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1.
Int J Syst Evol Microbiol ; 70(6): 3656-3664, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32416738

RESUMO

Four strains (9CBEGH2T, 9BBH35, 6BBH38 and 6EGH11) of Gram-stain-positive, obligately anaerobic, rod-shaped bacteria were isolated from faecal samples from healthy Japanese humans. The results of 16S rRNA gene sequence analysis indicated that the four strains represented members of the family Erysipelotrichaceae and formed a monophyletic cluster with 'Absiella argi' strain N6H1-5 (99.4% sequence similarity) and Eubacterium sp. Marseille-P5640 (99.3 %). Eubacterium dolichum JCM 10413T (94.2 %) and Eubacterium tortuosum ATCC 25548T (93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2T, 'A. argi' JCM 30884 and Eubacterium sp. Marseille-P5640 shared 98.7-99.1% average nucleotide identity (ANI) with each other. Moreover, the in silico DNA-DNA hybridization (DDH) values among three strains were 88.4-90.6%, indicating that these strains represent the same species. Strain 9CBEGH2T showed 21.5-24.1 % in silico DDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2T and other related taxa ranged from 71.2 % to 73.5 %, indicating that this strain should be considered as representing a novel species on the basis of whole-genome relatedness. Therefore, we formally propose a novel name for 'A. argi' strains identified because the name 'A. argi' has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2T represents a novel species of a novel genus, for which the name Amedibacterium intestinale gen. nov., sp. nov. is proposed. The type strain of A. intestinale is 9CBEGH2T (=JCM 33778T=DSM 110575T).


Assuntos
Fezes/microbiologia , Firmicutes/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Eubacterium/classificação , Ácidos Graxos/química , Firmicutes/isolamento & purificação , Humanos , Japão , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
2.
Bull Exp Biol Med ; 167(5): 645-649, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31625063

RESUMO

Infectious process even at the initial stage after aerosol infection with Mycobacterium tuberculosis induced rapid changes in vaginal microbiota in mice. Rapid decrease in both the quantity and diversity of microbiota was noted, and then, partial recovery of normal flora was observed. Changes in vaginal microbiota was detected as soon as in 3-7 days after lung infection, while inflammatory changes appeared by day 35. At the early stage of infection, no signs of inflammation were observed, neither M. tuberculosis nor its DNA were detected in mouse genital organs.


Assuntos
Disbiose/microbiologia , Pulmão/microbiologia , Microbiota , Mycobacterium tuberculosis/patogenicidade , Tuberculose Pulmonar/microbiologia , Vagina/microbiologia , Animais , Carga Bacteriana , Clostridium/isolamento & purificação , Disbiose/patologia , Eubacterium/isolamento & purificação , Feminino , Inflamação , Pulmão/patologia , Camundongos , Camundongos Endogâmicos C57BL , Mycobacterium tuberculosis/fisiologia , Peptostreptococcus/isolamento & purificação , Porphyromonas/isolamento & purificação , Prevotella/isolamento & purificação , Streptococcus/isolamento & purificação , Tuberculose Pulmonar/patologia
3.
Int J Mol Sci ; 20(16)2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31434224

RESUMO

Psychrotrophic foodborne pathogens, such as enteropathogenic Yersinia, which are able to survive and multiply at low temperatures, require cold shock proteins (Csps). The Csp superfamily consists of a diverse group of homologous proteins, which have been found throughout the eubacteria. They are related to cold shock tolerance and other cellular processes. Csps are mainly named following the convention of those in Escherichia coli. However, the nomenclature of certain Csps reflects neither their sequences nor functions, which can be confusing. Here, we performed phylogenetic analyses on Csp sequences in psychrotrophic enteropathogenic Yersinia and E. coli. We found that representative Csps in enteropathogenic Yersinia and E. coli can be clustered into six phylogenetic groups. When we extended the analysis to cover Enterobacteriales, the same major groups formed. Moreover, we investigated the evolutionary and structural relationships and the origin time of Csp superfamily members in eubacteria using nucleotide-level comparisons. Csps in eubacteria were classified into five clades and 12 subclades. The most recent common ancestor of Csp genes was estimated to have existed 3585 million years ago, indicating that Csps have been important since the beginning of evolution and have enabled bacterial growth in unfavorable conditions.


Assuntos
Proteínas de Bactérias/classificação , Proteínas de Bactérias/metabolismo , Proteínas e Peptídeos de Choque Frio/classificação , Proteínas e Peptídeos de Choque Frio/metabolismo , Escherichia coli/metabolismo , Eubacterium/metabolismo , Yersinia/metabolismo , Proteínas de Bactérias/genética , Proteínas e Peptídeos de Choque Frio/genética , Escherichia coli/genética , Eubacterium/genética , Filogenia , Yersinia/genética
4.
Chem Commun (Camb) ; 55(61): 8935-8938, 2019 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-31286126

RESUMO

The Eubacterium saburreum serine protease inhibitor from the human gut microbiota inhibits the eukaryotic pancreatic elastase associated with acute pancreatitis. Interestingly, the inhibition efficiency and stability are markedly increased by the para-sulphonato-calix[8]arene capped silver nanoparticles. Moreover, this enzyme is distinguishable by its high inhibitory effect at broad pH range between 2-10 and temperatures from 10 to 40 °C, in the presence of para-sulphonato-calix[8]arene capped silver nanoparticles the enzyme remains active even at 70 °C.


Assuntos
Calixarenos/química , Nanopartículas Metálicas/química , Elastase Pancreática/antagonistas & inibidores , Serpinas/química , Prata/química , Sequência de Aminoácidos , Animais , Ensaios Enzimáticos , Eubacterium/química , Concentração de Íons de Hidrogênio , Estabilidade Proteica , Alinhamento de Sequência , Serpinas/isolamento & purificação , Ácidos Sulfônicos/química , Suínos , Temperatura
5.
J Biol Chem ; 294(37): 13697-13707, 2019 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-31341018

RESUMO

The trimethylamine methyltransferase MttB is the founding member of a widely distributed superfamily of microbial proteins. Genes encoding most members of the MttB superfamily lack the codon for pyrrolysine that distinguishes previously characterized trimethylamine methyltransferases, leaving the function(s) of most of the enzymes in this superfamily unknown. Here, investigating the MttB family member MtpB from the human intestinal isolate Eubacterium limosum ATCC 8486, an acetogen that excretes N-methyl proline during growth on proline betaine, we demonstrate that MtpB catalyzes anoxic demethylation of proline betaine. MtpB along with MtqC (a corrinoid protein) and MtqA (a methylcorrinoid:tetrahydrofolate methyltransferase) was much more abundant in E. limosum cells grown on proline betaine than on lactate. We observed that recombinant MtpB methylates Co(I)-MtqC in the presence of proline betaine and that other quaternary amines are much less preferred substrates. MtpB, MtqC, and MtqA catalyze tetrahydrofolate methylation with proline betaine, thereby forming a key intermediate in the Wood-Ljungdahl acetogenesis pathway. To our knowledge, MtpB methylation of Co(I)-MtqC for the subsequent methylation of tetrahydrofolate represents the first described anoxic mechanism of proline betaine demethylation. The activities of MtpB and associated proteins in acetogens or other anaerobes provide a possible mechanism for the production of N-methyl proline by the gut microbiome. MtpB's activity characterized here strengthens the hypothesis that much of the MttB superfamily comprises quaternary amine-dependent methyltransferases.


Assuntos
Betaína/metabolismo , Eubacterium/metabolismo , Metiltransferases/metabolismo , Prolina/metabolismo , Desmetilação , Metabolismo Energético , Eubacterium/enzimologia , Ácido Fólico/metabolismo , Humanos , Intestinos/microbiologia , Metilaminas/metabolismo , Metilação , Microbiota , Prolina/análogos & derivados , Tetra-Hidrofolatos/metabolismo
6.
Anaerobe ; 59: 131-140, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31228669

RESUMO

Commensal butyrate-producing bacteria in the Firmicutes phylum are abundant in the human intestine and are important for maintaining health. However, understanding of the metabolism and host interaction of these bacteria is limited by the lack of genetic modification techniques. Here we establish a protocol enabling the transfer of autonomously-replicating shuttle vectors by conjugative plasmid transfer from an Escherichia coli donor into representatives of an important sub-group of strictly anaerobic human colonic Firmicutes. Five different plasmid shuttle vectors were tested, each carrying a different origin of replication from Gram-positive bacteria. Plasmid pMTL83151 (pCB102 replicon) were successfully transferred into two strains of Eubacterium rectale, while pMTL83151 and pMTL82151 (pBP1 replicon) were transferred into Roseburia inulinivorans A2-194. Plasmids that carried a Streptococcus bovis JB1 glycoside hydrolase family 16 ß-(1,3-1,4)-glucanase gene were constructed and conjugated into Roseburia inulinivorans A2-194 and Eubacterium rectale T1-815, resulting in successful heterologous expression of this introduced enzymatic activity in these two strains of butyrate-producing Firmicutes.


Assuntos
Clostridiales/genética , Conjugação Genética , Eubacterium/genética , Expressão Gênica , Técnicas de Transferência de Genes , Genética Microbiana/métodos , Plasmídeos , Escherichia coli/genética , Vetores Genéticos , Humanos , Transformação Bacteriana
7.
Gut Microbes ; 10(6): 712-719, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30991877

RESUMO

Background: A western high fat, high carbohydrate diet has been shown to be associated with decreased gut bacterial diversity and reductions in beneficial bacteria. This gut bacteria dysbiosis could develop in early life and contribute to chronic disease risk such as obesity, type 2 diabetes and non-alcoholic fatty liver disease.Objective: To determine how dietary macronutrients are associated with the relative abundance of gut bacteria in healthy adolescents.Methods: Fifty-two obese participants (12-19 years) from two studies, many who were primarily of Hispanic background, provided fecal samples for 16S rRNA gene sequencing. Dietary macronutrients were assessed using 24-hour diet recalls and body composition was assessed using DEXA. General regression models assuming a negative binomial distribution were used to examine the associations between gut bacteria and dietary fiber, saturated fat, unsaturated fats, protein, added sugar, total sugar and free fructose after adjusting for age, gender, race/ethnicity, body fat percentage, study and caloric intake.Results: The genera Eubacterium (Benjamini-Hochberg (BH) corrected p-value = 0.10) and Streptococcus (BH corrected p-value = 0.04) were inversely associated with dietary fructose intake. There were no other significant associations between abundances of gut microbes and other dietary macronutrients, including fiber, fat, protein, total sugar or added sugar.Conclusions: High dietary fructose was associated with lower abundance of the beneficial microbes Eubacterium and Streptococcus, which are involved with carbohydrate metabolism.


Assuntos
Açúcares da Dieta/efeitos adversos , Eubacterium/crescimento & desenvolvimento , Frutose/efeitos adversos , Obesidade/etiologia , Obesidade/microbiologia , Streptococcus/crescimento & desenvolvimento , Adolescente , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Composição Corporal , Criança , Dieta , Açúcares da Dieta/análise , Feminino , Microbioma Gastrointestinal/genética , Humanos , Masculino , Obesidade/patologia , RNA Ribossômico 16S/genética , Adulto Jovem
8.
Nature ; 568(7750): 43-48, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30918406

RESUMO

Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.


Assuntos
Bactérias/genética , Suscetibilidade a Doenças/microbiologia , Microbioma Gastrointestinal/genética , Genes Bacterianos/genética , Variação Genética , Saúde , Interações entre Hospedeiro e Microrganismos/genética , Adaptação Fisiológica/genética , Bactérias/classificação , Bactérias/crescimento & desenvolvimento , Bactérias/metabolismo , Butiratos/metabolismo , Estudos de Coortes , Ecossistema , Eubacterium/genética , Eubacterium/metabolismo , Fezes/microbiologia , Microbioma Gastrointestinal/fisiologia , Interações entre Hospedeiro e Microrganismos/fisiologia , Humanos , Inositol/metabolismo , Metagenômica , Viabilidade Microbiana/genética , Fatores de Risco
9.
Biotechnol Adv ; 37(5): 599-615, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30849433

RESUMO

Alternative chemicals to diverse fossil-fuel-based products is urgently needed to mitigate the adverse impacts of fossil fuel depletion on human development. To this end, researchers have focused on the production of biochemical from readily available and affordable waste biomass. This is consistent with current guidelines for sustainable development and provides great advantages related to economy and environment. The search for suitable biochemical products is in progress worldwide. Therefore, this review recommends a biochemical (i.e., medium chain carboxylic acids (MCCAs)) utilizing an emerging biotechnological production platform called the chain elongation (CE) process. This work covers comprehensive introduction of the CE mechanism, functional microbes, available feedstock types and corresponding utilization strategies, major methods to enhance the performance of MCCAs production, and the challenges that need to be addressed for practical application. This work is expected to provide a thorough understanding of the CE technology, to guide and inspire researchers to solve existing problems in depth, and motivate large-scale MCCAs production.


Assuntos
Biotecnologia/métodos , Ácidos Carboxílicos/metabolismo , Biocombustíveis , Biomassa , Reatores Biológicos , Biotecnologia/instrumentação , Ácidos Carboxílicos/química , Clostridium kluyveri/metabolismo , Eubacterium/metabolismo , Fermentação , Microbiologia Industrial/métodos , Megasphaera elsdenii/metabolismo , Resíduos
10.
Biochim Biophys Acta Proteins Proteom ; 1867(4): 426-433, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30716506

RESUMO

The thioredoxin system is a ubiquitous oxidoreductase system that consists of the enzyme thioredoxin reductase (TrxR), its cofactor nicotinamide adenine dinucleotide phosphate (NAD(P)H) and the protein thioredoxin (Trx). The system has been comprehensively studied from many organisms, such as Escherichia coli (E. coli); however, structural and functional analysis of this system from thermophilic bacteria has not been as extensive. In this study, Thermosipho africanus, a thermophilic eubacterium, Trx1 (TaTrx1) was successfully cloned, overexpressed and purified, to greater than 95% purity. Inspection of the amino acid sequence of TaTrx1 categorized the protein as a putative Trx. Its ability to reduce the interchain disulfides of insulin, in the presence of dithiothreitol, provided further evidence to suggest that it was a Trx. The three dimensional structure of the protein, determined using X-ray crystallography, provided additional evidence for this. The crystal structure was solved in space group P212121 to 1.8 A resolution and showed the characteristic thioredoxin fold; four ß-strands surrounded by three α-helices. The active site of TaTrx1 contained two cysteines that formed a disulfide bridge, and was structurally similar to the active site of EcTrx1. Further studies indicated that TaTrx1 was far more stable than Trx1 of E. coli (EcTrx1). The protein could withstand both higher temperatures and higher concentrations of guanidine hydrochloride before denaturing. Our studies have therefore identified a novel thermophilic putative Trx that structurally and functionally behaves like a Trx.


Assuntos
Proteínas de Bactérias/química , Eubacterium , Tiorredoxinas/química , Sequência de Aminoácidos , Insulina/química , Conformação Proteica , Estabilidade Proteica
11.
Pharmacol Res ; 139: 41-49, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30391354

RESUMO

Irinotecan (CPT-11), a first-line chemotherapy for advanced colorectal cancer, causes serious diarrhea in patients receiving treatment. The underlying mechanism has been shown that the active metabolite of CPT-11, SN-38, is metabolized to the inactive metabolite SN-38 glucuronide (SN-38 G) during hepatic glucuronidation, and subsequently is exported into the intestine, where SN-38 G is hydrolyzed by bacterial ß-glucuronidase (ßG) to be SN-38, thus leading to intestinal toxicity. Thus, inhibition of the intestinal bacterial ßG activity is expected to prevent CPT-11-induced diarrhea. However, the effects of such inhibition on serum pharmacokinetics of SN-38, the key determinant of CPT-11 treatment, are uncertain. Here, we determined the effects of a potent E. coli ßG (eßG)-specific inhibitor pyrazolo[4,3-c]quinoline derivative (TCH-3562) for the potential use in preventing CPT-11-induced diarrhea. TCH-3562 exhibited efficacious inhibitory potency of endogenous ßG activity in two anaerobes, Eubacteriumsp. and Peptostreptococcus anaerobius. Oral administration of TCH-3562 also effectively reduced the bacterial ßG activity in mice intestine. Moreover, pharmacokinetic analysis of TCH-3562 revealed a relatively low amount of TCH-3562 was detected in the plasma whereas the majority of TCH-3562 was found in the feces. Importantly, co-treatment of CPT-11 and TCH-3562 did not decrease active SN-38 level in mice plasma. Finally, we established that TCH-3562 as an adjuvant treatment showed protective effects on CPT-11-induced diarrhea and had no negative effects on the therapeutic efficacy of CPT-11 in tumor-bearing mice. Therefore, inhibition of the intestinal bacterial ßG activity by the specific inhibitor, TCH-3562, is promising to prevent CPT-11-induced diarrhea while maintaining its anti-tumor efficacy that may have clinical potentials for the treatment with CPT-11.


Assuntos
Antineoplásicos Fitogênicos/uso terapêutico , Proteínas de Bactérias/antagonistas & inibidores , Neoplasias do Colo/tratamento farmacológico , Diarreia/prevenção & controle , Glucuronidase/antagonistas & inibidores , Irinotecano/uso terapêutico , Quinolinas/farmacologia , Animais , Linhagem Celular Tumoral , Diarreia/induzido quimicamente , Escherichia coli/efeitos dos fármacos , Escherichia coli/crescimento & desenvolvimento , Eubacterium/enzimologia , Células HEK293 , Humanos , Masculino , Camundongos Endogâmicos BALB C , Peptostreptococcus/enzimologia
12.
Mol Nutr Food Res ; 63(2): e1800923, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30471194

RESUMO

SCOPE: The intestinal microbiota transforms a wide range of available substrates, including polyphenols. Microbial catabolites of polyphenols can contribute in significant ways to the health-promoting properties of their parent polyphenols. This work aims to identify intestinal metabolites of xanthohumol (XN), a prenylated flavonoid found in hops (Humulus lupulus) and beer, as well as to identify pathways of metabolism of XN in the gut. METHODS AND RESULTS: To investigate intestinal metabolism, XN and related prenylated flavonoids, isoxanthohumol (IX), and 8-prenylnaringenin (8PN) were added to growing cultures of intestinal bacteria, Eubacterium ramulus and E. limosum. Liquid chromatography coupled with mass spectrometry was used to identify metabolites of the flavonoids from the cultures. The metabolic capacity of E. limosum appears to be limited to O-demethylation. Evidence from the study indicates that E. ramulus hydrogenates XN to form α,ß-dihydroxanthohumol (DXN) and metabolizes the potent phytoestrogen 8PN into the chalcones, O-desmethylxanthohumol (DMX) and O-desmethyl-α,ß-dihydroxanthohumol (DDXN). CONCLUSION: Microbial metabolism is likely to affect both activity and toxicity of XN and derivatives. This study along with others highlights that attention should be focused on metabolites, in particular, products of intestinal microbial metabolism.


Assuntos
Eubacterium/metabolismo , Flavanonas/metabolismo , Flavonoides/metabolismo , Intestinos/microbiologia , Propiofenonas/metabolismo , Espectrometria de Massas em Tandem , Xantonas/metabolismo
13.
Exp Mol Med ; 50(12): 1-14, 2018 11 30.
Artigo em Inglês | MEDLINE | ID: mdl-30504803

RESUMO

The link between antibiotic treatment and IF-associated liver disease (IFALD) is unclear. Here, we study the effect of antibiotic treatment on bile acid (BA) metabolism and investigate the involved mechanisms. The results showed that pediatric IF patients with cholestasis had a significantly lower abundance of BA-biotransforming bacteria than patients without cholestasis. In addition, the BA composition was altered in the serum, feces, and liver of pediatric IF patients with cholestasis, as reflected by the increased proportion of primary BAs. In the ileum, farnesoid X receptor (FXR) expression was reduced in patients with cholestasis. Correspondingly, the serum FGF19 levels decreased significantly in patients with cholestasis. In the liver, the expression of the rate-limiting enzyme in bile salt synthesis, cytochrome P450 7a1 (CYP7A1), increased noticeably in IF patients with cholestasis. In mice, we showed that oral antibiotics (gentamicin, GM or vancomycin, VCM) reduced colonic microbial diversity, with a decrease in both Gram-negative bacteria (GM affected Eubacterium and Bacteroides) and Gram-positive bacteria (VCM affected Clostridium, Bifidobacterium and Lactobacillus). Concomitantly, treatment with GM or VCM decreased secondary BAs in the colonic contents, with a simultaneous increase in primary BAs in plasma. Moreover, the changes in the colonic BA profile especially that of tauro-beta-muricholic acid (TßMCA), were predominantly associated with the inhibition of the FXR and further altered BA synthesis and transport. In conclusion, the administration of antibiotics significantly decreased the intestinal microbiota diversity and subsequently altered the BA composition. The alterations in BA composition contributed to cholestasis in IF patients by regulating FXR signaling.


Assuntos
Bacteroides/fisiologia , Eubacterium/fisiologia , Microbioma Gastrointestinal/imunologia , Gentamicinas/efeitos adversos , Bactérias Gram-Positivas/fisiologia , Intestinos/patologia , Fígado/metabolismo , Receptores Citoplasmáticos e Nucleares/metabolismo , Vancomicina/efeitos adversos , Animais , Proteínas de Bactérias/metabolismo , Doença Hepática Induzida por Substâncias e Drogas , Criança , Pré-Escolar , Colestase/etiologia , Sistema Enzimático do Citocromo P-450/metabolismo , Feminino , Fatores de Crescimento de Fibroblastos/metabolismo , Gentamicinas/administração & dosagem , Humanos , Lactente , Intestinos/microbiologia , Fígado/patologia , Masculino , Camundongos , Transdução de Sinais , Ácido Taurocólico/análogos & derivados , Ácido Taurocólico/metabolismo , Vancomicina/administração & dosagem
14.
J Microbiol ; 56(12): 886-892, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30484158

RESUMO

Statin response shows great interindividual variations. Recently, emerging studies have shown that gut microbiota is linked to therapeutic responses to drugs, including statins. However, the association between the gut bacteria composition and statin response is still unclear. In this study, gut microbiota of 202 hyperlipidemic patients with statin sensitive (SS) response and statin resistant (SR) response in East China were investigated by high throughput sequencing to compare the gut bacteria composition and biodiversity in distinct statin response patients. Higher biodiversity was detected in Group SS than Group SR. Specifically, group SS showed significantly increased proportion of genera Lactobacillus (P = 0.001), Eubacterium (P = 0.004), Faecalibacterium (P = 0.005), and Bifidobacterium (P = 0.002) and decreased proportion of genus Clostridium (P = 0.001) compared to Group SR. The results indicated that higher gut biodiversity was associated with statin sensitive response. The increased genera Lactobacillus, Eubacterium, Faecalibacterium, Bifidobacterium, and decreased genus Clostridium in patient gut microbiota may predict patient's statin response, and hence may guide statin dosage adjustments.


Assuntos
Bactérias/classificação , Bactérias/efeitos dos fármacos , Microbioma Gastrointestinal/efeitos dos fármacos , Trato Gastrointestinal/microbiologia , Inibidores de Hidroximetilglutaril-CoA Redutases/farmacologia , Bactérias/genética , Bifidobacterium/efeitos dos fármacos , Biodiversidade , China , Clostridium/efeitos dos fármacos , DNA Bacteriano/genética , Eubacterium/efeitos dos fármacos , Faecalibacterium/efeitos dos fármacos , Fezes/microbiologia , Microbioma Gastrointestinal/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Hipercolesterolemia/tratamento farmacológico , Lactobacillus/efeitos dos fármacos , Masculino , Pessoa de Meia-Idade
15.
BMC Genomics ; 19(1): 837, 2018 Nov 23.
Artigo em Inglês | MEDLINE | ID: mdl-30470174

RESUMO

BACKGROUND: Acetogenic bacteria constitute promising biocatalysts for the conversion of CO2/H2 or synthesis gas (H2/CO/CO2) into biofuels and value-added biochemicals. These microorganisms are naturally capable of autotrophic growth via unique acetogenesis metabolism. Despite their biosynthetic potential for commercial applications, a systemic understanding of the transcriptional and translational regulation of the acetogenesis metabolism remains unclear. RESULTS: By integrating genome-scale transcriptomic and translatomic data, we explored the regulatory logic of the acetogenesis to convert CO2 into biomass and metabolites in Eubacterium limosum. The results indicate that majority of genes associated with autotrophic growth including the Wood-Ljungdahl pathway, the reduction of electron carriers, the energy conservation system, and gluconeogenesis were transcriptionally upregulated. The translation efficiency of genes in cellular respiration and electron bifurcation was also highly enhanced. In contrast, the transcriptionally abundant genes involved in the carbonyl branch of the Wood-Ljungdahl pathway, as well as the ion-translocating complex and ATP synthase complex in the energy conservation system, showed decreased translation efficiency. The translation efficiencies of genes were regulated by 5'UTR secondary structure under the autotrophic growth condition. CONCLUSIONS: The results illustrated that the acetogenic bacteria reallocate protein synthesis, focusing more on the translation of genes for the generation of reduced electron carriers via electron bifurcation, rather than on those for carbon metabolism under autotrophic growth.


Assuntos
Acetatos/metabolismo , Proteínas de Bactérias/genética , Eubacterium/crescimento & desenvolvimento , Fermentação , Regulação Bacteriana da Expressão Gênica , Processos Autotróficos , Biocombustíveis , Ciclo do Carbono , Metabolismo Energético , Eubacterium/genética , Eubacterium/metabolismo , Gases/análise , Genoma Bacteriano , Transcriptoma
16.
Int J Syst Evol Microbiol ; 68(12): 3741-3746, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30351260

RESUMO

A bacterial strain designated L2-7T, phylogenetically related to Eubacterium hallii DSM 3353T, was previously isolated from infant faeces. The complete genome of strain L2-7T contains eight copies of the 16S rRNA gene with only 98.0-98.5 % similarity to the 16S rRNA gene of the previously described type strain E. hallii. The next closest validly described species is Anaerostipes hadrus DSM 3319T (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7T to be a novel species, related to type strain E. hallii DSM 3353T. The experimentally observed DNA-DNA hybridization value between strain L2-7T and E. hallii DSM 3353T was 26.25 %, close to that calculated from the genomes (34.3 %). The G+C content of the chromosomal DNA of strain L2-7T was 38.6 mol%. The major fatty acids were C16 : 0, C16 : 1cis9 and a component with summed feature 10 (C18 : 1c11/t9/t6c). Strain L2-7T had higher amounts of C16 : 0 (30.6 %) compared to E. hallii DSM 3353T (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E. hallii DSM 3353T. Furthermore, 16S rRNA gene phylogenetic analysis advocates that E. hallii DSM 3353T is misclassified, and its reclassification as a member of the family Lachnospiraceae is necessary. Using a polyphasic approach, we propose that E. hallii (=DSM 3353T=ATCC 27751T) be reclassified as the type strain of a novel genus Anaerobutyricum sp. nov., comb. nov. and we propose that strain L2-7T should be classified as a novel species, Anaerobutyricum soehngenii sp. nov. The type strain is L2-7T (=DSM 17630T=KCTC 15707T).


Assuntos
Eubacterium/classificação , Fezes/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Butiratos/metabolismo , DNA Bacteriano/genética , Eubacterium/metabolismo , Ácidos Graxos/química , Humanos , Lactente , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas/química , Fosfatidilgliceróis/química , Propionatos/metabolismo , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
17.
Br J Nutr ; 120(9): 1014-1022, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30355393

RESUMO

Increasing evidence indicates that gut microbiota may influence colorectal cancer risk. Diet, particularly fibre intake, may modify gut microbiota composition, which may affect cancer risk. We investigated the relationship between dietary fibre intake and gut microbiota in adults. Using 16S rRNA gene sequencing, we assessed gut microbiota in faecal samples from 151 adults in two independent study populations: National Cancer Institute (NCI), n 75, and New York University (NYU), n 76. We calculated energy-adjusted fibre intake based on FFQ. For each study population with adjustment for age, sex, race, BMI and smoking, we evaluated the relationship between fibre intake and gut microbiota community composition and taxon abundance. Total fibre intake was significantly associated with overall microbial community composition in NYU (P=0·008) but not in NCI (P=0·81). In a meta-analysis of both study populations, higher fibre intake tended to be associated with genera of class Clostridia, including higher abundance of SMB53 (fold change (FC)=1·04, P=0·04), Lachnospira (FC=1·03, P=0·05) and Faecalibacterium (FC=1·03, P=0·06), and lower abundance of Actinomyces (FC=0·95, P=0·002), Odoribacter (FC=0·95, P=0·03) and Oscillospira (FC=0·96, P=0·06). A species-level meta-analysis showed that higher fibre intake was marginally associated with greater abundance of Faecalibacterium prausnitzii (FC=1·03, P=0·07) and lower abundance of Eubacterium dolichum (FC=0·96, P=0·04) and Bacteroides uniformis (FC=0·97, P=0·05). Thus, dietary fibre intake may impact gut microbiota composition, particularly class Clostridia, and may favour putatively beneficial bacteria such as F. prausnitzii. These findings warrant further understanding of diet-microbiota relationships for future development of colorectal cancer prevention strategies.


Assuntos
Bactérias/classificação , Fibras na Dieta/análise , Fezes/microbiologia , Microbioma Gastrointestinal , RNA Ribossômico 16S/genética , Bacteroides , Clostridiales , Dieta , Ingestão de Energia , Eubacterium , Feminino , Fermentação , Humanos , Lactobacillales , Masculino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes
18.
Biochim Biophys Acta Gen Subj ; 1862(12): 2797-2805, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30251668

RESUMO

Peroxiredoxins (Prxs) are thiol peroxidases that scavenge various peroxide substrates such as hydrogen peroxide (H2O2), alkyl hydroperoxides and peroxinitrite. They also function as chaperones and are involved in signal transduction by H2O2 in eukaryotic cells. The genome of Aquifex aeolicus, a microaerophilic, hyperthermophilic eubacterium, encodes four Prxs, among them an alkyl hydroperoxide reductase AhpC2 which was found to be closely related to archaeal 1-Cys peroxiredoxins. We determined the crystal structure of AhpC2 at 1.8 Šresolution and investigated its oligomeric state in solution by electron microscopy. AhpC2 is arranged as a toroid-shaped dodecamer instead of the typically observed decamer. The basic folding topology and the active site structure are conserved and possess a high structural similarity to other 1-Cys Prxs. However, the C-terminal region adopts an opposite orientation. AhpC2 contains three cysteines, Cys49, Cys212, and Cys218. The peroxidatic cysteine CP49 was found to be hyperoxidized to the sulfonic acid (SO3H) form, while Cys212 forms an intra-monomer disulfide bond with Cys218. Mutagenesis experiments indicate that Cys212 and Cys218 play important roles in the oligomerization of AhpC2. Based on these structural characteristics, we proposed the catalytic mechanism of AhpC2. This study provides novel insights into the structure and reaction mechanism of 1-Cys peroxiredoxins.


Assuntos
Eubacterium/química , Peroxirredoxinas/química , Catálise , Domínio Catalítico , Dissulfetos/química , Oxirredução , Peroxirredoxinas/genética , Peroxirredoxinas/isolamento & purificação , Polimerização , Conformação Proteica , Soluções
19.
Cell Syst ; 7(3): 245-257.e7, 2018 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-30195437

RESUMO

The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.


Assuntos
Clostridium/fisiologia , Eubacterium/fisiologia , Microbioma Gastrointestinal/fisiologia , Lactobacillus/fisiologia , Interações Microbianas , Animais , Técnicas de Cocultura , Simulação por Computador , Humanos , Redes e Vias Metabólicas , Metaboloma , Camundongos , Modelos Biológicos , Modelos Teóricos , Análise de Componente Principal
20.
Carbohydr Polym ; 199: 482-491, 2018 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-30143153

RESUMO

The suitability of artichoke and sunflower by-products as renewable sources of pectic compounds with prebiotic potential was evaluated by studying their ability to modulate the human faecal microbiota in vitro. Bacterial populations and short-chain fatty acid (SCFA) production were measured. Reduction of the molecular weight of artichoke pectin resulted in greater stimulation of the growth of Bifidobacterium, Lactobacillus and Bacteroides/Prevotella, whilst this effect was observed only in Bacteroides/Prevotella for sunflower samples. In contrast, the degree of methoxylation did not have any impact on fermentability properties or SCFA production, regardless of the origin of pectic compounds. Although further in vivo studies should be conducted, either pectin or enzymatically-modified pectin from sunflower and artichoke by-products might be considered as prebiotic candidates for human consumption showing similar ability to promote the in vitro growth of beneficial gut bacteria as compared to well-recognized prebiotics such as inulin or fructo-oligosaccharides.


Assuntos
Fermentação , Pectinas/metabolismo , Adulto , Bacteroides/crescimento & desenvolvimento , Bacteroides/metabolismo , Bifidobacterium/crescimento & desenvolvimento , Bifidobacterium/metabolismo , Citrus/química , Cynara scolymus/química , Enterococcus/crescimento & desenvolvimento , Enterococcus/metabolismo , Eubacterium/crescimento & desenvolvimento , Eubacterium/metabolismo , Ácidos Graxos Voláteis/análise , Fezes/microbiologia , Feminino , Microbioma Gastrointestinal/efeitos dos fármacos , Helianthus/química , Humanos , Lactobacillus/crescimento & desenvolvimento , Lactobacillus/metabolismo , Masculino , Pectinas/química , Pectinas/isolamento & purificação , Prebióticos , Prevotella/crescimento & desenvolvimento , Prevotella/metabolismo
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