Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov

Enorma shizhengliae sp. nov. and Eggerthella guodeyinii sp. nov., two new members of the family Coriobacteriaceae

Four obligatory anaerobic, Gram-stain-positive, non-motile and rod-shaped organisms (HF-1365^T, HF-1362, HF-1101^T and HF-4214) were isolated from faecal samples of healthy Chinese subjects. Results of 16S rRNA gene sequence analyses showed that these isolates belong to the genera Enorma (strains HF-1365^T and HF-1362) and Eggerthella (strains HF-1101^T and HF-4214), closest to Enorma massiliensis (both 98.6 %) and Eggerthella sinensis (98.0 and 97.8 %), respectively. The whole genome sequences of strains HF-1365^T and HF-1101^T were 2.3 and 4.2 Mb in size with 61.7 and 66.2 mol% DNA G+C content, respectively. The average nucleotide identity and digital DNA-DNA hybridization values indicated that strains HF-1365^T and HF-1101^T represent novel species in the genera Enorma and Eggerthella. Major fatty acid constituents (>10 %) of strains HF-1365^T and HF-1362 were C_12 : 0 (24.7 and 23.9 %), C_14 : 0 (21.9 and 20.6 %) and summed feature 1 (C_15 : 1iso H/C_13 : 0 3OH; 12.8 and 10.8 %); those of strains HF-1101^T and HF-4214 were C_18 : 1  ω9c (32.4 and 33.1 %) and C_16 : 0 (13.9 and 14.0 %). Strain HF-1365^T had phospholipid, glycolipid, lipid and phosphoglycolipid without any known quinones, while strain HF-1101^T had diphosphatidylglycerol as the major polar lipid and MK-7 (80.7 %) as the predominant quinone. On the basis of their phylogenetic and phenotypic characteristics, strains HF-1365^T and HF-1101^T represent two distinct species, respectively, in the genera Enorma and Eggerthella, for which the names Enorma shizhengliae sp. nov. (type strain HF-1365^T=CGMCC 1.17435^T=GDMCC 1.1705^T=JCM 33601^T) and Eggerthella guodeyinii sp. nov. (type strain HF-1101^T=CGMCC 1.17436^T=GDMCC 1.1668^T=JCM 33773^T) are proposed.

Genome Sequence of Enorma sp. Strain Marseille-P9525 T , a Member of a Human Gut Microbiome

Strain Marseille-P9525^T was isolated from the gut microbiota of a 28-year-old woman and exhibits a 2.23-Mb (G+C content, 66.8%) draft genome sequence containing 1,902 protein-coding genes, 49 tRNAs, and 3 rRNAs. The 16S rRNA sequencing and in silico DNA-DNA hybridization indicated that strain Marseille-P9525^T represents a new species to be described.

Strain Marseille-P9525^T was isolated from the gut microbiota of a 28-year-old woman and exhibits a 2.23-Mb (G+C content, 66.8%) draft genome sequence containing 1,902 protein-coding genes, 49 tRNAs, and 3 rRNAs. The 16S rRNA sequencing and in silico DNA-DNA hybridization indicated that strain Marseille-P9525^T represents a new species to be described.

Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11(T), the type strain of Paenibacillus antibioticophila

Paenibacillus antibioticophila strain GD11^T sp. nov. is the type strain of a new species within the genus Paenibacillus. This strain, whose genome is described here, was isolated from human faeces of a 63-year-old woman with multidrug-resistant tuberculosis who was receiving numerous antibiotics at the time of stool collection. P. antibioticophila is a Gram-positive aerobic bacterium. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 5 562 631 bp long genome contains 5084 protein-coding and 71 RNA genes.

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.