Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut

Abstract

The human gut is composed of a large diversity of microorganisms, which have been poorly described. Here, using culturomics, a new concept based on the variation in culture conditions and MALDI‐TOF MS identification, we proceed to explore the microbial diversity of the complex ecosystem of the human gut. Using this approach, we isolated strain AT8T (=CSUR P2118 = DSM 101782) from stool specimens collected from a 51‐year‐old obese French woman. Strain AT8T is a strictly anaerobic, nonmotile, nonspore‐forming gram‐positive coccus that do not exhibit catalase and oxidase activities. 16S rDNA‐based identification of strain AT8T demonstrated 92% gene sequence similarity with Eggerthella lenta DSM 2243, the phylogenetically closed validly named type species. Here, we present a set of features for the strain AT8T and the description of its complete genome sequence and annotation. The 2,091,845 bp long genome has a G+C content of 63.46% and encodes1,849 predicted genes; 1,781 were protein‐coding genes, and 68 were RNAs. On the basis of the characteristics reported here, we propose the creation of a new bacterial genus Hugonella gen. nov., belonging to the Eggerthellaceae family and including Hugonella massiliensis gen. nov., sp. nov., strain AT8T as the type strain.

Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool

“…To date, more than 2000 different bacterial species belonging to the human gut microbiota have been reported [4] . In our laboratory, we have developed a new technique named culturomics to isolate previously uncultured human gut bacteria [5] , [6] . Basically, stool samples are cultured under various conditions and all isolated colonies are identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).…”

Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut

“…A wet mount was performed to determine motility of both bacteria and a Leica DM 1000 photonic microscope (Leica Microsystems) at a 1,000× total magnification. A Tecnai G20 (FEI company, Limeil‐Brevannes, France) electron microscope was used for bacterial cell imaging at an operating voltage of 60 kV, as previously described (Elsawi et al, ).…”

Taxonogenomics description of Parabacteroides timonensis sp. nov. isolated from a human stool sample

“…Isolated bacterial colonies identification trials were done first by using MALDI‐TOF MS analysis as previously described (Elsawi et al., ). In case of MALDI‐TOF MS identification failure, complete 16S rRNA sequencing was performed for further analysis with the same protocol used in our previous studies (Elsawi et al., ). Complete 16S rRNA nucleotide sequence are assembled and manipulated using CodonCode Aligner software (http://www.codoncode.com) and blasted in the online PubMed National Center for Biotechnology Information (NCBI) database for phylogenetic analysis.…”

“…Genomic DNA (gDNA) of Marseille‐P3236 T strain was extracted as previously described with 50 μL being eluted (Elsawi et al., ). Quantification was done using the Qubit assay with the high sensitivity kit (Life technologies, Carlsbad, CA, USA) and determined to be 134 ng/μl.…”

“…Genomic DNA (gDNA) of Marseille-P3236 T strain was extracted as previously described with 50 μL being eluted (Elsawi et al, 2017).…”