BackgroundThe dietary methylamines choline, carnitine, and phosphatidylcholine are used by the gut microbiota to produce a range of metabolites, including trimethylamine (TMA). However, little is known about the use of trimethylamine N-oxide (TMAO) by this consortium of microbes.ResultsA feeding study using deuterated TMAO in C57BL6/J mice demonstrated microbial conversion of TMAO to TMA, with uptake of TMA into the bloodstream and its conversion to TMAO. Microbial activity necessary to convert TMAO to TMA was suppressed in antibiotic-treated mice, with deuterated TMAO being taken up directly into the bloodstream. In batch-culture fermentation systems inoculated with human faeces, growth of Enterobacteriaceae was stimulated in the presence of TMAO. Human-derived faecal and caecal bacteria (n = 66 isolates) were screened on solid and liquid media for their ability to use TMAO, with metabolites in spent media analysed by 1H-NMR. As with the in vitro fermentation experiments, TMAO stimulated the growth of Enterobacteriaceae; these bacteria produced most TMA from TMAO. Caecal/small intestinal isolates of Escherichia coli produced more TMA from TMAO than their faecal counterparts. Lactic acid bacteria produced increased amounts of lactate when grown in the presence of TMAO but did not produce large amounts of TMA. Clostridia (sensu stricto), bifidobacteria, and coriobacteria were significantly correlated with TMA production in the mixed fermentation system but did not produce notable quantities of TMA from TMAO in pure culture.ConclusionsReduction of TMAO by the gut microbiota (predominantly Enterobacteriaceae) to TMA followed by host uptake of TMA into the bloodstream from the intestine and its conversion back to TMAO by host hepatic enzymes is an example of metabolic retroconversion. TMAO influences microbial metabolism depending on isolation source and taxon of gut bacterium. Correlation of metabolomic and abundance data from mixed microbiota fermentation systems did not give a true picture of which members of the gut microbiota were responsible for converting TMAO to TMA; only by supplementing the study with pure culture work and additional metabolomics was it possible to increase our understanding of TMAO bioconversions by the human gut microbiota.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0461-0) contains supplementary material, which is available to authorized users.

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A Gram-negative, non-spore-forming, motile, moderately halophilic, aerobic, rod-shaped bacterium, designated strain FP2.5T , was isolated from the inland hypersaline lake Fuente de Piedra, a saline-wetland wildfowl reserve located in the province of Má laga in southern Spain. Strain FP2.5 T was subjected to a polyphasic taxonomic study. It produced colonies with a lightyellow pigment. Strain FP2.5 T grew at salinities of 3-15 % (w/v) and at temperatures of 20-40 6C. The pH range for growth was 5-9. Strain FP2.5 T was able to utilize various organic acids as sole carbon and energy source. Its major fatty acids were C 16 : 0 , C 18 : 1 v9c and C 16 : 1 v9c. The DNA G+C content was 58.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FP2.5 T appeared to be a member of the genus Marinobacter and clustered closely with the type strains of Marinobacter segnicrescens, Marinobacter bryozoorum and Marinobacter gudaonensis (levels of 16S rRNA gene sequence similarity of 98.1, 97.4 and 97.2 %, respectively). However, DNA-DNA relatedness between the new isolate and the type strains of its closest related Marinobacter species was low; levels of DNA-DNA relatedness between strain FP2. During the course of screening of halophilic microorganisms originating from water samples taken from the inland hypersaline lake Fuente de Piedra, a saline-wetland wildfowl reserve located in the province of Málaga (4 u 469 W 37 u 079 N), in southern Spain, a moderately halophilic, Gram-negative bacterium, designated strain FP2.5 T , was isolated. Strain FP2.5 T is characterized herein by using a polyphasic approach, including phylogenetic analysis based on 16S rRNA gene sequences, genomic relatedness, and chemotaxonomic and phenotypic properties. The results indicate that strain FP2.5T represents a novel species of the genus Marinobacter.Strain FP2.5T was isolated on MH complex medium supplemented with a balanced mixture of sea salts. This medium contained (per litre distilled water) 10 g yeast extract (Difco), 5 g proteose peptone no. 3 (Difco) and 1 g glucose (Ventosa et al., 1982), and was supplemented with the balanced mixture of sea salts of Subov (1931). The pH was adjusted to 7.2 with 1 M NaOH. The medium was solidified with 20 g Bacto agar (Difco) per litre. The isolate was maintained and routinely grown aerobically on MH complex medium with 7.5 % (w/v) total salts at 35 u C except where indicated otherwise.The methods used for phenotypic characterization have been described previously in detail (Ventosa et al., 1982;Quesada et al., 1983;Prado et al., 1991Prado et al., , 2006Mata et al., 2002;Kharroub et al., 2006). NaCl tolerance was determined at 35 u C in MH growth medium prepared with 0, 0.5, 1, 3, 5, 7.5, 10, 15, 20, 25 or 30 % (w/v) NaCl. Each 50-ml batch of medium was inoculated with 0.1 ml (approximately 10 5 cells ml -1) from an appropriate dilution of a 20-h culture of the novel micro-organism grown in MH medium containing 7.5 % (w/v) salts. The cultures were incubated in a rotary shaker. Viabl...

A Gram-negative, aerobic, moderately halophilic bacterium, designated Set74 T , was isolated from brine of a salt concentrator at Ain Oulmene, Algeria. The strain grew optimally at 37-40 6C, at pH 6.5-7.0 and with 5-7.5 % (w/v) NaCl and used various organic compounds as sole carbon, nitrogen and energy sources. Ubiquinone 9 (Q-9) was the major lipoquinone. The main cellular fatty acids were C 16 : 0 , C 18 : 1 v9c, summed feature 7 (ECL 18.846; C 19 : 0 cyclo v10c and/or C 19 : 1 v6c), C 12 : 0 3-OH, C 16 : 1 v9c, C 18 : 0 and C 12 : 0 . The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 57.4 mol%. The 16S rRNA gene sequence analysis indicated that strain Set74 T was a member of the genus Marinobacter. The closest relatives of strain Set74 T were Marinobacter santoriniensis NKSG1 T (97.5 % 16S rRNA gene sequence similarity) and Marinobacter koreensis DD-M3 T (97.4 %). DNA-DNA relatedness between strain Set74 T and M. santoriniensis DSM 21262 T and M. koreensis DSM 17924 T was 45 and 37 %, respectively. On the basis of the phenotypic, chemotaxonomic and phylogenetic features, a novel species, Marinobacter oulmenensis sp. nov., is proposed. The type strain is Set74 T (5CECT 7499 T 5DSM 22359 T ).The family Alteromonadaceae was created by Ivanova & Mikhailov (2001) to accommodate an assemblage of marine Gram-negative, chemoheterotrophic, straight or curved rods. Members of this group include the genera Aestuariibacter, Agarivorans, Aliagarivorans, Alishewanella, Alteromonas, Bowmanella, Glaciecola, Haliea, Marinimicrobium, Marinobacter, Marinobacterium, Melitea, Microbulbifer, Saccharophagus and Salinimonas (Baumann et al., 1972;Bowman et al., 1998; Ekborg et al., 2005;Gauthier et al., 1992; González et al., 1997;Jean et al., 2006Jean et al., , 2009Jeon et al., 2005;Kurahashi & Yokota, 2004;Lim et al., 2006; Urios et al., 2008a, b;Vogel et al., 2000;Yi et al., 2004). The genus Marinobacter was proposed by Gauthier et al. (1992) with the type species Marinobacter hydrocarbonoclasticus. Members of this genus can be found in different habitats, including marine environments, hypersaline lakes, saline soils and hydrothermal sediments (Martín et al., 2003;Yoon et al., 2004;Handley et al., 2009;Aguilera et al., 2009).A strain, designated Set74 T , was obtained from brine samples collected from the Ain Oulmene salt concentrator (35 u 559 230 N 5 u 179 360 E) in north-eastern Algeria. Isolation was performed in MH medium (containing per litre distilled water: 1 g glucose, 5 g proteose peptone, 5 g yeast extract) and supplemented with 7.5 % (w/v) total salts. The total salts stock solution was prepared at 30 % (w/v) as described by Subov (1931) . The medium was adjusted to pH 7.0 with NaOH and the medium was solidified with 2.0 % agar (Difco). Incubation was at 37 u C and a single colony was streaked at least three times on MH agar to obtain a pure culture. Unless otherwise stated, MH medium was routinely used for cultivation and ph...