RESUMEN
Interspecies pathways in the gut microbiome have been shown to metabolize levodopa, the primary treatment for Parkinson's disease, and reduce its bioavailability. While the enzymatic reactions have been identified, the ability to establish the resulting macromolecules as biomarkers of microbial metabolism remains technically challenging. In this study, we leveraged an untargeted mass spectrometry-based approach to investigate volatile organic compounds (VOCs) produced during levodopa metabolism by Enterococcus faecalis, Clostridium sporogenes, and Eggerthella lenta. We cultured these organisms with and without their respective bioactive metabolites and detected levodopa-induced shifts in VOC profiles. We then utilized bioinformatics to identify significant differences in 2,6-dimethylpyrazine, 4,6-dimethylpyrimidine, and 4,5-dimethylpyrimidine associated with its biotransformation. Supplementing cultures with inhibitors of levodopa-metabolizing enzymes revealed specific modulation of levodopa-associated diazines, verifying their relationship to its metabolism. Furthermore, functional group analysis depicts strain-specific VOC profiles that reflect interspecies differences in metabolic activity that can be leveraged to assess microbiome functionality in individual patients. Collectively, this work identifies previously uncharacterized metabolites of microbe-mediated levodopa metabolism to determine potential indicators of this activity and further elucidate the metabolic capabilities of different gut bacteria.
Asunto(s)
Enterococcus faecalis , Microbioma Gastrointestinal , Levodopa , Compuestos Orgánicos Volátiles , Levodopa/metabolismo , Compuestos Orgánicos Volátiles/metabolismo , Enterococcus faecalis/metabolismo , Humanos , Bacterias/metabolismo , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Clostridium/metabolismo , Clostridium/clasificación , Espectrometría de Masas , BiotransformaciónRESUMEN
A novel thermotolerant caproic acid-producing bacterial strain, Clostridium M1NH, was successfully isolated from sewage sludge. Ethanol and acetic acid at a molar ratio of 4:1 proved to be the optimal substrates, yielding a maximum caproic acid production of 3.5 g/L. Clostridium M1NH exhibited remarkable tolerance to high concentrations of ethanol (up to 5% v/v), acetic acid (up to 5% w/v), and caproic acid (up to 2% w/v). The strain also demonstrated a wide pH tolerance range (pH 5.5-7.5) and an elevated temperature optimum between 35 and 40 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that Clostridium M1NH shares a 98% similarity with Clostridium luticellarii DSM 29923 T. The robustness of strain M1NH and its efficient caproic acid production from low-cost substrates highlight its potential for sustainable bio-based chemical production. The maximum caproic acid yield achieved by Clostridium M1NH was 1.6-fold higher than that reported for C. kluyveri under similar fermentation conditions. This study opens new avenues for valorizing waste streams and advancing a circular economy model in the chemical industry.
Asunto(s)
Ácido Acético , Clostridium , Etanol , Fermentación , Filogenia , ARN Ribosómico 16S , Ácido Acético/metabolismo , Etanol/metabolismo , Clostridium/genética , Clostridium/metabolismo , Clostridium/clasificación , ARN Ribosómico 16S/genética , Termotolerancia , Aguas del Alcantarillado/microbiología , Concentración de Iones de Hidrógeno , Caprilatos/metabolismo , Temperatura , CaproatosRESUMEN
Reductive soil disinfestation (RSD), also known as biological soil disinfestation, is a bioremediation method used to suppress soil-borne plant pathogens by stimulating the activity of indigenous anaerobic bacteria in the soil. An anaerobic bacterial strain (E14T) was isolated from an anoxic soil sample subjected to RSD treatment and then comprehensively characterized. Cells of the strain were Gram-stain-positive, curved to sigmoid, and spore-forming rods. Cells were motile with a polar flagellum. Strain E14T grew in peptone-yeast extract broth, indicating that it utilized proteinous compounds. Strain E14T was also saccharolytic and produced acetate, isobutyrate, butyrate, isovalerate and gases (H2 and CO2) as fermentation products. The strain did not decompose any of examined polysaccharides except for starch. The major cellular fatty acids of strain E14T were iso-C15:0 and iso-C15:0 DMA. The closest relative to strain E14T, based on 16S rRNA gene sequences, was Clostridium thermarum SYSU GA15002T (96.2â%) in the Clostridiaceae. Whole-genome analysis of strain E14T showed that its genome was 4.66 Mb long with a genomic DNA G+C content of 32.5 mol%. The average nucleotide identity (ANIb) between strain E14T and C. thermarum SYSU GA15002T was 69.0â%. The presence of the genes encoding glycolysis and butyrate production via the acetyl-CoA pathway was confirmed through genome analysis. Based on the obtained phylogenetic, genomic and phenotypic data, we propose that strain E14T should be assigned to the genus Clostridium in the family Clostridiaceae as Clostridium omnivorum sp. nov. The type strain is E14T (=NBRC 115133T=DSM 114974T).
Asunto(s)
Técnicas de Tipificación Bacteriana , Composición de Base , Clostridium , ADN Bacteriano , Ácidos Grasos , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Microbiología del Suelo , ARN Ribosómico 16S/genética , Clostridium/genética , Clostridium/aislamiento & purificación , Clostridium/clasificación , ADN Bacteriano/genética , Genoma Bacteriano , Anaerobiosis , Biodegradación AmbientalRESUMEN
A Gram-stain-positive, strictly anaerobic, endospore-forming and rod-shaped (0.6-0.8×2.7-13.1 µm) bacterium, designated as 5 N-1T, was isolated from a yellow water sample collected from the manufacturing process of Nongxiangxing baijiu in the Yibin region of Sichuan, PR China. Growth occurred at 15-40â°C (optimum growth at 37â°C), at pH 6.0-9.0 (optimum growth at pH 7.0) and in NaCl concentrations of 0-1â% (w/v) and ethanol concentrations of 0-2â% (v/v). The major fatty acids in strain 5 N-1T were C16â:â0, C18â:â0 and C14â:â0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids and one unidentified lipid. Phylogenetic analysis of its 16S rRNA gene sequence indicated that strain 5 N-1T was most closely related to Clostridium weizhouense YB-6T (97.70â%) and Clostridium uliginosum DSM 12992T (97.56â%). The average nucleotide identity and digital DNAâDNA hybridization values between strain 5 N-1T and the above two type strains were 80.89 and 80.05â% and 25.80 and 25.30â%, respectively, which were all below the species thresholds. The genome size of strain 5 N-1T was 3.5 Mbp and the DNA G+C content was 27.5 mol%. Based on the results of phenotypic and genotypic analyses, strain 5 N-1T represents a novel species of the genus Clostridium, for which the name Clostridium aquiflavi sp. nov. is proposed. The type strain is Clostridium aquiflavi 5 N-1T (=CICC 24886T=JCM 35355T).
Asunto(s)
Técnicas de Tipificación Bacteriana , Composición de Base , Clostridium , ADN Bacteriano , Ácidos Grasos , Hibridación de Ácido Nucleico , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , China , ARN Ribosómico 16S/genética , Ácidos Grasos/análisis , ADN Bacteriano/genética , Clostridium/genética , Clostridium/aislamiento & purificación , Clostridium/clasificación , Microbiología del Agua , Fosfolípidos/análisisRESUMEN
A strictly anaerobic, Gram-stain-negative rod-shaped bacterium, designated A1-XYC3T, was isolated from the faeces of an alpaca (Lama pacos). On the basis of the results of a comparative 16S rRNA gene sequence analysis, the isolate was assigned to the genus Clostridium with the highest sequence similarities to Clostridium magnum DSM 2767T (96.8â%), Clostridium carboxidivorans P7T (96.3â%) and Clostridium aciditolerans JW/YJL-B3T (96.1â%). The average nucleotide identity between A1-XYC3T, C. magnum, C. carboxidivorans and C. aciditolerans was 77.4, 76.1 and 76.6ââ%, respectively. The predominant components of the cellular fatty acids of A1-XYC3T were C14â:â0, C16â:â0 and summed feature 10, containing C18:0/C17:0 cyclo. The DNA G+C content was 32.4 mol%. On the basis of biochemical, phylogenetic, genotypic and chemotaxonomic criteria, this isolate represents a novel species within Clostridium sensu stricto for which the name Clostridium tanneri sp. nov. is proposed. The type strain of this species is strain A1-XYC3T (=CCM 9376T=NRRL B-65691T).
Asunto(s)
Técnicas de Tipificación Bacteriana , Composición de Base , Camélidos del Nuevo Mundo , Clostridium , ADN Bacteriano , Ácidos Grasos , Heces , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Camélidos del Nuevo Mundo/microbiología , Heces/microbiología , ARN Ribosómico 16S/genética , Animales , Clostridium/genética , Clostridium/clasificación , Clostridium/aislamiento & purificación , ADN Bacteriano/genética , Ácidos Grasos/análisis , Datos de Secuencia MolecularRESUMEN
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs and as commensals or infecting pathogens in human and animal populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
Asunto(s)
Infecciones por Clostridium , Salud Única , Humanos , Infecciones por Clostridium/microbiología , Infecciones por Clostridium/epidemiología , Animales , Clostridium/genética , Clostridium/aislamiento & purificación , Clostridium/clasificación , Brotes de Enfermedades/prevención & control , Genómica/métodos , Toxinas Bacterianas/genéticaRESUMEN
Members of the genus Clostridium are frequently associated with meat spoilage. The ability for low numbers of spores of certain Clostridium species to germinate in cold-stored vacuum-packed meat can result in blown pack spoilage. However, little is known about the germination process of these clostridia, despite this characteristic being important for their ability to cause spoilage. This study sought to determine the genomic conditions for germination of 37 representative Clostridium strains from seven species (C. estertheticum, C. tagluense, C. frigoris, C. gasigenes, C. putrefaciens, C. aligidicarnis and C. frigdicarnis) by comparison with previously characterized germination genes from C. perfringens, C. sporogenes and C. botulinum. All the genomes analysed contained at least one gerX operon. Seven different gerX operon configuration types were identified across genomes from C. estertheticum, C. tagluense and C. gasigenes. Differences arose between the C. gasigenes genomes and those belonging to C. tagluense/C. estertheticum in the number and type of genes coding for cortex lytic enzymes, suggesting the germination pathway of C. gasigenes is different. However, the core components of the germination pathway were conserved in all the Clostridium genomes analysed, suggesting that these species undergo the same major steps as Bacillus subtilis for germination to occur.
Asunto(s)
Clostridium/crecimiento & desarrollo , Clostridium/genética , Carne/microbiología , Esporas Bacterianas/crecimiento & desarrollo , Esporas Bacterianas/genética , Clostridium/clasificación , Hibridación Genómica Comparativa , ADN Bacteriano , Microbiología de Alimentos , Genes Bacterianos , Genoma BacterianoRESUMEN
Some species of the genus Clostridium are efficient acetate producers and have been deemed useful for upgrading industrial biogas. An acetogenic, strictly anaerobic, Gram-stain-positive, subterminal endospore-forming bacterium designated strain PL3T was isolated from peatland soil enrichments with H2 and CO2. Cells of strain PL3T were 0.8-1.0×4.0-10.0 µm in size and rod-shaped. Growth of strain PL3T occurred at pH 6.0-7.5 (optimum, pH 7.0), at 20-40 °C (optimum, 30 °C) and with 0-1.5â% (w/v) NaCl (optimum, 0.5%). Biochemical analyses revealed that strain PL3T metabolized lactose, maltose, raffinose, rhamnose, lactic acid, sorbitol, arabinose and glycerol. Acetic acid was the predominant metabolite under anaerobic respiration with H2/CO2. The major cellular fatty acids were C16â:â0, C16â:â1 cis 9 and C17â:â0 cyc. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, aminolipid and aminophospholipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PL3T belongs to the genus Clostridium with the highest sequence similarity to Clostridium aciditolerans DSM 17425T (98.6â%) followed by Clostridium nitrophenolicum (97.8â%). The genomic DNA G+C content of strain PL3T was 31.1 mol%.The genomic in silico DNA-DNA hybridization value between strain PL3T and C. aciditolerans DSM 17425T was 25.1â%, with an average nucleotide identity of 80.2â%. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain PL3T was suggested to represent a novel species of the genus Clostridium, for which the name Clostridium thailandense sp. nov. is proposed. The type strain is PL3T (=DSM 111812T=TISTR 2984T).
Asunto(s)
Dióxido de Carbono , Clostridium/clasificación , Filogenia , Microbiología del Suelo , Sphagnopsida/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , Dióxido de Carbono/metabolismo , Clostridium/aislamiento & purificación , ADN Bacteriano/genética , Ácidos Grasos/química , Hibridación de Ácido Nucleico , Fosfolípidos/química , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
A rod-shaped, Gram-stain-negative, strictly anaerobic, catalase-negative and endospore-forming bacterial strain CSC2T was isolated from corn silage preserved in Tochigi, Japan. The strain CSC2T grew at 15-40 °C, at pH 5.0-7.7 and with up to 0.5â% (w/v) NaCl. The main cellular fatty acids were C14â:â0, C16â:â0 and C16â:â0 dimethyl acetal. The cellular polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidic acid, lysophosphatidylethanolamine, phosphatidylserine, lysophosphatidylcholine and two unidentified polar lipids. Phylogenetic analysis of the 16S rRNA gene showed that strain CSC2T was a member of the genus Clostridium and closely related to Clostridium polyendosporum DSM 57272T (95.6â% gene sequence similarity) and Clostridium fallax ATCC 19400T (95.3â%). The genomic DNA G+C content of strain CSC2T was 31.1âmol% (whole genome analysis). The average nucleotide identity based on blast and digital DNA-DNA hybridization values between strain CSC2T and the type strains of phylogenetically related species were below 71 and 24â%, respectively. On the basis of the genotypic, phenotypic and chemotaxonomic characteristics, it is proposed to designate strain CSC2T as representing Clostridium zeae sp. nov. The type strain is CSC2T (=MAFF212476T=JCM 33766T=DSM 111242T).
Asunto(s)
Clostridium/clasificación , Filogenia , Ensilaje , Zea mays , Técnicas de Tipificación Bacteriana , Composición de Base , Clostridium/aislamiento & purificación , ADN Bacteriano/genética , Ácidos Grasos/química , Japón , Fosfolípidos/química , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Ensilaje/microbiología , Zea mays/microbiologíaRESUMEN
The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection (C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi. Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA-DNA hybridization values of 98.3 and 87.9â%, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis.
Asunto(s)
Clostridium , Filogenia , Técnicas de Tipificación Bacteriana , Composición de Base , Clostridium/clasificación , Clostridium/aislamiento & purificación , ADN Bacteriano/genética , Ácidos Grasos/química , Hibridación de Ácido Nucleico , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
The transfer of blown pack spoilage causing Clostridium spores from the farm to the meat plant is of growing concern to the meat industry. This study investigated the environmental niches of these Clostridium spp., specifically Clostridium estertheticum and Clostridium gasigenes in the beef and sheep farm environments in New Zealand. Faecal, soil, grass, drinking water, puddle water and feed (fodder beet, hay, bailage and silage, where available) samples were collected on five beef and sheep farms during Winter and Spring in 2018, in North and South Island, respectively. Beef and sheep farm samples were tested for C. estertheticum and C. gasigenes using enrichment plus PCR, qPCR and direct plating. C. estertheticum was detected in bovine faecal (4%), soil (2-18%) and grass (0-12%) samples at concentration of up to 2.0 log10 cfu/g. C. gasigenes were found in 18-46% of faecal, 16-82% of soil, 12-44% of grass, 0-44.4% of drinking water and 0-58.3% of puddle water samples tested and the direct counts ranged from 2.4 log10 cfu/ml in puddle water to 3.4 log10 cfu/g in soil. C. estertheticum were detected by qPCR in sheep farms in ovine feces (2.3%), soil (2.3%) and fodder beet (10%). All other sample types (grass, drinking water, puddle water, baleage, hay, silage and fodder beet) were negative using direct and enrichment plus PCR methods. In contrast C. gasigenes was detected in of faecal (22.7-38.6%), soil (22.7-84.1%), grass (17.5-34.1%) drinking water (35.7-78.6%), puddle water (33.3-40%), hay baleage (57%), silage (2%) and fodder beet (10%) at concentrations of up to 3.7 log10 cfu/g/ml. It was concluded that C. estertheticum and C. gasigenes were common on beef and sheep farms with the latter having higher incidence and mean concentration.
Asunto(s)
Clostridium/crecimiento & desarrollo , Microbiología Ambiental , Carne/microbiología , Mataderos , Crianza de Animales Domésticos , Animales , Bovinos , Clostridium/clasificación , Clostridium/genética , Clostridium/aislamiento & purificación , Granjas , Heces/microbiología , Contaminación de Alimentos/análisis , Embalaje de Alimentos/instrumentación , Embalaje de Alimentos/métodos , Carne/análisis , Nueva Zelanda , Reacción en Cadena en Tiempo Real de la Polimerasa , Estaciones del Año , OvinosRESUMEN
Fatty liver disease is the most common liver disease in the world. Its connection with the gut microbiome has been known for at least 80 y, but this association remains mostly unstudied in the general population because of underdiagnosis and small sample sizes. To address this knowledge gap, we studied the link between the Fatty Liver Index (FLI), a well-established proxy for fatty liver disease, and gut microbiome composition in a representative, ethnically homogeneous population sample of 6,269 Finnish participants. We based our models on biometric covariates and gut microbiome compositions from shallow metagenome sequencing. Our classification models could discriminate between individuals with a high FLI (≥60, indicates likely liver steatosis) and low FLI (<60) in internal cross-region validation, consisting of 30% of the data not used in model training, with an average AUC of 0.75 and AUPRC of 0.56 (baseline at 0.30). In addition to age and sex, our models included differences in 11 microbial groups from class Clostridia, mostly belonging to orders Lachnospirales and Oscillospirales. Our models were also predictive of the high FLI group in a different Finnish cohort, consisting of 258 participants, with an average AUC of 0.77 and AUPRC of 0.51 (baseline at 0.21). Pathway analysis of representative genomes of the positively FLI-associated taxa in (NCBI) Clostridium subclusters IV and XIVa indicated the presence of, e.g., ethanol fermentation pathways. These results support several findings from smaller case-control studies, such as the role of endogenous ethanol producers in the development of the fatty liver.
Asunto(s)
Bacterias/clasificación , Bacterias/crecimiento & desarrollo , Hígado Graso/microbiología , Microbioma Gastrointestinal , Adulto , Factores de Edad , Bacterias/genética , Bacterias/metabolismo , Clostridium/clasificación , Clostridium/genética , Clostridium/crecimiento & desarrollo , Clostridium/metabolismo , Estudios de Cohortes , Etanol/metabolismo , Femenino , Fermentación , Genoma Bacteriano , Humanos , Masculino , Metagenoma , Persona de Mediana Edad , Filogenia , Factores SexualesRESUMEN
Clostridioides difficile is an emerging One Health pathogen and a common etiologic agent of diarrhea, both in healthcare settings and the community. This bacterial species is highly diverse, and its global population has been classified in eight clades by multilocus sequence typing (MLST). The C. difficile MLST Clade 2 includes the NAP1/RT027/ST01 strain, which is highly recognized due to its epidemicity and association with severe disease presentation and mortality. By contrast, the remaining 83 sequence types (STs) that compose this clade have received much less attention. In response to this shortcoming, we reviewed articles published in English between 1999 and 2020 and collected information for 27 Clade 2 STs, with an emphasis on STs 01, 67, 41 and 188/231/365. Our analysis provides evidence of large phenotypic differences that preclude support of the rather widespread notion that ST01 and Clade 2 strains are "hypervirulent". Moreover, it revealed a profound lack of (meta)data for nearly 70% of the Clade 2 STs that have been identified in surveillance efforts. Targeted studies aiming to relate wet-lab and bioinformatics results to patient and clinical parameters should be performed to gain a more in-depth insight into the biology of this intriguing group of C. difficile isolates.
Asunto(s)
Infecciones por Clostridium/epidemiología , Infecciones por Clostridium/fisiopatología , Clostridium/clasificación , Clostridium/genética , Virulencia/genética , Técnicas de Tipificación Bacteriana , Variación Genética , Genotipo , Humanos , Epidemiología Molecular , FilogeniaRESUMEN
Bacterial species belonging to the genus Clostridium have been recognized as causative agents of blown pack spoilage (BPS) in vacuum packed meat products. Whole-genome sequencing of six New Zealand psychrotolerant clostridia isolates derived from three meat production animal types and their environments was performed to examine their roles in BPS. Comparative genome analyses have provided insight into the genomic diversity and physiology of these bacteria and divides clostridia into two separate species clusters. BPS-associated clostridia encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) that enable them to utilize the intramuscular carbohydrate stores and facilitate sporulation. In total, 516 glycoside hydrolases (GHs), 93 carbohydrate esterases (CEs), 21 polysaccharide lyases (PLs), 434 glycosyl transferases (GTs) and 211 carbohydrate-binding protein modules (CBM) with predicted activities involved in the breakdown and transport of carbohydrates were identified. Clostridia genomes have different patterns of CAZyme families and vary greatly in the number of genes within each CAZy category, suggesting some level of functional redundancy. These results suggest that BPS-associated clostridia occupy similar environmental niches but apply different carbohydrate metabolism strategies to be able to co-exist and cause meat spoilage.
Asunto(s)
Clostridium/genética , Clostridium/aislamiento & purificación , Productos de la Carne/microbiología , Animales , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Bovinos , Clostridium/clasificación , Esterasas/genética , Esterasas/metabolismo , Embalaje de Alimentos , Inocuidad de los Alimentos , Genoma Bacteriano , Glicósido Hidrolasas/genética , Glicósido Hidrolasas/metabolismo , Productos de la Carne/análisis , Nueva Zelanda , Polisacárido Liasas/genética , Polisacárido Liasas/metabolismo , VacioRESUMEN
Sixty vacuum-packed beef samples retailed in Germany were investigated for the occurrence of cold-tolerant Clostridium spp. After a storage period at 4 °C for eight weeks, meat juice from all samples was processed for culturing, DNA extraction and SYBR green qPCR for Clostridium species. After that, a previously developed multiplex qPCR, sequence analysis of the 16S rRNA gene, and MALDI-TOF MS were applied in order to identify Clostridium spp. found in samples. Subsequently, 23 samples were found positive for C. frigoriphilum (n = 19), C. estertheticum (n = 2), C. tagluense (n = 1) and C. lacusfryxellense/C. frigoris (n = 1). By using a new multiplex qPCR and a new RFLP method developed in this study, a further 15 meat juice samples were revealed to be contaminated with C. algidicarnis. With some samples being co-contaminated with two different species, 53% (n = 32) of all investigated vacuum-packed beef samples were found to be positive for cold-tolerant clostridia. This is the first report of detection and identification of C. algidicarnis in meat samples in Germany and Central Europe.
Asunto(s)
Clostridium/aislamiento & purificación , Embalaje de Alimentos , Carne Roja/microbiología , Animales , Bovinos , Clostridium/clasificación , Clostridium/fisiología , Frío , Europa (Continente) , Alemania , Reacción en Cadena de la Polimerasa Multiplex , ARN Ribosómico 16S/genética , VacioRESUMEN
An obligately anaerobic, Gram-stain-positive and spore-forming strain, SNUG30386T was isolated from a faecal sample of a healthy Korean subject. The strain formed a round ivory-coloured colony and cells were chained rods with tapered ends, approximately 2.0-2.5×0.6-0.8 µm in size. The taxonomic analysis indicated that strain SNUG30386T was within the family Lachnospiraceae. According to the 16S rRNA gene sequence similarity, the closest species to strain SNUG30386T was Clostridium symbiosum (95.6â%), followed by Enterocloster asparagiformis (94.8â%), Enterocloster clostridioformis (94.8â%) and Enterocloster lavalensis (94.6â%). The evolutionary tree based on 16S rRNA gene sequences demonstrated that strain SNUG30386T had split apart at a unique branch point far from other close relatives. Its DNA G+C content was 48.3âmol% calculated from the whole genome sequence. The major cellular fatty acids were C16â:â0 and C14â:â0. Compared to those of the closely related species, strain SNUG30386T showed distinct biochemical activities such as being unable to utilize most of carbon sources except d-glucose and l-arabinose. As a result, based on its unique phylogenetic clade and taxonomic characteristics, we conclude that strain SNUG30386T represents a novel species within the genus Clostridium, for which the name Clostridium fessum sp. nov. is proposed. The type strain of the novel species is SNUG30386T (=KCTC 15633T= JCM 32258T).
Asunto(s)
Clostridium/clasificación , Heces/microbiología , Filogenia , Técnicas de Tipificación Bacteriana , Composición de Base , Clostridium/aislamiento & purificación , ADN Bacteriano/genética , Ácidos Grasos/química , Humanos , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADNRESUMEN
Clostridium diolis DSM 15410 is a type strain of solventogenic clostridium capable of conducting isopropanol-butanol-ethanol fermentation. By studying its growth on different carbohydrates, we verified its ability to utilize glycerol and produce 1,3-propanediol and discovered its ability to produced isopropanol. Complete genome sequencing showed that its genome is a single circular chromosome and belongs to the cluster I (sensu scricto) of the genus Clostridium. By cultivation analysis we highlighted its specific behavior in comparison to two selected closely related strains. Despite the fact that several CRISPR loci were found, 16 putative prophages showed the ability to receive foreign DNA. Thus, the strain has the necessary features for future engineering of its 1,3-propanediol biosynthetic pathway and for the possible industrial utilization in the production of biofuels.
Asunto(s)
2-Propanol/metabolismo , Clostridium/genética , Genoma Bacteriano , Filogenia , Glicoles de Propileno/metabolismo , Biocombustibles , Clostridium/clasificación , Clostridium/metabolismo , Microbiología Industrial , FenotipoRESUMEN
Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.
Asunto(s)
Bacterias/clasificación , Bacterias/aislamiento & purificación , Microbioma Gastrointestinal , Intestinos/microbiología , Filogenia , Porcinos/microbiología , Anciano de 80 o más Años , Animales , Bacterias/genética , Bacterias/metabolismo , Ácidos y Sales Biliares/metabolismo , Biodiversidad , Clostridium/clasificación , Clostridium/genética , Clostridium/aislamiento & purificación , Heces/microbiología , Femenino , Microbioma Gastrointestinal/genética , Genes Bacterianos/genética , Especificidad del Huésped , Humanos , Masculino , Metagenoma , Familia de Multigenes , ARN Ribosómico 16SRESUMEN
Overweight and obese individuals may have leaky intestinal barrier and microbiome dysbiosis. The aim of this study was to determine whether body mass reduction with diet and synbiotics in an adult person with excess body mass has an influence on the gut microbiota and zonulin concentration. The study was a single blinded trial. 60 persons with excess body mass were examined. Based on randomization, patients were qualified either to the intervention group (Synbiotic group) or to the control group (Placebo group). Anthropometric measurements, microbiological assessment of faecal samples and zonulin concentration in the stool were performed before and after observation. After 3-months, an increase in the variety of intestinal bacteria (increase in the Shannon-Weaver index and the Simpson index) and a decrease in concentration of zonulin in faecal samples were observed in the Synbiotic group. Also, statistically significant correlation between zonulin and Bifidobacterium spp. (Spearman test, R=-0.51; p=0.0040) was noticed. There were no significant relationships between the body mass, BMI and changes in the intestinal microbiota or zonulin concentrations. The use of diet and synbiotics improved the condition of the microbiota and intestinal barrier in patients in the Synbiotic group.
Asunto(s)
Microbioma Gastrointestinal/fisiología , Obesidad/dietoterapia , Simbióticos/administración & dosificación , Adulto , Bacteroides/clasificación , Bacteroides/aislamiento & purificación , Bacteroides/fisiología , Bifidobacterium/clasificación , Bifidobacterium/aislamiento & purificación , Bifidobacterium/fisiología , Índice de Masa Corporal , Clostridium/clasificación , Clostridium/aislamiento & purificación , Clostridium/fisiología , Dieta/métodos , Enterococcus/clasificación , Enterococcus/aislamiento & purificación , Enterococcus/fisiología , Escherichia coli/clasificación , Escherichia coli/aislamiento & purificación , Escherichia coli/fisiología , Heces/microbiología , Femenino , Haptoglobinas/metabolismo , Humanos , Intestinos/microbiología , Lactobacillus/clasificación , Lactobacillus/aislamiento & purificación , Lactobacillus/fisiología , Masculino , Persona de Mediana Edad , Obesidad/microbiología , Permeabilidad , Estudios Prospectivos , Precursores de Proteínas/metabolismo , Proteus/clasificación , Proteus/aislamiento & purificación , Proteus/fisiología , Pseudomonas/clasificación , Pseudomonas/aislamiento & purificación , Pseudomonas/fisiologíaRESUMEN
Clostridium like species, particularly Clostridium perfrigens, are the second most common causes of human anaerobic infections, including myonecrosis and bacteremia. Clostridium paraputrificum is an infrequent isolate, which has been identified in only 1% of reported cases of clostridial infections. We herein report a rare case of C. paraputrificum bacteremia in a 78-year-old Caucasian man diagnosed with an intestinal carcinoma and liver neoplastic lesions. The isolate was susceptible to chloramphenicol, meropenem, metronidazole, vancomycin, and resistant to clindamycin and penicillin, and the patient was successfully treated with metronidazole. Malignancy and inflammatory bowel diseases are often associated with clostridial bacteremia, which cannot be neglected.