identify three additional species. To increase the growth of bacteria under culture conditions that mimic their natural environment, and drawing from previous studies on environmental bacteria [ 9 ], we used sterile rumen fluid [ 3 ] Fig.
The majority of the isolated species These results provide guidance for future culturomics studies, which will benefit from using the set of conditions shown to be efficient in this study before developing new culture approaches. The typical diameter of the isolated bacteria ranged from 0.
However, the largest isolated bacterium, Microvirga massiliensis , reached 2. S3 , suggesting that this is a new strain of Marseillevirus. Preliminary work indicates the presence of antibodies against this virus in the serum and stool of the subject. The genome sizes of the new bacteria ranged from 1. Among the predicted gene products of the new genomes, 2. Altogether, the present study yielded c. For the three stools taken together, the microbial culturomics approach yielded bacterial species from seven phyla and genera, whereas pyrosequencing identified species from six phyla and 91 genera.
Altogether, phylotypes of previously uncultured bacteria were identified. Finally, the molecular techniques did not identify pathogenic bacteria, such as Salmonella , that were detected by culturomics Fig. Identification of bacteria in the human gut by culturomics and metagenomics. The overlap between the two sets of species, i.
The dashed coloured lines show the phylum membership of the respective genus node. The two shapes with dashed lines at left and right represent the bacterial and fungal genera identified by only one technique pyrosequencing or culturomics , whereas the shape in the middle represents the genera identified by both culturomics and pyrosequencing. The detection thresholds of metagenomic and culturomic approaches. The detection threshold of metagenomic methods correlates with the concentration of bacteria in the investigated sample divided by the number of generated sequences.
The blue pointed shapes show the detection depth of different published metagenomic analyses of the human gut microbiome. The upper dotted red line shows the detection threshold of the most powerful available metagenomic methods, the middle line shows the detection threshold of PCR, and the lower line shows the detection threshold of culturomics. The latter two thresholds were determined by detection of Staphylococcus aureus that was added to the samples in varying concentrations indicated by green pointed shapes.
Among the cultivated bacterial species, 29 were identified only after several days of incubation in an anaerobic blood culture bottle, so their concentrations in the original samples could not be estimated. Metagenomics is currently thought of as the mainstream of microbiome studies, in particular as applied to the human gut. Unexpectedly, however, in a direct comparison, we described more known bacterial species by systematically applying a large sample of culture conditions the approach we denoted culturomics than by pyrosequencing Fig.
Moreover, we found a dramatic divergence between the sets of bacteria identified by the two approaches at the level of both species and genera. The detection by culturomics of numerous bacteria that go undetected in genomic and metagenomic studies is far from being trivial, even if most of these microorganisms are of low abundance. Undoubtedly, a minority population, as in the famous short story [ 28 ], can have a substantial effect on the ecology of the gut microbiota and on human health. Indeed, c. In support of this conclusion, culture methods allowed the detection of Staphylococcus aureus that was added to the stools at a concentration that was times lower than the concentration detectable by molecular tools Fig.
Nevertheless, this limited effort yielded bacterial species that have not been previously reported from the human gut microbiota. Genome sequencing of these bacteria would increase by c. The present limited culturomics study shows that microbial biodiversity in the human gut is substantially broader than predicted on the basis of genomic and metagenomic analyses [ 27 , 30 ].
In fact, each isolated microorganism is one among the possible viable solutions to the evolutionary equation whose constants are the selective constraints of the environment, corresponding here to the human gut. In the future, the use of the most effective conditions and automatic colony picking will further deepen this field of research. The authors wish to thank B. Davoust for the sheep rumen collection, R.
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