Metabolism of Daidzein and Genistein by Gut Bacteria of the Class Coriobacteriia.

The intake of isoflavones is presumed to be associated with health benefits in humans, but also potential adverse effects of isoflavones are controversially discussed. Isoflavones can be metabolized by gut bacteria leading to modulation of the bioactivity, such as estrogenic effects. Especially bacterial strains of the Eggerthellaceae, a well-known bacterial family of the human gut microbiota, are able to convert the isoflavone daidzein into equol. In addition, metabolization of genistein is also described for strains of the Eggerthellaceae. The aim of this study was to identify and investigate gut bacterial strains of the family Eggerthellaceae as well as the narrowly related family Coriobacteriaceae which are able to metabolize daidzein and genistein. This study provides a comprehensive, polyphasic approach comprising in silico analysis of the equol gene cluster, detection of genes associated with the daidzein, and genistein metabolism via PCR and fermentation of these isoflavones. The in silico search for protein sequences that are associated with daidzein metabolism identified sequences with high similarity values in already well-known equol-producing strains. Furthermore, protein sequences that are presumed to be associated with daidzein and genistein metabolism were detected in the two type strains 'Hugonella massiliensis' and Senegalimassilia faecalis which were not yet described to metabolize these isoflavones. An alignment of these protein sequences showed that the equol gene cluster is highly conserved. In addition, PCR amplification supported the presence of genes associated with daidzein and genistein metabolism. Furthermore, the metabolism of daidzein and genistein was investigated in fermentations of pure bacterial cultures under strictly anaerobic conditions and proofed the metabolism of daidzein and genistein by the strains 'Hugonella massiliensis' DSM 101782T and Senegalimassilia faecalis KGMB04484T.

Adlercreutzia rubneri sp. nov., a resveratrol-metabolizing bacterium isolated from human faeces and emended description of the genus Adlercreutzia.

The novel, anaerobic, Gram-positive, rod-shaped bacterial strain, ResAG-91T, was isolated from a faecal sample of a male human volunteer. Analysis of the 16S rRNA gene sequence revealed that strain ResAG-91T showed high similarity to the type strains of Adlercreutzia equolifaciens subsp. equolifaciens and Adlercreutzia equolifaciens subsp. celatus. Analysis of the whole draft genome sequences, i.e. digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), of strain ResAG-91T and the type strains of Adlercreutzia species revealed that strain ResAG-91T represents a novel species of the genus Adlercreutzia. The genome size of strain ResAG-91T is 2.8 Mbp and the G+C content is 63.3 mol%. The major respiratory quinone of strain ResAG-91T was MMK-5 (methylmenaquinone). Major cellular fatty acids were C15 : 0 anteiso, C14 : 0 iso and C14 : 0 2-OH. Galactose and ribose were detected as major whole cell sugars. Furthermore, the peptidoglycan type of strain ResAG-91T was A1γ with meso-diaminopimelic acid. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and five unidentified glycolipids. Strain ResAG-91T was able to metabolize the stilbene resveratrol into dihydroresveratrol. On the basis of this polyphasic approach, including phenotypical, molecular (16S rRNA gene and whole genome sequencing) and biochemical (fatty acids, quinones, polar lipids, peptidoglycan, whole cell sugars, Rapid ID32A and API20A) analyses, we propose the novel species Adlercreutzia rubneri sp. nov. with the type and only strain ResAG-91T (=DSM 111416T=JCM 34176T=LMG 31897T).

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria. However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

Draft Genome Sequences of 13 Isolates of Adlercreutzia equolifaciens, Eggerthella lenta, and Gordonibacter urolithinfaciens, Isolated from Human Fecal Samples in Karlsruhe, Germany.

Here, we report the annotated draft genome sequences of 13 Eggerthellaceae strains isolated from fecal samples from two healthy human volunteers in Karlsruhe, Germany, i.e., Adlercreutzia equolifaciens ResAG-91, Eggerthella lenta MRI-F 36, MRI-F 37, MRI-F 40, ResAG-49, ResAG-88, ResAG-121, and ResAG-145, and Gordonibacter urolithinfaciens ResAG-5, ResAG-26, ResAG-43, ResAG-50, and ResAG-59.

The Putative Caloric Restriction Mimetic Resveratrol has Moderate Impact on Insulin Sensitivity, Body Composition, and the Metabolome in Mice.

SCOPE: Data on resveratrol-(trans-3,5,4'-trihydroxystilbene)-induced caloric-restriction-(CR)-mimicking effects in mice receiving a high-fat diet (HFD) are contradictory. It is hypothesized that this can possibly stem from different bioactivities of resveratrol (RSV) microbial metabolites. METHODS AND RESULTS: C57BL/6Rj mice are fed an ad-libitum HFD supplemented with RSV or its metabolites, dihydroresveratrol (DHR) and lunularin (LUN) (≈28 mg (dihydro)stilbene kg-1 mouse per day). A 40% CR group was included in the study. While CR mice show robust changes in bodyweight and composition, hormone levels and mRNA expression, slight changes are found (more muscle, less adipose tissue) in body composition, leptin, and insulin levels in RSV-supplemented mice compared to ad libitum controls. LUN hardly and DHR does not change the hormone levels measured. Metabolome analysis of serum shows changes in CR mice but only slight, if any, changes in RSV-, DHR-, or LUN-supplemented mice compared to the controls. Evaluating the capability of RSV and its metabolites to inhibit carbohydrate-hydrolyzing enzymes in vitro, it is found that RSV reduced α-glucosidase activity to a stronger extent than DHR and LUN. CONCLUSION: Decelerated carbohydrate breakdown by RSV may have contributed to the moderate impact of dietary RSV on mouse insulin sensitivity (lowered fasting and post-glucose-bolus insulin levels).

Draft Genome Sequences of Type Strains of Adlercreutzia muris and Ellagibacter urolithinifaciens, Belonging to the Family Eggerthellaceae.

Here, we report the annotated draft genome sequences of two type strains belonging to the family Eggerthellaceae within the class Coriobacteriia (phylum Actinobacteria), Adlercreutzia muris WCA-131-CoC-2 (= DSM 29508 = KCTC 15543) and Ellagibacter urolithinifaciens CEBAS 4A (= CCUG 70284 = DSM 104140).

Gordonibacter faecihominis is a later heterotypic synonym of Gordonibacter urolithinfaciens.

In this study, the phylogenetic position of Gordonibacter faecihominis and Gordonibacter urolithinfaciens was investigated using phenotypic and molecular (rep-PCR, ARDRA, 16S rRNA gene sequencing and whole-genome sequencing) methods. Our results show that Gordonibacter faecihominis cannot be distinguished from Gordonibacter urolithinfaciens on the basis of the results of this polyphasic approach. Therefore, it is proposed that the two species Gordonibacter faecihominis and Gordonibacter urolithinfaciens belong to the same species.

Resveratrol, lunularin and dihydroresveratrol do not act as caloric restriction mimetics when administered intraperitoneally in mice.

Resveratrol as well as caloric restriction were shown to extend lifespan in some model organisms and may possibly delay onset of ageing-related diseases in humans. Yet, resveratrol supplementation does not always extend lifespan of animal models or improve health status of humans. Because of interindividual differences in human microbiota, resveratrol metabolite production in the gut differs. While some individuals produce lunularin and dihydroresveratrol in their gut, others produce dihydroresveratrol only. Therefore, we addressed the question whether these metabolites differ in their biological impact on ageing and intraperitoneally injected 13-month-old C57BL/6JRj mice on an ad-libitum (AL) HFD with resveratrol, dihydroresveratrol or lunularin (24 mg/kg bodyweight; 3 times/week). Compared to mice injected with vehicle (AL-control), resveratrol and dihydroresveratrol did not change bodyweight and had no impact on insulin or glucose levels while lunularin slightly reduced feed intake and bodyweight gain. CR-mice showed lowered cholesterol, insulin and leptin levels, elevated adiponectin and phosphorylated AMPK levels in liver as well as increased transcription of Pck1 and Pgc1α when compared to the AL-control. In contrast, injections with the test substances did not change these parameters. We therefore conclude that in our model, resveratrol, lunularin and dihydroresveratrol did not act as CR mimetics.

Draft Genome Sequences of Type Strains of Gordonibacter faecihominis, Paraeggerthella hongkongensis, Parvibacter caecicola,Slackia equolifaciens, Slackia faecicanis, and Slackia isoflavoniconvertens.

Here, we report the annotated draft genome sequences of six type strains of the family Eggerthellaceae, Gordonibacter faecihominis JCM 16058, Paraeggerthella hongkongensis DSM 16106, Parvibacter caecicola DSM 22242, Slackia equolifaciens DSM 24851, Slackia faecicanis DSM 17537, and Slackia isoflavoniconvertens DSM 22006.

Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis MS 501, a Potential Human Pathogen Isolated from Red Lettuce (Lactuca sativa var. capitata) in Karlsruhe, Germany.

We report here the genome sequence of Salmonella enterica subsp. enterica serovar Enteritidis MS 501, a potential human pathogen isolated from red lettuce (Lactuca sativa var. capitata) in Karlsruhe, Germany. The assembled genome size was 4,700,322 bp. A total of 4,560 coding genes, 16 rRNAs, 78 tRNAs, and 15 noncoding RNAs were predicted.

Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces.

Two novel, anaerobic, Gram-positive, rod-shaped bacterial strains, ResAG-85T and ResAG-96T, were isolated from a faecal sample of a male human. 16S rRNA gene sequences analyses indicated that these strains represent a distinct lineage within the family Eggerthellaceae. Strain ResAG-85T showed 92.3 % similarity to the type strains of the genera Eggerthella and Gordonibacter. Strain ResAG-96T clustered together with Paraeggerthella hongkongensis and the newly (but not validly) published genus 'Arabia massiliensis' (94.8 % similarity). Analysis of quinones revealed that MK-5 (21 % in ResAG-85T and 95 % in ResAG-96T) and MK-7 (53 % in strain ResAG-85T) were present, which were described for the first time for members of the Eggerthellaceae. Furthermore, MK-6 was present in both strains (25 % ResAG-85T and 5 % in ResAG-96T). The polar lipids detected in ResAG-85T and ResAG-96T consisted of eight and six glycolipids, respectively. Both strains possessed three phospholipids, one phosphatidylglycerol and one diphosphatidylglycerol. Analysis of fatty acids revealed that the percentage of total branched fatty acids was relatively high in comparison to related strains with 42 and 50 % of strains ResAG-85T and ResAG-96T but comparable to the value obtained for Gordonibacter pamelaeae DSM 19378T. On the basis of this polyphasic approach including molecular (16S rRNA gene sequencing) and biochemical methods (analysis of fatty acids, quinones, polar lipids, Rapid ID 32A and API 20A), the new genera and species Rubneribacter badeniensis with ResAG-85T (=DSM 105129T=JCM 32272T) and Enteroscipio rubneri with ResAG-96T (=DSM 105130T=JCM 32273T) as the type and only strains are described.