RESUMEN
Shotgun metagenomics is a powerful, high-resolution technique enabling the study of microbial communities in situ. However, species-level resolution is only achieved after a process of 'binning' where contigs predicted to originate from the same genome are clustered. Such culture-independent sequencing frequently unearths novel microbes, and so various methods have been devised for reference-free binning. As novel microbiomes of increasing complexity are explored, sometimes associated with non-model hosts, robust automated binning methods are required. Existing methods struggle with eukaryotic contamination and cannot handle highly complex single metagenomes. We therefore developed an automated binning pipeline, termed 'Autometa', to address these issues. This command-line application integrates sequence homology, nucleotide composition, coverage and the presence of single-copy marker genes to separate microbial genomes from non-model host genomes and other eukaryotic contaminants, before deconvoluting individual genomes from single metagenomes. The method is able to effectively separate over 1000 genomes from a metagenome, allowing the study of previously intractably complex environments at the level of single species. Autometa is freely available at https://bitbucket.org/jason_c_kwan/autometa and as a docker image at https://hub.docker.com/r/jasonkwan/autometa under the GNU Affero General Public License 3 (AGPL 3).
Asunto(s)
Algoritmos , Biología Computacional/métodos , Genoma Microbiano/genética , Metagenoma/genética , Metagenómica/métodos , Animales , Bacterias/clasificación , Bacterias/genética , Análisis por Conglomerados , Genoma Bacteriano/genética , Humanos , Internet , Reproducibilidad de los ResultadosRESUMEN
Gut bacterial metabolism of dietary flavonoids results in the production of a variety of phenolic acids, whose contributions to health remain poorly understood. Here, we show that supplementation with the commonly consumed flavonoid quercetin impacted gut microbiome composition and resulted in a significant reduction in atherosclerosis burden in conventionally-raised (ConvR) Apolipoprotein E (ApoE) knockout (KO) mice fed a high-MAC (microbiota-accessible carbohydrates) diet. However, this effect was not observed in animals consuming a defined diet containing low levels of MAC. Furthermore, we found that the effect of quercetin on atherosclerosis required gut microbes, as supplementation of this flavonoid to germ-free (GF) ApoE KO mice consuming the high-MAC diet did not affect the development of atherosclerosis. Metabolomic analysis revealed that consumption of quercetin significantly increased plasma levels of benzoylglutamic acid and protocatechuic acid in ConvR mice exposed to the high-MAC diet, while these increases were not observed in GF mice or conventional animals consuming the low-MAC diet supplemented with the flavonoid. Furthermore, levels of these metabolites were negatively associated with atherosclerosis burden. Altogether, these results suggest that the beneficial effects of quercetin on atherosclerosis are influenced by gut microbes and dietary MAC.
RESUMEN
The microbes and microbial pathways that influence host inflammatory disease progression remain largely undefined. Here, we show that variation in atherosclerosis burden is partially driven by gut microbiota and is associated with circulating levels of uric acid (UA) in mice and humans. We identify gut bacterial taxa spanning multiple phyla, including Bacillota, Fusobacteriota, and Pseudomonadota, that use multiple purines, including UA as carbon and energy sources anaerobically. We identify a gene cluster that encodes key steps of anaerobic purine degradation and that is widely distributed among gut-dwelling bacteria. Furthermore, we show that colonization of gnotobiotic mice with purine-degrading bacteria modulates levels of UA and other purines in the gut and systemically. Thus, gut microbes are important drivers of host global purine homeostasis and serum UA levels, and gut bacterial catabolism of purines may represent a mechanism by which gut bacteria influence health.
Asunto(s)
Microbioma Gastrointestinal , Humanos , Animales , Ratones , Homeostasis , Purinas/metabolismo , Bacterias/genética , Bacterias/metabolismo , Ácido Úrico/metabolismoRESUMEN
Age-related disease may be mediated by low levels of chronic inflammation ("inflammaging"). Recent work suggests that gut microbes can contribute to inflammation via degradation of the intestinal barrier. While aging and age-related diseases including Alzheimer's disease (AD) are linked to altered microbiome composition and higher levels of gut microbial components in systemic circulation, the role of intestinal inflammation remains unclear. To investigate whether greater gut inflammation is associated with advanced age and AD pathology, we assessed fecal samples from older adults to measure calprotectin, an established marker of intestinal inflammation which is elevated in diseases of gut barrier integrity. Multiple regression with maximum likelihood estimation and Satorra-Bentler corrections were used to test relationships between fecal calprotectin and clinical diagnosis, participant age, cerebrospinal fluid biomarkers of AD pathology, amyloid burden measured using 11C-Pittsburgh compound B positron emission tomography (PiB PET) imaging, and performance on cognitive tests measuring executive function and verbal learning and recall. Calprotectin levels were elevated in advanced age and were higher in participants diagnosed with amyloid-confirmed AD dementia. Additionally, among individuals with AD dementia, higher calprotectin was associated with greater amyloid burden as measured with PiB PET. Exploratory analyses indicated that calprotectin levels were also associated with cerebrospinal fluid markers of AD, and with lower verbal memory function even among cognitively unimpaired participants. Taken together, these findings suggest that intestinal inflammation is linked with brain pathology even in the earliest disease stages. Moreover, intestinal inflammation may exacerbate the progression toward AD.
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Enfermedad de Alzheimer , Disfunción Cognitiva , Humanos , Anciano , Enfermedad de Alzheimer/metabolismo , Estudios de Cohortes , Péptidos beta-Amiloides/metabolismo , Encéfalo/metabolismo , Tomografía Computarizada por Rayos X , Tomografía de Emisión de Positrones/métodos , Amiloide/metabolismo , Complejo de Antígeno L1 de Leucocito/metabolismo , Biomarcadores/metabolismo , Proteínas tau/metabolismo , Disfunción Cognitiva/patologíaRESUMEN
Soluble human lectins are critical components of innate immunity. Genetic models suggest that lectins influence host-resident microbiota, but their specificity for commensal and mutualist species is understudied. Elucidating lectins' roles in regulating microbiota requires an understanding of which microbial species they bind within native communities. To profile human lectin recognition, we developed Lectin-Seq. We apply Lectin-Seq to human fecal microbiota using the soluble mannose-binding lectin (MBL) and intelectin-1 (hItln1). Although each lectin binds a substantial percentage of the samples (10 to 20%), the microbial interactomes of MBL and hItln1 differ markedly in composition and diversity. MBL binding is highly selective for a small subset of species commonly associated with humans. In contrast, hItln1's interaction profile encompasses a broad range of lower-abundance species. Our data uncover stark differences in the commensal recognition properties of human lectins.
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Inmunidad Innata , Lectinas , Humanos , Lectinas/genéticaRESUMEN
The molecular bases of how host genetic variation impacts the gut microbiome remain largely unknown. Here we used a genetically diverse mouse population and applied systems genetics strategies to identify interactions between host and microbe phenotypes including microbial functions, using faecal metagenomics, small intestinal transcripts and caecal lipids that influence microbe-host dynamics. Quantitative trait locus (QTL) mapping identified murine genomic regions associated with variations in bacterial taxa; bacterial functions including motility, sporulation and lipopolysaccharide production and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and caecal levels of ornithine lipids. Follow-up in vitro and in vivo studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that ornithine lipids have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits including Atf3, which encodes for a transcription factor that plays vital roles in modulating metabolism and immunity. Collectively, these results suggest that ornithine lipids are potentially important for A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.
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Microbioma Gastrointestinal , Verrucomicrobia , Ratones , Animales , Verrucomicrobia/genética , Microbioma Gastrointestinal/genética , Akkermansia/genética , FenotipoRESUMEN
The single-component RcoM transcription factor couples an N-terminally bound heme cofactor with a C-terminal "LytTR" DNA-binding domain. Here the RcoM(Bx)-1 protein from Burkholderia xenovorans LB400 was heterologously expressed and then purified in a form with minimal bound CO (~10%) and was found to stably bind this effector with a nanomolar affinity. DNase I protection assays demonstrated that the CO-associated form binds with a micromolar affinity to two ~60-bp DNA regions, each comprised of a novel set of three direct-repeat binding sites spaced 21 bp apart on center. Binding to each region was independent, while binding to the triplet binding sites within a region was cooperative, depended upon spacing and sequence, and was marked by phased DNase I hyperactivity and protection patterns consistent with considerable changes in the DNA conformation of the nucleoprotein complex. Each protected binding site spanned a conserved motif (5'-TTnnnG-3') that was present, in triplicate, in putative RcoM-binding regions of more than a dozen organisms. In vivo screens confirmed the functional importance of the conserved "TTnnnG" motif residues and their triplet arrangement and were also used to determine an improved binding motif [5'-CnnC(C/A)(G/A)TTCAnG-3'] that more closely corresponds to canonical LytTR domain/DNA-binding sites. A low-affinity but CO-dependent binding of RcoM(Bx)-1 to a variety of DNA probes was demonstrated in vitro. We posit that for the RcoM(Bx)-1 protein, the high CO affinity combined with multiple low-affinity DNA-binding events constitutes a transcriptional "accumulating switch" that senses low but persistent CO levels.
Asunto(s)
Proteínas Bacterianas/metabolismo , Burkholderia/metabolismo , Monóxido de Carbono/metabolismo , Factores de Transcripción/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/aislamiento & purificación , Burkholderia/genética , Clonación Molecular , Huella de ADN , ADN Bacteriano/metabolismo , Expresión Génica , Regulación Bacteriana de la Expresión Génica , Unión Proteica , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/aislamiento & purificaciónRESUMEN
The CO-responsive transcriptional regulator RcoM from Burkholderia xenovorans (BxRcoM) was recently identified as a Cys(thiolate)-ligated heme protein that undergoes a redox-mediated ligand switch; however, the Cys bound to the Fe(III) heme was not identified. To that end, we generated and purified three Cys-to-Ser variants of BxRcoM-2--C94S, C127S, and C130S--and examined their spectroscopic properties in order to identify the native Cys(thiolate) ligand. Electronic absorption, resonance Raman, and electron paramagnetic resonance (EPR) spectroscopies demonstrate that the C127S and C130S variants, like wild-type BxRcoM-2, bind a six-coordinate low-spin Fe(III) heme using a Cys/His ligation motif. In contrast, electronic absorption and resonance Raman spectra of the C94S variant are most consistent with a mixture of five-coordinate high-spin and six-coordinate low-spin Fe(III) heme, neither of which are ligated by a Cys(thiolate) ligand. The EPR spectrum of C94S is dominated by a large, axial high-spin Fe(III) signal, confirming that the native ligation motif is not maintained in this variant. Together, these data reveal that Cys(94) is the distal Fe(III) heme ligand in BxRcoM-2; by sequence alignment, Cys(94) is also implicated as the distal Fe(III) heme ligand in BxRcoM-1, another homologue found in the same organism.
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Burkholderia/química , Cisteína/química , Hemoproteínas/química , Elementos Reguladores de la Transcripción/genética , Secuencia de Aminoácidos , Burkholderia/genética , Cisteína/genética , Variación Genética , Hemoproteínas/genética , Ligandos , Datos de Secuencia Molecular , Estructura Molecular , Alineación de Secuencia , Espectrometría RamanRESUMEN
Low levels of carbon monoxide inhibit the N(2)-dependent growth of Rhodospirillum rubrum unless the â¼100-residue CowN protein is expressed. Expression requires the CO-responsive regulator RcoM and is maximal in cells grown in the presence of CO and a poor nitrogen source, consistent with the role of CowN in N(2) fixation.
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Monóxido de Carbono/metabolismo , Nitrógeno/metabolismo , Rhodospirillum rubrum/crecimiento & desarrollo , Rhodospirillum rubrum/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/biosíntesis , Expresión Génica , Datos de Secuencia Molecular , Fijación del Nitrógeno , Homología de Secuencia de Aminoácido , Factores de Transcripción/metabolismoRESUMEN
Elderberries are good sources of anthocyanins, which are poorly absorbed in the upper gastrointestinal tract but extensively transformed into phenolic metabolites at the colonic level. Because different gut microbiota strains have different metabolism, the catabolism of anthocyanins may lead to interindividual differences in metabolite production. In this work, an anthocyanin-rich elderberry extract was incubated with three single gut microbial strains (Enterobacter cancerogenous, Bifidobacterium dentium, and Dorea longicatena) up to 4 days, to assess differences in their phenolic metabolism. All of the strains degraded the elderberry anthocyanins, but the metabolic pathways followed were different. Although some metabolites were common for all of the strains, a wide disparity was observed in the kind and amount of several phenolic metabolites produced by each species. These in vitro preliminary results may be of help in the interpretation of the bioavailability of anthocyanins and give a clue to understand interindividual variability in metabolite production.
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Antocianinas/metabolismo , Bifidobacterium/metabolismo , Clostridiales/metabolismo , Enterobacter/metabolismo , Microbioma Gastrointestinal , Extractos Vegetales/metabolismo , Sambucus/metabolismo , Colon/metabolismo , Colon/microbiología , Frutas/metabolismo , Humanos , Redes y Vías MetabólicasRESUMEN
SCOPE: Increased fruit consumption is associated with reduced risk of colitis. It has been investigated whether the anti-colitic effects of the polyphenol-rich aronia berry (Aronia mitschurinii 'Viking') are mediated through Th17 and Treg. METHODS AND RESULTS: Colitis is induced in recombinase activating gene-1 deficient mice injected with syngeneic CD4+ CD62L+ naïve T cells. Mice consume either 4.5% w/w aronia-berry-supplemented or a control diet concurrent with T cell transfer. The extent of colitis and immunocyte populations are evaluated at weeks 3 to 7 after transfer. Aronia consumption prevents colitic wasting and reduces colon weight/length ratios relative to the control diet at weeks 5 and 7. Compared to the control diet, aronia feeding increases Treg in mesenteric lymph node at all colitis stages. Treg and regulatory Th17 subpopulations (IL-17A+ IL-10+ and IL-17A+ IL-22+ ) are increased in lamina propria and spleen at week 5 in aronia-fed mice. Aronia feeding also decreases total CD4+ cells but increases colonic Tregs. The ability of aronia to modulate colonic cytokines is associated with functional T cell IL-10 and increased diversity of microbiota. CONCLUSIONS: Aronia berry consumption inhibits adoptive transfer colitis by increasing Treg and regulatory Th17 cells. Dietary modulation of T cells is dynamic and precedes colitic wasting.
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Colitis/dietoterapia , Photinia , Linfocitos T Reguladores , Células Th17 , Animales , Linfocitos T CD4-Positivos/patología , Diferenciación Celular , Colitis/patología , Colitis/prevención & control , Citocinas/metabolismo , Modelos Animales de Enfermedad , Femenino , Microbioma Gastrointestinal , Interleucina-10/metabolismo , Masculino , Ratones Endogámicos C57BL , Ratones Mutantes , Bazo/citología , Linfocitos T Reguladores/metabolismoRESUMEN
Social relationships shape human health and mortality via behavioral, psychosocial, and physiological mechanisms, including inflammatory and immune responses. Though not tested in human studies, recent primate studies indicate that the gut microbiome may also be a biological mechanism linking relationships to health. Integrating microbiota data into the 60-year-old Wisconsin Longitudinal Study, we found that socialness with family and friends is associated with differences in the human fecal microbiota. Analysis of spouse (N = 94) and sibling pairs (N = 83) further revealed that spouses have more similar microbiota and more bacterial taxa in common than siblings, with no observed differences between sibling and unrelated pairs. These differences held even after accounting for dietary factors. The differences between unrelated individuals and married couples was driven entirely by couples who reported close relationships; there were no differences in similarity between couples reporting somewhat close relationships and unrelated individuals. Moreover, married individuals harbor microbial communities of greater diversity and richness relative to those living alone, with the greatest diversity among couples reporting close relationships, which is notable given decades of research documenting the health benefits of marriage. These results suggest that human interactions, especially sustained, close marital relationships, influence the gut microbiota.
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Bacterias/clasificación , Bacterias/genética , Heces/microbiología , Microbioma Gastrointestinal/genética , Relaciones Interpersonales , Hermanos , Esposos/estadística & datos numéricos , Anciano , ADN Bacteriano/análisis , ADN Bacteriano/genética , Femenino , Amigos , Humanos , Estudios Longitudinales , Masculino , Persona de Mediana Edad , WisconsinRESUMEN
Carbon monoxide (CO) has long been known to have dramatic physiological effects on organisms ranging from bacteria to humans, but recently there have a number of suggestions that organisms might have specific sensors for CO. This article reviews the current evidence for a variety of proteins with demonstrated or potential CO-sensing ability. Particular emphasis is placed on the molecular description of CooA, a heme-containing CO sensor from Rhodospirillum rubrum, since its biological role as a CO sensor is clear and we have substantial insight into the basis of its sensing ability.
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Proteínas Bacterianas/metabolismo , Monóxido de Carbono/metabolismo , Regulación de la Expresión Génica , Hemoproteínas/metabolismo , Transducción de Señal , Transactivadores/metabolismo , Secuencia de Aminoácidos , Animales , Bacterias/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Monóxido de Carbono/análisis , Células Eucariotas/fisiología , Hemoproteínas/química , Hemoproteínas/genética , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Transactivadores/química , Transactivadores/genéticaRESUMEN
Genomic analysis suggested the existence of a CO-sensing bacterial transcriptional regulator that couples an N-terminal PAS fold domain to a C-terminal DNA-binding LytTR domain. UV/visible-light spectral analyses of heterologously expressed, purified full-length proteins indicated that they contained a hexacoordinated b-type heme moiety that avidly binds CO and NO. Studies of protein variants strongly suggested that the PAS domain residues His74 and Met104 serve as the heme Fe(II) axial ligands, with displacement of Met104 upon binding of the gaseous effectors. Two RcoM (regulator of CO metabolism) homologs were shown to function in vivo as CO sensors capable of regulating an aerobic CO oxidation (cox) regulon. The genetic linkage of rcoM with both aerobic (cox) and anaerobic (coo) CO oxidation systems suggests that in different organisms RcoM proteins may control either regulon type.
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Proteínas Bacterianas/metabolismo , Monóxido de Carbono/metabolismo , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano , Factores de Transcripción/metabolismo , Aerobiosis/genética , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Burkholderia/genética , Burkholderia/metabolismo , Escherichia coli/genética , Genómica , Hemo/metabolismo , Ligandos , Datos de Secuencia Molecular , Óxido Nítrico/metabolismo , Oxidación-Reducción , Oxígeno/metabolismo , Estructura Terciaria de Proteína/genética , Regulón , Factores de Transcripción/química , Factores de Transcripción/genéticaRESUMEN
Spectroscopic characterization of the newly discovered heme-PAS domain sensor protein BxRcoM-2 reveals that this protein undergoes redox-dependent ligand switching and CO- and NO-induced ligand displacement. The aerobic bacterium Burkholderia xenovorans expresses two homologous heme-containing proteins that promote CO-dependent transcription in vivo. These regulators of CO metabolism, BxRcoM-1 and BxRcoM-2, are gas-responsive heme-PAS domain proteins like mammalian neuronal PAS domain protein 2 (NPAS2) and the direct oxygen sensor from Escherichia coli ( EcDos). BxRcoM-2 was studied using electronic absorption, MCD, resonance Raman, and EPR spectroscopies. In the Fe(III) oxidation state, the heme is low-spin and six-coordinate with a cysteine(thiolate) as one of the two ligands. The sixth ligand is a histidine (His (74)), which is present in all states of the protein that were studied. Reduction to the Fe(II) oxidation state results in replacement of the cysteine(thiolate) with a neutral thioether ligand, Met (104). CO and NO bind to the Fe(II) BxRcoM-2 heme opposite the histidine ligand. Thus, BxRcoM-2 employs coordination state changes similar to those known for CO-sensing CooA, with redox-dependent loss of a cysteine(thiolate) ligand and displacement of a relatively weakly bound axial ligand by the effector gas molecule. Like EcDos, the weakly bound axial ligand that is displaced is methionine.
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Proteínas Bacterianas/metabolismo , Burkholderia/metabolismo , Cisteína/metabolismo , Hemoproteínas/metabolismo , Proteínas Bacterianas/química , Burkholderia/genética , Monóxido de Carbono/química , Monóxido de Carbono/metabolismo , Cisteína/química , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , Espectroscopía de Resonancia por Spin del Electrón , Hemoproteínas/química , Histidina/química , Histidina/metabolismo , Hierro/química , Hierro/metabolismo , Estructura Molecular , Óxido Nítrico/química , Óxido Nítrico/metabolismo , Oxidación-Reducción , Unión Proteica , Espectrometría Raman , Transactivadores/química , Transactivadores/metabolismoRESUMEN
Huntington's disease is one of nine known neurodegenerative diseases in which a disease-specific protein contains an unusually long polyglutamine (polyQ) stretch. The proteins associated with each disease are unrelated in sequence, size, structure, function or location of the mutation. In all cases, there is an apparent critical number of glutamines below which individuals do not develop disease. Expansion of the polyQ domain is closely associated with misfolding and aggregation of the protein. It is not yet well understood how the length of the polyQ tract, and its location within a given protein, is related to misfolding and to disease. In this work we developed a strategy for generating length libraries of polyQ-containing proteins, with the polyQ inserted at an arbitrary location. This strategy facilitates systematic, detailed study of the relationship among polyQ length, context and misfolding.
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Péptidos/química , Enfermedad de Huntington/metabolismo , Mioglobina/química , Mioglobina/genética , Mioglobina/metabolismo , Pliegue de Proteína , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismoRESUMEN
BACKGROUND: Convenient, reproducible, and rapid preservation of unique biological specimens is pivotal to their use in microbiome analyses. As an increasing number of human studies incorporate the gut microbiome in their design, there is a high demand for streamlined sample collection and storage methods that are amenable to different settings and experimental needs. While several commercial kits address collection/shipping needs for sequence-based studies, these methods do not preserve samples properly for studies that require viable microbes. RESULTS: We describe the Fecal Aliquot Straw Technique (FAST) of fecal sample processing for storage and subsampling. This method uses a straw to collect fecal material from samples recently voided or preserved at low temperature but not frozen (i.e., 4 °C). Different straw aliquots collected from the same sample yielded highly reproducible communities as disclosed by 16S rRNA gene sequencing; operational taxonomic units that were lost, or gained, between the two aliquots represented very low-abundance taxa (i.e., < 0.3% of the community). FAST-processed samples inoculated into germ-free animals resulted in gut communities that retained on average ~ 80% of the donor's bacterial community. Assessment of choline metabolism and trimethylamine-N-oxide accumulation in transplanted mice suggests large interpersonal variation. CONCLUSIONS: Overall, FAST allows for repetitive subsampling without thawing of the specimens and requires minimal supplies and storage space, making it convenient to utilize both in the lab and in the field. FAST has the potential to advance microbiome research through easy, reproducible sample processing.
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Bacterias/clasificación , Bacterias/genética , Heces/microbiología , Microbioma Gastrointestinal/genética , Metilaminas/metabolismo , Manejo de Especímenes/métodos , Animales , Bacterias/aislamiento & purificación , Secuencia de Bases , Humanos , Ratones , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
Humans with metabolic and inflammatory diseases frequently harbour lower levels of butyrate-producing bacteria in their gut. However, it is not known whether variation in the levels of these organisms is causally linked with disease development and whether diet modifies the impact of these bacteria on health. Here we show that a prominent gut-associated butyrate-producing bacterial genus (Roseburia) is inversely correlated with atherosclerotic lesion development in a genetically diverse mouse population. We use germ-free apolipoprotein E-deficient mice colonized with synthetic microbial communities that differ in their capacity to generate butyrate to demonstrate that Roseburia intestinalis interacts with dietary plant polysaccharides to: impact gene expression in the intestine, directing metabolism away from glycolysis and toward fatty acid utilization; lower systemic inflammation; and ameliorate atherosclerosis. Furthermore, intestinal administration of butyrate reduces endotoxaemia and atherosclerosis development. Together, our results illustrate how modifiable diet-by-microbiota interactions impact cardiovascular disease, and suggest that interventions aimed at increasing the representation of butyrate-producing bacteria may provide protection against atherosclerosis.
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Aterosclerosis , Clostridiales/metabolismo , Dieta , Microbioma Gastrointestinal , Intestinos/microbiología , Animales , Apolipoproteínas E/genética , Aterosclerosis/tratamiento farmacológico , Aterosclerosis/patología , Butiratos/metabolismo , Butiratos/farmacología , Enfermedades Cardiovasculares , Clostridiales/genética , Colon/metabolismo , Colon/microbiología , Carbohidratos de la Dieta/metabolismo , Modelos Animales de Enfermedad , Endotoxemia , Metabolismo Energético , Ácidos Grasos/metabolismo , Heces/microbiología , Expresión Génica , Vida Libre de Gérmenes , Masculino , Metaboloma , Ratones , Ratones Noqueados , ARN Ribosómico 16S/genéticaRESUMEN
Using an untargeted metabolomics approach in initial (N = 99 subjects) and replication cohorts (N = 1,162), we discovered and structurally identified a plasma metabolite associated with cardiovascular disease (CVD) risks, N6,N6,N6-trimethyl-L-lysine (trimethyllysine, TML). Stable-isotope-dilution tandem mass spectrometry analyses of an independent validation cohort (N = 2,140) confirmed TML levels are independently associated with incident (3-year) major adverse cardiovascular event risks (hazards ratio [HR], 2.4; 95% CI, 1.7-3.4) and incident (5-year) mortality risk (HR, 2.9; 95% CI, 2.0-4.2). Genome-wide association studies identified several suggestive loci for TML levels, but none reached genome-wide significance; and d9(trimethyl)-TML isotope tracer studies confirmed TML can serve as a nutrient precursor for gut microbiota-dependent generation of trimethylamine (TMA) and the atherogenic metabolite trimethylamine N-oxide (TMAO). Although TML was shown to be abundant in both plant- and animal-derived foods, mouse and human fecal cultures (omnivores and vegans) showed slow conversion of TML to TMA. Furthermore, unlike chronic dietary choline, TML supplementation in mice failed to elevate plasma TMAO or heighten thrombosis potential in vivo. Thus, TML is identified as a strong predictor of incident CVD risks in subjects and to serve as a dietary precursor for gut microbiota-dependent generation of TMAO; however, TML does not appear to be a major microbial source for TMAO generation in vivo.