Schaedlerella arabinosiphila gen. nov., sp. nov., a D-arabinose-utilizing bacterium isolated from faeces of C57BL/6J mice that is a close relative of Clostridium species ASF 502
The use of gnotobiotics has attracted wide interest in recent years due to technological advances that have revealed the importance of host-associated microbiomes for host physiology and health. One of the oldest and most important gnotobiotic mouse model, the altered Schaedler flora (ASF) has been used for several decades. ASF comprises eight different bacterial strains, which have been characterized to different extent, but only a few are available through public strain collections. Here, the isolation of a close relative of one of the less-studied ASF strains, Clostridium species ASF 502, from faeces of C57BL/6J mice is reported. Isolate TLL-A1T shares 99.5 % 16S rRNA gene sequence identity with Clostridium species ASF 502 and phylogenetic analyses indicate that both strains belong to the uncultured so-called ‘Lachnospiraceae UCG 006’ clade. The rare sugar d-arabinose was used as a sole carbon source in the anaerobic isolation medium. Results of growth experiments with TLL-A1T on different carbon sources and analysis of its ~6.5 Gb indicate that TLL-A1T harbours a large gene repertoire that enables it to utilize a variety of carbohydrates for growth. Comparative genome analyses of TLL-A1T and Clostridium species ASF 502 reveal differences in genome content between the two strains, in particular with regards to carbohydrate-activating enzymes. Based on genomic, molecular and phenotypic differences, we propose to classify strain TLL-A1T (DSM 106076T=KCTC 15657T) as a representative of a new genus and a new species, for which we propose the name Schaedlerella arabinosiphila gen. nov., sp. nov.
DewhirstFE,
ChienCC,
PasterBJ,
EricsonRL,
OrcuttRP et al. Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl Environ Microbiol1999; 65:3287–3292[PubMed]
CollinsMD,
LawsonPA,
WillemsA,
CordobaJJ,
Fernandez-GarayzabalJ et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol1994; 44:812–826 [View Article][PubMed]
LawsonPA,
RaineyFA.
Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol2016; 66:1009–1016 [View Article][PubMed]
ParksDH,
ChuvochinaM,
WaiteDW,
RinkeC,
SkarshewskiA et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol2018; 36:996–1004 [View Article][PubMed]
StamatakisA.
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics2006; 22:2688–2690 [View Article][PubMed]
YarzaP,
YilmazP,
PruesseE,
GlöcknerFO,
LudwigW et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol2014; 12:635–645 [View Article][PubMed]
WannemuehlerMJ,
OverstreetAM,
WardDV,
PhillipsGJ.
Draft genome sequences of the altered schaedler flora, a defined bacterial community from gnotobiotic mice. Genome Announc2014; 2:e0028700214 [View Article][PubMed]
ParksDH,
ImelfortM,
SkennertonCT,
HugenholtzP,
TysonGW.
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res2015; 25:1043–1055 [View Article][PubMed]
CarattoliA,
ZankariE,
García-FernándezA,
Voldby LarsenM,
LundO et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother2014; 58:3895–3903 [View Article][PubMed]
BrettinT,
DavisJJ,
DiszT,
EdwardsRA,
GerdesS et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep2015; 5:8365 [View Article][PubMed]
ZhangH,
YoheT,
HuangL,
EntwistleS,
WuP et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res2018; 46:W95–W101 [View Article][PubMed]
BuskPK,
PilgaardB,
LezykMJ,
MeyerAS,
LangeL.
Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function. BMC Bioinformatics2017; 18:214 [View Article][PubMed]
QinQL,
XieBB,
ZhangXY,
ChenXL,
ZhouBC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol2014; 196:2210–2215 [View Article][PubMed]
YoonSH,
HaSM,
LimJ,
KwonS,
ChunJ.
A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek2017; 110:1281–1286 [View Article][PubMed]
BrownDP,
Ganova-RaevaL,
GreenBD,
WilkinsonSR,
YoungM et al. Characterization of spo0A homologues in diverse Bacillus and Clostridium species identifies a probable DNA-binding domain. Mol Microbiol1994; 14:411–426 [View Article][PubMed]
KitaharaM,
TakamineF,
ImamuraT,
BennoY.
Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7alpha-dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces. Int J Syst Evol Microbiol2000; 50:971–978 [View Article][PubMed]
MorrisGN,
WinterJ,
CatoEP,
RitchieAE,
BokkenheuserVD.
Clostridium scindens sp. nov., a Human Intestinal Bacterium with Desmolytic Activity on Corticoids. Int J Syst Bacteriol1985; 35:478–481 [View Article]
SakamotoM,
IinoT,
OhkumaM.
Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int J Syst Evol Microbiol2017; 67:1219–1227 [View Article][PubMed]
TogoAH,
DiopA,
BittarF,
MaraninchiM,
ValeroR et al. Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov. Antonie van Leeuwenhoek2018; 111:2107–2128 [View Article][PubMed]
Schaedlerella arabinosiphila gen. nov., sp. nov., a D-arabinose-utilizing bacterium isolated from faeces of C57BL/6J mice that is a close relative of Clostridium species ASF 502