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.

Togo, Amadou Hamidou; Diop, Awa; Bittar, Fadi; Maraninchi, Marie; Valéro, René; Armstrong, Nicholas; Dubourg, Grégory; Labas, N.; Richez, Magali; Delerce, Jérémy; Levasseur, Anthony; Fournier, Pierre‐Edouard; Raoult, Didier; Million, Matthieu

doi:10.1007/s10482-018-1104-y

“…Ruminococcus torques represented by two strains in the analyzed set of genomes shows the highest variability of vitamin phenotypes (NVP = 6; OPVS = 3), suggesting that these strains could be incorrectly classified. Indeed, based on phenotypic, biochemical, phylogenetic and genomic evidence one of these strains has recently been reclassified as Mediterraneibacter torques ATCC 27756 (Togo et al, 2018). From an evolutionary perspective, the observed cases of intraspecies variability of vitamin phenotypes can be explained by either loss or acquisition of vitamin biosynthesis genes, which are often co-localized into gene clusters on the chromosome.…”

Section: Resultsmentioning

confidence: 99%

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

Rodionov

¹

,

Arzamasov

²

,

Khoroshkin

³

et al. 2019

View full text Add to dashboard Cite

The human gut microbiome harbors a diverse array of metabolic pathways contributing to its development and homeostasis via a complex web of diet-dependent metabolic interactions within the microbial community and host. Genomics-based reconstruction and predictive modeling of these interactions would provide a framework for diagnostics and treatment of dysbiosis-related syndromes via rational selection of therapeutic prebiotics and dietary nutrients. Of particular interest are micronutrients, such as B-group vitamins, precursors of indispensable metabolic cofactors, that are produced de novo by some gut bacteria (prototrophs) but must be provided exogenously in the diet for many other bacterial species (auxotrophs) as well as for the mammalian host. Cross-feeding of B vitamins between prototrophic and auxotrophic species is expected to strongly contribute to the homeostasis of microbial communities in the distal gut given the efficient absorption of dietary vitamins in the upper gastrointestinal tract. To confidently estimate the balance of microbiome micronutrient biosynthetic capabilities and requirements using available genomic data, we have performed a subsystems-based reconstruction of biogenesis, salvage and uptake for eight B vitamins (B1, B2, B3, B5, B6, B7, B9, and B12) and queuosine (essential factor in tRNA modification) over a reference set of 2,228 bacterial genomes representing 690 cultured species of the human gastrointestinal microbiota. This allowed us to classify the studied organisms with respect to their pathway variants and infer their prototrophic vs. auxotrophic phenotypes. In addition to canonical vitamin pathways, several conserved partial pathways were identified pointing to alternative routes of syntrophic metabolism and expanding a microbial vitamin “menu” by several pathway intermediates (vitamers) such as thiazole, quinolinate, dethiobiotin, pantoate. A cross-species comparison was applied to assess the extent of conservation of vitamin phenotypes at distinct taxonomic levels (from strains to families). The obtained reference collection combined with 16S rRNA gene-based phylogenetic profiles was used to deduce phenotype profiles of the human gut microbiota across in two large cohorts. This analysis provided the first estimate of B-vitamin requirements, production and sharing capabilities in the human gut microbiome establishing predictive phenotype profiling as a new approach to classification of microbiome samples. Future expansion of our reference genomic collection of metabolic phenotypes will allow further improvement in coverage and accuracy of predictive phenotype profiling of the human microbiome.

show abstract

“…The 16S rRNA gene sequence of WCA-9-b2 T was ≥98 % similar to already published sequences of uncultured bacteria isolated from the caecum of both lean (DQ815562 [26], JQ084505 [27] and EF602954 [28]) and obese (EF098864 [29]) laboratory mice. All the closest relatives with a validly published name at EzBioCloud belonged to the order Clostridiales : Dorea longicatena (AAXB02000032, 94.9 % sequence identity), Ruminococcus gnavus (proposed but not validated as Mediterraneibacter gnavus [30]; AAYG02000025, 94.8%), Clostridium scindens (ABFY02000057, 94.3%), Dorea formicigenerans (AAXA02000006, 94.2%), Ruminococcus lactaris (proposed but not validated as Mediterraneibacter lactaris [30]; ABOU02000049, 93.8%), Clostridium hylemonae (AB023972, 93.7%), Merdimonas faecis (KP966093, 93.7%) , Faecalicatena contorta (FR749945, 93.5%) and Faecalicatena fissicatena (LDAQ01000152, 92.9%) ().…”

Section: S Rrna Gene Phylogenymentioning

confidence: 99%

Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

Rasmussen

¹

,

Streidl

²

,

Hitch

³

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

A bacterial strain, designated WCA-9-b2T, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate was rod-shaped, strictly anaerobic, spore-forming, non-motile and Gram-stain-positive, under the conditions tested. Colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the order Clostridiales with Dorea longicatena ATCC 27755T (94.9 % sequence identity), Ruminococcus gnavus ATCC 29149T (94.8%) and Clostridium scindens ATCC 35704T (94.3%) being the closest relatives. Whole genome sequencing showed an average nucleotide identity <74.23 %, average amino acid identity <64.52–74.67 % and percentage of conserved proteins values <50 % against the nine closest relatives ( D. longicatena , Ruminococcus gnavus , C. scindens , Dorea formicigenerans , Ruminococcus lactaris , Clostridium hylemonae , Merdimonas faecis , Faecalicatena contorta and Faecalicatena fissicatena ). The genome-based G+C content of genomic DNA was 44.4 mol%. The major cellular fatty acids were C16 : 0 (24.5%), C18 : 1 cis9 (19.8 %), C16 : 0 DMA (11.7%), C18 : 0 (8.4%) and C14 : 0 (6.6%). Respiratory quinones were not detected. The predominant metabolic end products of glucose fermentation were acetate and succinate. Production of CO2 and H2 were detected. Based on these data, we propose that strain WCA-9-b2T represents a novel species within a novel genus, for which the name Sporofaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T=CECT 30156T).

show abstract

“…Genome sequencing, assemblage, annotation and comparison were performed as previously described [22], [23], [25]. The genomes of Solobacterium moorei strain RCA59-74 T (NZ_AUKY00000000) [19], Bulleidia extructa strain W 1219 T (NZ_ADFR00000000) [26], Anaerorhabdus furcosa strain VPI 3253 T (NZ_FUWY00000000) [27], Holdemania filiformis strain J1-31B-1 T (NZ_ACCF01000000) [28] and Holdemania massiliensis strain AP2 T (CALK01000000) [29] were used for genome comparison of the strains Marseille-P4301, Marseille-P4302 and Marseille-P4641.…”

Section: Methodsmentioning

confidence: 99%

Lactimicrobium massiliense gen. nov., sp. nov.; Anaerolactibacter massiliensis gen. nov., sp. nov.; Galactobacillus timonensis gen. nov., sp. nov. and Acidipropionibacterium timonense sp. nov. isolated from breast milk from healthy breastfeeding African women

Togo¹,

Diop²,

Camara³

et al. 2019

New Microbes and New Infections

View full text Add to dashboard Cite

Four strains isolated by microbial culturomics from breast milk of healthy mothers from Mali were not identified and characterized by taxono-genomics. This led us to propose the new genera and species Lactimicrobium massiliense , Anaerolactibacter massiliensis and Galactobacillus timonensis containing type strain Marseille-P4301 T (CSUR P4301 T ), Marseille-P4302 T (CSUR P4302 T ) and Marseille-P4641 T (CSUR P4641 T ), respectively. The strain Marseille-P4482 represents a novel species, Acidipropionibacterium timonense, in a previously known genus with type strain being Marseille-P4482 T (CSUR P4482 T ).

show abstract

Cited by 75 publications

References 56 publications

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

Lactimicrobium massiliense gen. nov., sp. nov.; Anaerolactibacter massiliensis gen. nov., sp. nov.; Galactobacillus timonensis gen. nov., sp. nov. and Acidipropionibacterium timonense sp. nov. isolated from breast milk from healthy breastfeeding African women

Contact Info

Product

Resources

About