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1.
Artigo em Inglês | MEDLINE | ID: mdl-38728064

RESUMO

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 (96.8 %), Clostridium carboxidivorans P7T (96.3 %) and Clostridium aciditolerans JW/YJL-B3T (96.1 %). The average nucleotide identity between A1-XYC3T, C. magnum, C. carboxidivorans and C. aciditolerans was 77.4, 76.1 and 76.6  %, respectively. The predominant components of the cellular fatty acids of A1-XYC3T were C14 : 0, C16 : 0 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).


Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , Camelídeos Americanos , Clostridium , DNA Bacteriano , Ácidos Graxos , Fezes , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , Camelídeos Americanos/microbiologia , Fezes/microbiologia , RNA Ribossômico 16S/genética , Animais , Clostridium/genética , Clostridium/classificação , Clostridium/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/análise , Dados de Sequência Molecular
2.
Artigo em Inglês | MEDLINE | ID: mdl-35188883

RESUMO

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 0-1.5 % (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 C16 : 0, C16 : 1 cis 9 and C17 : 0 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 (98.6 %) followed by Clostridium nitrophenolicum (97.8 %). 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 25.1 %, with an average nucleotide identity of 80.2 %. 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).


Assuntos
Dióxido de Carbono , Clostridium/classificação , Filogenia , Microbiologia do Solo , Sphagnopsida/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Dióxido de Carbono/metabolismo , Clostridium/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
3.
Microb Genom ; 8(2)2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-35166653

RESUMO

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.


Assuntos
Clostridium/crescimento & desenvolvimento , Clostridium/genética , Carne/microbiologia , Esporos Bacterianos/crescimento & desenvolvimento , Esporos Bacterianos/genética , Clostridium/classificação , Hibridização Genômica Comparativa , DNA Bacteriano , Microbiologia de Alimentos , Genes Bacterianos , Genoma Bacteriano
4.
Int J Syst Evol Microbiol ; 71(11)2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34748474

RESUMO

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 0.5 % (w/v) NaCl. The main cellular fatty acids were C14 : 0, C16 : 0 and C16 : 0 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 (95.6 % gene sequence similarity) and Clostridium fallax ATCC 19400T (95.3 %). The genomic DNA G+C content of strain CSC2T was 31.1 mol% (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 24 %, 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).


Assuntos
Clostridium/classificação , Filogenia , Silagem , Zea mays , Técnicas de Tipagem Bacteriana , Composição de Bases , Clostridium/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Japão , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Silagem/microbiologia , Zea mays/microbiologia
5.
Artigo em Inglês | MEDLINE | ID: mdl-34379581

RESUMO

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 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis.


Assuntos
Clostridium , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Clostridium/classificação , Clostridium/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
6.
Food Microbiol ; 98: 103769, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-33875205

RESUMO

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.


Assuntos
Clostridium/crescimento & desenvolvimento , Microbiologia Ambiental , Carne/microbiologia , Matadouros , Criação de Animais Domésticos , Animais , Bovinos , Clostridium/classificação , Clostridium/genética , Clostridium/isolamento & purificação , Fazendas , Fezes/microbiologia , Contaminação de Alimentos/análise , Embalagem de Alimentos/instrumentação , Embalagem de Alimentos/métodos , Carne/análise , Nova Zelândia , Reação em Cadeia da Polimerase em Tempo Real , Estações do Ano , Ovinos
7.
Anaerobe ; 69: 102355, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33711422

RESUMO

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.


Assuntos
Infecções por Clostridium/epidemiologia , Infecções por Clostridium/fisiopatologia , Clostridium/classificação , Clostridium/genética , Virulência/genética , Técnicas de Tipagem Bacteriana , Variação Genética , Genótipo , Humanos , Epidemiologia Molecular , Filogenia
8.
Gut Microbes ; 13(1): 1-22, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33651661

RESUMO

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.


Assuntos
Bactérias/classificação , Bactérias/crescimento & desenvolvimento , Fígado Gorduroso/microbiologia , Microbioma Gastrointestinal , Adulto , Fatores Etários , Bactérias/genética , Bactérias/metabolismo , Clostridium/classificação , Clostridium/genética , Clostridium/crescimento & desenvolvimento , Clostridium/metabolismo , Estudos de Coortes , Etanol/metabolismo , Feminino , Fermentação , Genoma Bacteriano , Humanos , Masculino , Metagenoma , Pessoa de Meia-Idade , Filogenia , Fatores Sexuais
9.
Int J Food Microbiol ; 340: 109053, 2021 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-33461000

RESUMO

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.


Assuntos
Clostridium/isolamento & purificação , Embalagem de Alimentos , Carne Vermelha/microbiologia , Animais , Bovinos , Clostridium/classificação , Clostridium/fisiologia , Temperatura Baixa , Europa (Continente) , Alemanha , Reação em Cadeia da Polimerase Multiplex , RNA Ribossômico 16S/genética , Vácuo
10.
Food Microbiol ; 95: 103687, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33397617

RESUMO

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.


Assuntos
Clostridium/genética , Clostridium/isolamento & purificação , Produtos da Carne/microbiologia , Animais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bovinos , Clostridium/classificação , Esterases/genética , Esterases/metabolismo , Embalagem de Alimentos , Inocuidade dos Alimentos , Genoma Bacteriano , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Produtos da Carne/análise , Nova Zelândia , Polissacarídeo-Liases/genética , Polissacarídeo-Liases/metabolismo , Vácuo
11.
Artigo em Inglês | MEDLINE | ID: mdl-33253079

RESUMO

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 (95.6 %), followed by Enterocloster asparagiformis (94.8 %), Enterocloster clostridioformis (94.8 %) and Enterocloster lavalensis (94.6 %). 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 48.3 mol% calculated from the whole genome sequence. The major cellular fatty acids were C16 : 0 and C14 : 0. 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).


Assuntos
Clostridium/classificação , Fezes/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Clostridium/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Humanos , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA
12.
Genomics ; 113(1 Pt 2): 1109-1119, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33166602

RESUMO

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.


Assuntos
2-Propanol/metabolismo , Clostridium/genética , Genoma Bacteriano , Filogenia , Propilenoglicóis/metabolismo , Biocombustíveis , Clostridium/classificação , Clostridium/metabolismo , Microbiologia Industrial , Fenótipo
13.
Acta Biochim Pol ; 67(4): 571-578, 2020 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-33326198

RESUMO

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.


Assuntos
Microbioma Gastrointestinal/fisiologia , Obesidade/dietoterapia , Simbióticos/administração & dosagem , Adulto , Bacteroides/classificação , Bacteroides/isolamento & purificação , Bacteroides/fisiologia , Bifidobacterium/classificação , Bifidobacterium/isolamento & purificação , Bifidobacterium/fisiologia , Índice de Massa Corporal , Clostridium/classificação , Clostridium/isolamento & purificação , Clostridium/fisiologia , Dieta/métodos , Enterococcus/classificação , Enterococcus/isolamento & purificação , Enterococcus/fisiologia , Escherichia coli/classificação , Escherichia coli/isolamento & purificação , Escherichia coli/fisiologia , Fezes/microbiologia , Feminino , Haptoglobinas/metabolismo , Humanos , Intestinos/microbiologia , Lactobacillus/classificação , Lactobacillus/isolamento & purificação , Lactobacillus/fisiologia , Masculino , Pessoa de Meia-Idade , Obesidade/microbiologia , Permeabilidade , Estudos Prospectivos , Precursores de Proteínas/metabolismo , Proteus/classificação , Proteus/isolamento & purificação , Proteus/fisiologia , Pseudomonas/classificação , Pseudomonas/isolamento & purificação , Pseudomonas/fisiologia
14.
Nat Commun ; 11(1): 6389, 2020 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-33319778

RESUMO

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.


Assuntos
Bactérias/classificação , Bactérias/isolamento & purificação , Microbioma Gastrointestinal , Intestinos/microbiologia , Filogenia , Suínos/microbiologia , Idoso de 80 Anos ou mais , Animais , Bactérias/genética , Bactérias/metabolismo , Ácidos e Sais Biliares/metabolismo , Biodiversidade , Clostridium/classificação , Clostridium/genética , Clostridium/isolamento & purificação , Fezes/microbiologia , Feminino , Microbioma Gastrointestinal/genética , Genes Bacterianos/genética , Especificidade de Hospedeiro , Humanos , Masculino , Metagenoma , Família Multigênica , RNA Ribossômico 16S
15.
Anaerobe ; 66: 102292, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33171286

RESUMO

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.


Assuntos
Infecções por Clostridium/diagnóstico , Infecções por Clostridium/microbiologia , Idoso , Antibacterianos/uso terapêutico , Bacteriemia/diagnóstico , Bacteriemia/tratamento farmacológico , Bacteriemia/microbiologia , Clostridium/classificação , Clostridium/efeitos dos fármacos , Clostridium/isolamento & purificação , Infecções por Clostridium/tratamento farmacológico , Humanos , Doenças Inflamatórias Intestinais/complicações , Neoplasias Intestinais/complicações , Masculino , Testes de Sensibilidade Microbiana , Fatores de Risco , Resultado do Tratamento
16.
Int J Biol Macromol ; 165(Pt A): 665-674, 2020 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-32946938

RESUMO

The non-tasting form of the bitter taste receptor, TAS2R38, has been shown as a genetic risk factor associated with the development of Parkinson's disease (PD). Specific taste receptors that are expressed in the lower gastrointestinal tract may respond to alteration in gut microbiota composition, detecting bacterial molecules, and regulate immune responses. Given the importance of brain-gut-microbiota axis and gene-environment interactions in PD, we investigate the associations between the genetic variants of TAS2R38 and gut microbiota composition in 39 PD patients. The results confirm that the majority of PD patients have reduced sensitivity to 6-n-propylthiouracil (PROP) and are carriers of at least one non-functional TAS2R38 AVI haplotype. Moreover, we found this correlation to be associated with a reduction in bacteria alpha-diversity with a predominant reduction of Clostridium genus. We hypothesised that the high frequency of the non-taster form of TAS2R38 associated with a diminuition of Clostridium bacteria in PD might determine a reduction in the activation of protective signalling-molecules useful in preserving gut homeostasis. This pilot study, by identifying a decrease in specific bacteria associated with a reduced sensitivity to PROP, adds essential information that opens new avenues of research into the association of PD microbiota composition and sensory modification.


Assuntos
Clostridium/classificação , Microbioma Gastrointestinal , Variação Genética , Doença de Parkinson , Receptores Acoplados a Proteínas G/genética , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Doença de Parkinson/genética , Doença de Parkinson/microbiologia , Projetos Piloto , Fatores de Risco
17.
Syst Appl Microbiol ; 43(5): 126104, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32847779

RESUMO

Lignocellulose is considered a major source of renewable energy that serve as an alternative to the fossil fuels. Members of the genus Clostridium are some of the many microorganisms that have the ability to degrade lignocellulose efficiently to sugar, which can be further converted to biofuel. In this study, we isolated twelve Clostridium strains from hot spring samples of Yunnan and Tibet, of which isolates SYSU GA15002T and SYSU GA17076 showed low 16S rRNA gene sequence identity profiles to any of the validly named Clostridium strains (<94.0%). Studies using a polyphasic taxonomy approach concluded that the two isolates represent one novel species of the genus Clostridium, for which we propose the name Clostridium thermarum sp. nov., with SYSU GA15002T as the type strain of the species. Isolate SYSU GA15002T has an optimum growth temperature at 45°C. Fermentation of the substrates cellobiose, cellulose, xylan and untreated straw powder by this strain results in the production of ethanol, along with acetate and formate. The complete pathways for the conversion of cellulose and xylan to ethanol is also predicted from the genome of isolate SYSU GA15002T, which revealed a single step conversion of lignocellulosic biomass through consolidated bioprocessing. This paper is a comprehensive study encompassing isolation, polyphasic taxonomy, lignocellulose biodegradation and the genomic information of Clostridium in Yunnan-Tibet hot springs.


Assuntos
Clostridium/isolamento & purificação , Clostridium/metabolismo , Etanol/metabolismo , Fontes Termais/microbiologia , Lignina/metabolismo , Técnicas de Tipagem Bacteriana , Celobiose/metabolismo , Celulose/metabolismo , China , Clostridium/classificação , Clostridium/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , Fermentação , Genes de RNAr , Genoma Bacteriano , Lipídeos/análise , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tibet , Xilanos/metabolismo
18.
Lett Appl Microbiol ; 71(6): 660-666, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32608530

RESUMO

Blown pack spoilage (BPS) of vacuum packaged beef is caused by psychrotolerant and psychrophilic Clostridium species, primarily Clostridium estertheticum and Clostridium gasigenes. The aim of this study was to investigate the environmental niches and impact of season on these BPS Clostridium spp. on Irish beef farms. On each of five different beef farms, faecal (10), soil (5), silage (5), air (5), bedding straw (5), drinking water (5) and puddle/ditch water (5) samples were collected during Spring, Summer, Autumn and Winter and tested for C. estertheticum and C. gasigenes using culture (direct plating and enrichment) and molecular (conventional PCR and quantitative PCR (qPCR)) based techniques. C. estertheticum and C. gasigenes were detected in all sample types, with qPCR detection rates ranging from 4% to 50% and at concentrations of up to 1·5 log10 CFU per g and 3·5 log10 CFU per g, respectively. The impact of season was not clear as the results were mixed depending on the detection method used. It was concluded that BPS-causing C. estertheticum and C. gasigenes are widely distributed in the beef farm environment.


Assuntos
Clostridium/isolamento & purificação , Contaminação de Alimentos/análise , Carne/microbiologia , Animais , Bovinos , Clostridium/classificação , Clostridium/genética , Ecossistema , Microbiologia Ambiental , Fazendas , Fezes/microbiologia , Embalagem de Alimentos , Água Doce/microbiologia , Irlanda , Reação em Cadeia da Polimerase em Tempo Real , Estações do Ano , Microbiologia do Solo
19.
Sci Rep ; 10(1): 8048, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-32415178

RESUMO

Oil reservoirs have been shown to house numerous microbial lineages that differ based on the in-situ pH, salinity and temperature of the subsurface environment. Lineages of Firmicutes, including Clostridiales, have been frequently detected in oil reservoirs, but are typically not considered impactful or relevant due to their spore-forming nature. Here we show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales. These organisms form an oil-reservoir specific clade based on the phylogenies of both 16S rRNA genes and ribosomal proteins, which we propose to name UPetromonas tenebris, meaning they are single-celled organisms from dark rocks. Metagenome-assembled genomes (MAGs) of these Petromonas sp. were obtained and used to determine that these populations, while capable of spore-formation, were also likely replicating in situ in the reservoir. We compared these MAGs to closely related genomes and show that these subsurface Clostridiales differ, from the surface derived genomes, showing signatures of the ability to degrade plant-related compounds, whereas subsurface genomes only show the ability to process simple sugars. The estimation of in-situ replication from genomic data suggest that UPetromonas tenebris lineages are functional in-situ and may be specifically adapted to inhabit oil reservoirs.


Assuntos
Clostridium/classificação , Clostridium/genética , Microbiologia Ambiental , Metagenoma , Metagenômica , Campos de Petróleo e Gás/microbiologia , Metabolismo dos Carboidratos/genética , Clostridium/metabolismo , Biologia Computacional/métodos , Regulação Bacteriana da Expressão Gênica , Regulação Enzimológica da Expressão Gênica , Metagenômica/métodos , Filogenia
20.
Int J Syst Evol Microbiol ; 70(5): 2988-2997, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32369000

RESUMO

A novel, Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, obligately anaerobic bacterium, designated strain ZHW00191T, was isolated from human faeces and characterized by using a polyphasic taxonomic approach. Growth occurred at 25-45 °C (optimum, 37-42 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.0) and with 0-2 % (w/v) NaCl (optimum, 0 %). The end products of glucose fermentation were acetic acid, isobutyric acid and isovaleric acid and a small amount of propionic acid. The dominant cellular fatty acids (>10 %) of strain ZHW00191T were C16 : 0, C18 : 1 ω9с and C18 : 2ω6,9с. Its polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and ten unidentified glycolipids. Respiratory quinones were not detected. The cell-wall peptidoglycan contained meso-2,6-diaminopimelic acid, and the whole-cell sugars were ribose and glucose. The genomic DNA G+C content was 32.8 mol%. Analysis of the 16S rRNA gene sequence indicated that ZHW00191T was most closely related to Clostridium hiranonis TO-931T (95.3 % similarity). Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses with closely related reference strains indicated that reassociation values were both well below the thresholds of 95-96% and 70 % for species delineation, respectively. Based on phenotypic, chemotaxonomic and genetic studies, a novel genus, Peptacetobacter gen. nov., is proposed. The novel isolate ZHW00191T (=JCM 33482T=GDMCC 1.1530T) is proposed as the type strain of the type species Peptacetobacter hominis gen. nov., sp. nov. of the proposed new genus. Furthermore, it is proposed that Clostridium hiranonis be transferred to this novel genus, as Peptacetobacter hiranonis comb. nov.


Assuntos
Clostridium/classificação , Fezes/microbiologia , Bacilos Gram-Positivos Formadores de Endosporo/classificação , Filogenia , Adulto , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Glicolipídeos/química , Bacilos Gram-Positivos Formadores de Endosporo/isolamento & purificação , Humanos , Masculino , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
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