Intestinal Ralstonia pickettii augments glucose intolerance in obesity

An altered intestinal microbiota composition has been implicated in the pathogenesis of metabolic disease including obesity and type 2 diabetes mellitus (T2DM). Low grade inflammation, potentially initiated by the intestinal microbiota, has been suggested to be a driving force in the development of insulin resistance in obesity. Here, we report that bacterial DNA is present in mesenteric adipose tissue of obese but otherwise healthy human subjects. Pyrosequencing of bacterial 16S rRNA genes revealed that DNA from the Gram-negative species Ralstonia was most prevalent. Interestingly, fecal abundance of Ralstonia pickettii was increased in obese subjects with pre-diabetes and T2DM. To assess if R. pickettii was causally involved in development of obesity and T2DM, we performed a proof-of-concept study in diet-induced obese (DIO) mice. Compared to vehicle-treated control mice, R. pickettii-treated DIO mice had reduced glucose tolerance. In addition, circulating levels of endotoxin were increased in R. pickettii-treated mice. In conclusion, this study suggests that intestinal Ralstonia is increased in obese human subjects with T2DM and reciprocally worsens glucose tolerance in DIO mice.Peer reviewe

Antibiotics-induced monodominance of a novel gut bacterial order

OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species. DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria. RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals. CONCLUSION: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations

Preparation and preservation of viable Akkermansia muciniphila cells for therapeutic interventions

The anaerobic gut bacterium Akkermansia muciniphila is a well-characterised member of the mucosal microbiota and has shown to be a gut symbiont in human. A. muciniphila has been negatively associated with obesity and its associated metabolic disorders in various human cohorts while treatment with A. muciniphila cells reversed highfat diet-induced obesity and its associated metabolic disorders in mouse models. Therefore, administration of A. muciniphila has been suggested as a possible new therapeutic treatment for these omnipresent diseases. Here we describe a potentially scalable workflow for the preparation and preservation of high numbers of viable cells of A. muciniphila obtained from 1 l laboratory scale growth under strict anaerobic conditions for therapeutic interventions. This resulted in viable A. muciniphila cells with high yields and very high stability, with up to 97.9±4.5% survival for a time period of 1 year at -80 °C in glycerol-amended medium. Moreover, various quality assessment and control procedures were developed to ensure the use of viable cells of A. muciniphila. Several microscopic, culturing, and molecular approaches were applied to monitor the presence, abundance and recovery of A. muciniphila before, during, and after its administration to high-fat treated mice. We show that viable A. muciniphila cells can be recovered from caecal and colon content (up to 1×1010 cells/g), testifying for the efficiency of the described workflow

Mechanistic study on trophic interaction between mucosal keystone species and butyrogenic gut commensals

Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at the mucosal layer creates a steady niche space for bacteria colonization. Mucin, characterized by complex molecular structure, exerts selective nutritional pressure for mucin-degrading bacteria. Mucin degradation by keystone species subsequently drives the local trophic chain and shapes mucosal microbial assembly a.k.a. mucobiome. This study investigates mucin-driven trophic interaction between the specialized mucin-degrader, Akkermansia muciniphila and butyrogenic gut commensals. Co-cultures of A. muciniphila with non-mucolytic butyrogens (Anaerostipes caccae and Eubacterium hallii) were grown in minimal media supplemented with pure mucin. Metabolites (HPLC) and meta-transcriptome (RNA-seq) were studied. Mucin degradation by A. muciniphila produced mucin-derived monosaccharides and metabolites (galactose, fucose, mannose, GlcNAc and acetate) for the growth of butyrogens (A. caccae and E. hallii) resulted in 2mM butyrate production. Interestingly, co-culture of A. muciniphila with E. hallii demonstrated mutual relationship, in which pseudovitamin B12 production by E. hallii facilitated propionate production by A. muciniphila. Cobalamin-dependent methylmalonyl-CoA mutase genes (Amuc_1983 and Amuc_1984) were upregulated in A. muciniphila monoculture, indicated the attempt by A. muciniphila to activate propionate production pathway by synthesizing more key catalytic enzymes. Differential analysis (DESeq2) showed the presence of butyrogens resulted in an altered transcriptional profile of A. muciniphila. E. hallii in particular, incurred high functional impact on A. muciniphila gene expression. Mucosal subpopulation driven by A. muciniphila could result in butyrate and propionate production. Deciphering the underlying mechanism of this microbial tropism is crucial for the understanding of mucosal health and pathophysiology

Mechanistic study on trophic interaction between mucosal keystone species and butyrogenic gut commensals

Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at the mucosal layer creates a steady niche space for bacteria colonization. Mucin, characterized by complex molecular structure, exerts selective nutritional pressure for mucin-degrading bacteria. Mucin degradation by keystone species subsequently drives the local trophic chain and shapes mucosal microbial assembly a.k.a. mucobiome. This study investigates mucin-driven trophic interaction between the specialized mucin-degrader, Akkermansia muciniphila and butyrogenic gut commensals. Co-cultures of A. muciniphila with non-mucolytic butyrogens (Anaerostipes caccae and Eubacterium hallii) were grown in minimal media supplemented with pure mucin. Metabolites (HPLC) and meta-transcriptome (RNA-seq) were studied. Mucin degradation by A. muciniphila produced mucin-derived monosaccharides and metabolites (galactose, fucose, mannose, GlcNAc and acetate) for the growth of butyrogens (A. caccae and E. hallii) resulted in 2mM butyrate production. Interestingly, co-culture of A. muciniphila with E. hallii demonstrated mutual relationship, in which pseudovitamin B12 production by E. hallii facilitated propionate production by A. muciniphila. Cobalamin-dependent methylmalonyl-CoA mutase genes (Amuc_1983 and Amuc_1984) were upregulated in A. muciniphila monoculture, indicated the attempt by A. muciniphila to activate propionate production pathway by synthesizing more key catalytic enzymes. Differential analysis (DESeq2) showed the presence of butyrogens resulted in an altered transcriptional profile of A. muciniphila. E. hallii in particular, incurred high functional impact on A. muciniphila gene expression. Mucosal subpopulation driven by A. muciniphila could result in butyrate and propionate production. Deciphering the underlying mechanism of this microbial tropism is crucial for the understanding of mucosal health and pathophysiology

Genome assembly of a novel psychrotolerance bacterium, Trichococcus ART1 .

A psychrotolerant anaerobe, strain ART1T, was isolated from a psychrophilic anaerobic digester treating . 16S rRNA gene sequence of strain ART1T was highly similar to those of other Trichococcus species (> 99%), but digital DNA-DNA hybridization (dDDH) values were lower than 70% indicating that strain ART1 is a new species of the genus Trichococcus. Cells of strain ART1T were immotile cocci and stained Gram-positive. Growth was optimal at pH 7.5 and cells could grow in a temperature range of 0 to 37°C (optimum 30°C). Strain ART1T could degrade several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate, and ethanol.

Genome assembly of a novel psychrotolerance bacterium, Trichococcus ART1 .

A psychrotolerant anaerobe, strain ART1T, was isolated from a psychrophilic anaerobic digester treating . 16S rRNA gene sequence of strain ART1T was highly similar to those of other Trichococcus species (> 99%), but digital DNA-DNA hybridization (dDDH) values were lower than 70% indicating that strain ART1 is a new species of the genus Trichococcus. Cells of strain ART1T were immotile cocci and stained Gram-positive. Growth was optimal at pH 7.5 and cells could grow in a temperature range of 0 to 37°C (optimum 30°C). Strain ART1T could degrade several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate, and ethanol.

Genome assembly of a novel psychrotolerance bacterium, Trichococcus ART1 .

A psychrotolerant anaerobe, strain ART1T, was isolated from a psychrophilic anaerobic digester treating . 16S rRNA gene sequence of strain ART1T was highly similar to those of other Trichococcus species (> 99%), but digital DNA-DNA hybridization (dDDH) values were lower than 70% indicating that strain ART1 is a new species of the genus Trichococcus. Cells of strain ART1T were immotile cocci and stained Gram-positive. Growth was optimal at pH 7.5 and cells could grow in a temperature range of 0 to 37°C (optimum 30°C). Strain ART1T could degrade several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate, and ethanol.

Mechanistic study on trophic interaction between mucosal keystone species and butyrogenic gut commensals

Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at the mucosal layer creates a steady niche space for bacteria colonization. Mucin, characterized by complex molecular structure, exerts selective nutritional pressure for mucin-degrading bacteria. Mucin degradation by keystone species subsequently drives the local trophic chain and shapes mucosal microbial assembly a.k.a. mucobiome. This study investigates mucin-driven trophic interaction between the specialized mucin-degrader, Akkermansia muciniphila and butyrogenic gut commensals. Co-cultures of A. muciniphila with non-mucolytic butyrogens (Anaerostipes caccae and Eubacterium hallii) were grown in minimal media supplemented with pure mucin. Metabolites (HPLC) and meta-transcriptome (RNA-seq) were studied. Mucin degradation by A. muciniphila produced mucin-derived monosaccharides and metabolites (galactose, fucose, mannose, GlcNAc and acetate) for the growth of butyrogens (A. caccae and E. hallii) resulted in 2mM butyrate production. Interestingly, co-culture of A. muciniphila with E. hallii demonstrated mutual relationship, in which pseudovitamin B12 production by E. hallii facilitated propionate production by A. muciniphila. Cobalamin-dependent methylmalonyl-CoA mutase genes (Amuc_1983 and Amuc_1984) were upregulated in A. muciniphila monoculture, indicated the attempt by A. muciniphila to activate propionate production pathway by synthesizing more key catalytic enzymes. Differential analysis (DESeq2) showed the presence of butyrogens resulted in an altered transcriptional profile of A. muciniphila. E. hallii in particular, incurred high functional impact on A. muciniphila gene expression. Mucosal subpopulation driven by A. muciniphila could result in butyrate and propionate production. Deciphering the underlying mechanism of this microbial tropism is crucial for the understanding of mucosal health and pathophysiology

Bacteroides thetaiotaomicron fosters the growth of butyrate-producing anaerostipes caccae in the presence of lactose and total human milk carbohydrates

The development of infant gut microbiota is strongly influenced by nutrition. Human milk oligosaccharides (HMOSs) in breast milk selectively promote the growth of glycan-degrading microbes, which lays the basis of the microbial network. In this study, we investigated the trophic interaction between Bacteroides thetaiotaomicron and the butyrate-producing Anaerostipes caccae in the presence of early-life carbohydrates. Anaerobic bioreactors were set up to study the monocultures of B. thetaiotaomicron and the co-cultures of B. thetaiotaomicron with A. caccae in minimal media supplemented with lactose or a total human milk carbohydrate fraction. Bacterial growth (qPCR), metabolites (HPLC), and HMOS utilization (LC-ESI-MS2) were monitored. B. thetaiotaomicron displayed potent glycan catabolic capability with differential preference in degrading specific low molecular weight HMOSs, including the neutral trioses (2′-FL and 3-FL), neutral tetraoses (DFL, LNT, LNnT), neutral pentaoses (LNFP I, II, III, V), and acidic trioses (3′-SL and 6′-SL). In contrast, A. caccae was not able to utilize lactose and HMOSs. However, the signature metabolite of A. caccae, butyrate, was detected in co-culture with B. thetaiotaomicron. As such, A. caccae cross-fed on B. thetaiotaomicron-derived monosaccharides, acetate, and d-lactate for growth and concomitant butyrate production. This study provides a proof of concept that B. thetaiotaomicron could drive the butyrogenic metabolic network in the infant gut.</p