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1.
Int J Syst Evol Microbiol ; 65(11): 4134-4139, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26303147

RESUMO

An aerobic, Gram-stain-negative rod, designated strain A2P5T, was isolated from the Douro river, in Porto, Portugal. Cells were catalase- and oxidase-positive. Growth occurred at 15-30 °C, at pH 6-8 and in the presence of 1 % (w/v) NaCl. The major respiratory quinone was Q8, the genomic DNA had a G+C content of 47 ± 1 mol%, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain A2P5T was observed to be a member of the family Burkholderiaceae, but could not be identified as a member of any validly named genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa ( < 91 %), together with the comparative analysis of phenotypic and chemotaxonomic characteristics, supported the proposal of a novel species of a new genus within the family Burkholderiaceae. The name Hydromonas duriensis gen. nov., sp. nov. is proposed. The type strain of Hydromonas duriensis is A2P5T ( = LMG 28428T = CCUG 66137T).


Assuntos
Burkholderiaceae/classificação , Água Doce/microbiologia , Filogenia , Rios/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Burkholderiaceae/genética , Burkholderiaceae/isolamento & purificação , DNA Bacteriano/genética , Fosfolipídeos/química , Portugal , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
2.
Int J Syst Evol Microbiol ; 63(Pt 5): 1754-1759, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-22941299

RESUMO

A species diversity study of lactic acid bacteria occurring in traditional Vietnamese nem chua yielded an isolate, LMG 26767(T), that could not be assigned to a species with a validly published name. The isolate was initially investigated by 16S rRNA gene sequence analysis, which revealed that it belonged to the genus Lactobacillus, with Lactobacillus manihotivorans and Lactobacillus camelliae as the closest relatives (98.9 % and 96.9 % gene sequence similarity to the type strains, respectively). Comparative (GTG)5-PCR genomic fingerprinting confirmed the unique taxonomic status of the novel strain. DNA-DNA hybridization experiments, DNA G+C content determination, sequence analysis of the phenylalanyl-tRNA synthase (pheS) gene, and physiological and biochemical characterization demonstrated that strain LMG 26767(T) represents a novel species, for which the name Lactobacillus porcinae sp. nov. is proposed; the type strain is LMG 26767(T) ( = CCUG 62266(T)). Biochemically, L. porcinae can be distinguished from L. manihotivorans and L. camelliae by its carbohydrate fermentation profile, absence of growth at 45 °C, and production of d- and l-lactate as end products of glucose metabolism.


Assuntos
Microbiologia de Alimentos , Lactobacillus/classificação , Carne/microbiologia , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Fermentação , Lactobacillus/genética , Lactobacillus/isolamento & purificação , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Peptidoglicano/análise , Fenilalanina-tRNA Ligase/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Suínos , Vietnã
3.
Int J Syst Evol Microbiol ; 63(Pt 12): 4707-4718, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23959831

RESUMO

Analysis of partial gyrB gene sequences revealed six taxa in a group of 17 Burkholderia glathei-like isolates which were further examined by (GTG)5-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA-DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and an analysis of cell and colony morphology and more than 180 biochemical characteristics. The results demonstrated that one taxon consisting of three human clinical isolates represented Burkholderia zhejiangensis, a recently described methyl-parathion-degrading bacterium isolated from a wastewater-treatment system in China. The remaining taxa represented five novel species isolated from soil or rhizosphere soil samples, and could be distinguished by both genotypic and phenotypic characteristics. We therefore propose to formally classify these bacteria as Burkholderia humi sp. nov. (type strain, LMG 22934(T) = CCUG 63059(T)), Burkholderia choica sp. nov. (type strain, LMG 22940(T) = CCUG 63063(T)), Burkholderia telluris sp. nov. (type strain, LMG 22936(T) = CCUG 63060(T)), Burkholderia udeis sp. nov. (type strain, LMG 27134(T) = CCUG 63061(T)) and Burkholderia terrestris sp. nov. (type strain, LMG 22937(T) = CCUG 63062(T)).


Assuntos
Burkholderia/classificação , Filogenia , Rizosfera , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , Burkholderia/genética , Burkholderia/isolamento & purificação , China , DNA Girase/genética , DNA Bacteriano/genética , Ácidos Graxos/química , Humanos , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Águas Residuárias/microbiologia
4.
Int J Syst Evol Microbiol ; 63(Pt 9): 3250-3256, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23456811

RESUMO

Eight coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human clinical specimens at two different Belgian medical facilities. All strains were non-motile, Gram-stain-positive, catalase-positive cocci. DNA G+C content, peptidoglycan type, menaquinone pattern, the presence of teichoic acid and cellular fatty acid composition were in agreement with the characteristics of species of the genus Staphylococcus. Sequencing of the 16S rRNA gene and four housekeeping genes (dnaJ, tuf, gap and rpoB) demonstrated that these strains constitute a separate taxon within the genus Staphylococcus. Less than 41% DNA-DNA hybridization with the most closely related species of the genus Staphylococcus (Staphylococcus haemolyticus, Staphylococcus hominis and Staphlococcus lugdunensis) was observed. Key biochemical characteristics that allowed these bacteria to be distinguished from their nearest phylogenetic neighbours are arginine dihydrolase positivity, ornithine decarboxylase negativity and inability to produce acid aerobically from D-mannose, α-lactose and turanose. Acid is produced aerobically from trehalose. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus jettensis sp. nov. The type strain is SEQ110(T) ( =LMG 26879(T) =CCUG 62657(T) =DSM 26618(T)).


Assuntos
Filogenia , Staphylococcus/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Bélgica , Coagulase/metabolismo , DNA Bacteriano/genética , Ácidos Graxos/análise , Genes Bacterianos , Humanos , Dados de Sequência Molecular , Novobiocina/farmacologia , Hibridização de Ácido Nucleico , Peptidoglicano/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Staphylococcus/efeitos dos fármacos , Staphylococcus/genética , Staphylococcus/isolamento & purificação , Ácidos Teicoicos/análise , Vitamina K 2/análise
5.
Int J Syst Evol Microbiol ; 62(Pt 9): 2156-2159, 2012 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-22058318

RESUMO

Analysis of gyrB gene sequences, (GTG)(5)-primed PCR fingerprinting and biochemical characteristics determined in the Biolog GEN III microtest system were used to differentiate an unnamed Kerstersia species from Kerstersia gyiorum, the type and only named species in this genus. The inability to oxidize D-galacturonic and D-glucuronic acids and the ability to oxidize D-serine, along with gyrB gene sequence analysis and (GTG)(5)-PCR fingerprints, readily differentiated the unnamed taxon from the type species. Therefore, we propose to formally classify this unnamed taxon as Kerstersia similis sp. nov. with strain LMG 5890(T) (= CCUG 46999(T)), isolated from a leg wound in the USA in 1983, as the type strain.


Assuntos
Alcaligenaceae/classificação , Filogenia , Alcaligenaceae/genética , Alcaligenaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Bélgica , Impressões Digitais de DNA , DNA Bacteriano/genética , Genes Bacterianos , Humanos , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Análise de Sequência de DNA , Estados Unidos
6.
Int J Syst Evol Microbiol ; 61(Pt 9): 2238-2246, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-20952543

RESUMO

Two bacterial strains (SC-089(T) and SC-092(T)) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089(T) and SC-092(T), which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA-DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089(T) = LMG 24812(T) = CCUG 55806(T)) and Candidimonas humi sp. nov. (type strain, SC-092(T) = LMG 24813(T) = CCUG 55807(T)).


Assuntos
Alcaligenaceae/classificação , Alcaligenaceae/isolamento & purificação , Esgotos/microbiologia , Solo , Alcaligenaceae/genética , Alcaligenaceae/fisiologia , Técnicas de Tipagem Bacteriana , Catalase/metabolismo , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Concentração de Íons de Hidrogênio , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Oxirredutases/metabolismo , Fosfolipídeos/análise , Filogenia , Quinonas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Cloreto de Sódio/metabolismo , Temperatura
7.
Int J Food Microbiol ; 323: 108586, 2020 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-32199192

RESUMO

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS), a culture based alternative for microbial diversity studies, is an attractive tool to dereplicate large numbers of isolates to a smaller set of representatives for downstream characterization. In the present study, MALDI-TOF MS, combined with a database of reference spectra compiled in previous studies, was applied to identify 88 non-starter lactic acid bacteria (NSLAB) isolated from 18 samples of four different artisanal cheeses produced in the Island of Naxos, Greece, from raw sheep and goat milk without the addition of starters. Eighty-four isolates (95.5%) could be identified directly via MALDI-TOF MS. Lactobacillus brevis and Lactobacillus plantarum were the dominant species, followed by Lactococcus lactis, Leuconostoc mesenteroides Lactobacillus paracasei, Lactobacillus rhamnosus, Pediococcus pentosaceus and Enterococcus faecium. The remaining four isolates represented species present in the database; however, within-species diversity was insufficiently covered. Additionally, pheS sequencing was applied to confirm identification.


Assuntos
Queijo/microbiologia , Microbiologia de Alimentos/métodos , Lactobacillales/classificação , Lactobacillales/isolamento & purificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Animais , Biodiversidade , Grécia , Lactobacillales/química , Leite/microbiologia , Ovinos
8.
Front Microbiol ; 10: 2556, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31781066

RESUMO

Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The gyrB, recA, and gltB phylogenetic trees were used to select 27 strains for whole-genome sequence analysis and for a comparative genomics study that also included 41 publicly available Pandoraea genome sequences. The phylogenomic analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise digital DNA-DNA hybridization values and their confidence intervals, average nucleotide identity analyses using the OrthoANIu algorithm, and a whole-genome phylogeny reconstruction based on 107 single-copy core genes using bcgTree. These analyses, along with subsequent chemotaxonomic and traditional phenotypic analyses, revealed the presence of 17 novel Pandoraea species among the strains analyzed, and allowed the identification of several unclassified Pandoraea strains reported in the literature. The genus Pandoraea has an open pan genome that includes many orthogroups in the 'Xenobiotics biodegradation and metabolism' KEGG pathway, which likely explains the enrichment of these species in polluted soils and participation in the biodegradation of complex organic substances. We propose to formally classify the 17 novel Pandoraea species as P. anapnoica sp. nov. (type strain LMG 31117T = CCUG 73385T), P. anhela sp. nov. (type strain LMG 31108T = CCUG 73386T), P. aquatica sp. nov. (type strain LMG 31011T = CCUG 73384T), P. bronchicola sp. nov. (type strain LMG 20603T = ATCC BAA-110T), P. capi sp. nov. (type strain LMG 20602T = ATCC BAA-109T), P. captiosa sp. nov. (type strain LMG 31118T = CCUG 73387T), P. cepalis sp. nov. (type strain LMG 31106T = CCUG 39680T), P. commovens sp. nov. (type strain LMG 31010T = CCUG 73378T), P. communis sp. nov. (type strain LMG 31110T = CCUG 73383T), P. eparura sp. nov. (type strain LMG 31012T = CCUG 73380T), P. horticolens sp. nov. (type strain LMG 31112T = CCUG 73379T), P. iniqua sp. nov. (type strain LMG 31009T = CCUG 73377T), P. morbifera sp. nov. (type strain LMG 31116T = CCUG 73389T), P. nosoerga sp. nov. (type strain LMG 31109T = CCUG 73390T), P. pneumonica sp. nov. (type strain LMG 31114T = CCUG 73388T), P. soli sp. nov. (type strain LMG 31014T = CCUG 73382T), and P. terrigena sp. nov. (type strain LMG 31013T = CCUG 73381T).

9.
Res Microbiol ; 159(2): 88-93, 2008 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-18272350

RESUMO

The sensitivity and specificity of 7 PCR assays described for the identification of Campylobacter jejuni and Campylobacter coli were examined using alkaline cell lysates from a collection of 100 well characterized reference strains of C. jejuni, C. coli, Campylobacter lari and related Campylobacter, Helicobacter and Arcobacter species. Based on a preliminary evaluation, one multiplex test was excluded from further evaluation. The various assays differed considerably in sensitivity and specificity towards their target species. For C. coli, 4 of the 5 assays were 100% specific and sensitive, but for C. jejuni, none of the 5 assays were found to be 100% specific or sensitive. Subsequently, a statistically valid sample (n=263) was taken from a Belgian collection of 1906 human Campylobacter field isolates. This second collection was used to further evaluate two selected multiplex PCR assays. The present study indicates that PCR-based identification using each of the two selected multiplex PCR assays was highly reliable. The R-mPCR assay, followed by species-specific PCR assays or the ceu-oxr mPCR assay if necessary, is our current strategy of choice for the molecular identification of C. jejuni and C. coli. Results presented here should aid researchers in selecting a PCR assay suitable for their specific needs.


Assuntos
Técnicas de Tipagem Bacteriana , Campylobacter coli/isolamento & purificação , Campylobacter jejuni/isolamento & purificação , Reação em Cadeia da Polimerase/métodos , Infecções por Campylobacter/microbiologia , Campylobacter coli/genética , Campylobacter jejuni/genética , DNA Bacteriano/genética , Eletroforese em Gel de Poliacrilamida , Humanos , Sensibilidade e Especificidade
10.
Front Microbiol ; 7: 877, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27375597

RESUMO

Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extended multilocus sequence analysis (MLSA) approach. The results demonstrated that these 17 BGC isolates represented 13 novel Burkholderia species that could be distinguished by both genotypic and phenotypic characteristics. BGC strains exhibited a broad metabolic versatility and developed beneficial, symbiotic, and pathogenic interactions with different hosts. Our data also confirmed that there is no phylogenetic subdivision in the genus Burkholderia that distinguishes beneficial from pathogenic strains. We therefore propose to formally classify the 13 novel BGC Burkholderia species as Burkholderia arvi sp. nov. (type strain LMG 29317(T) = CCUG 68412(T)), Burkholderia hypogeia sp. nov. (type strain LMG 29322(T) = CCUG 68407(T)), Burkholderia ptereochthonis sp. nov. (type strain LMG 29326(T) = CCUG 68403(T)), Burkholderia glebae sp. nov. (type strain LMG 29325(T) = CCUG 68404(T)), Burkholderia pedi sp. nov. (type strain LMG 29323(T) = CCUG 68406(T)), Burkholderia arationis sp. nov. (type strain LMG 29324(T) = CCUG 68405(T)), Burkholderia fortuita sp. nov. (type strain LMG 29320(T) = CCUG 68409(T)), Burkholderia temeraria sp. nov. (type strain LMG 29319(T) = CCUG 68410(T)), Burkholderia calidae sp. nov. (type strain LMG 29321(T) = CCUG 68408(T)), Burkholderia concitans sp. nov. (type strain LMG 29315(T) = CCUG 68414(T)), Burkholderia turbans sp. nov. (type strain LMG 29316(T) = CCUG 68413(T)), Burkholderia catudaia sp. nov. (type strain LMG 29318(T) = CCUG 68411(T)) and Burkholderia peredens sp. nov. (type strain LMG 29314(T) = CCUG 68415(T)). Furthermore, we present emended descriptions of the species Burkholderia sordidicola, Burkholderia zhejiangensis and Burkholderia grimmiae. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and gyrB gene sequences determined in this study are LT158612-LT158624 and LT158625-LT158641, respectively.

11.
FEMS Microbiol Lett ; 249(1): 65-71, 2005 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-15979820

RESUMO

The large intestine of dogs contains a complex microbial ecosystem with predominance of streptococci, bifidobacteria, lactobacilli, Bacteroides and Clostridium. Generally, this predominant microbiota in dogs is relatively stable in time but much less is known about its taxonomic composition. Moreover, almost no studies have been conducted to investigate this stability of the faecal microbial population in dogs upon prebiotic administration. The objective of the present study was to monitor possible changes in faecal microbiota of seven healthy adult dogs related to the administration of two fructans, oligofructose and inulin. For this purpose, population fingerprints generated by denaturing gradient gel electrophoresis (DGGE) analysis of universal V3 16 S rRNA gene PCR amplicons were compared between control (baseline) samples and samples collected after prebiotic feeding. From these DGGE gels, marked changes were observed in the faecal microbiota between subjects and before and after fructan administration. One DGGE band that appeared or intensified after fructan intake was further analyzed. Sequence analysis could attribute this band to a member of the Streptococcus bovis-equinus group. Following cultivation on MRS medium, a set of faecal isolates that most likely represent the stimulated streptococci were allocated to the species Streptococcus lutetiensis by (GTG)(5)-PCR fingerprinting and partial 16 S rRNA and sodA gene sequencing. The data provided in this study demonstrate the ability of fructans to influence the bacterial composition of the gut microbiota in healthy dogs. More work is needed to unravel the relevance of S. lutetiensis or other autochthonous organisms of the dog gut as target groups for prebiotic supplementation.


Assuntos
Ecossistema , Fezes/microbiologia , Frutanos/administração & dosagem , Streptococcus/classificação , Animais , Técnicas de Tipagem Bacteriana , DNA Bacteriano/análise , DNA Bacteriano/isolamento & purificação , DNA Ribossômico/análise , Cães , Eletroforese em Gel de Poliacrilamida/métodos , Genes de RNAr , Inulina/administração & dosagem , Dados de Sequência Molecular , Oligossacarídeos/administração & dosagem , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie , Streptococcus/genética , Streptococcus/isolamento & purificação
12.
BMC Pharmacol Toxicol ; 14: 62, 2013 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-24325943

RESUMO

BACKGROUND: The gut microbiota is critical for intestinal homeostasis. Recent studies have revealed the links between different types of dysbiosis and diseases inside and outside the intestine. Environmental exposure to pollutants (such as heavy metals) can also impair various physiological functions for good health. Here, we studied the impact of up to 8 weeks of oral lead and cadmium ingestion on the composition of the murine intestinal microbiome. RESULTS: Pyrosequencing of 16S RNA sequences revealed minor but specific changes in bacterial commensal communities (at both family and genus levels) following oral exposure to the heavy metals, with notably low numbers of Lachnospiraceae and high numbers levels of Lactobacillaceae and Erysipelotrichaceacae (mainly due to changes in Turicibacter spp), relative to control animals. CONCLUSIONS: Non-absorbed heavy metals have a direct impact on the gut microbiota. In turn, this may impact the alimentary tract and overall gut homeostasis. Our results may enable more accurate assessment of the risk of intestinal disease associated with heavy metal ingestion.


Assuntos
Cádmio/toxicidade , Ceco/efeitos dos fármacos , Ecotoxicologia , Intoxicação por Metais Pesados , Chumbo/toxicidade , Microbiota/efeitos dos fármacos , Intoxicação/etiologia , Animais , Ceco/microbiologia , Eletroforese em Gel de Gradiente Desnaturante , Fezes/microbiologia , Feminino , Lactobacillaceae/genética , Camundongos , Camundongos Endogâmicos BALB C , Microbiota/genética , Intoxicação/microbiologia , RNA Ribossômico 16S/genética
13.
Int J Food Microbiol ; 163(1): 19-27, 2013 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-23500611

RESUMO

An important part of the daily nourishment in Vietnam constitutes of fermented vegetables. Bacteria and especially lactic acid bacteria play a central role in the production of many fermented vegetables. The current study was conducted to investigate the diversity of native lactic acid bacteria (LAB) populations in 'dua muoi' (mustard and beet fermentation) and 'ca muoi' (eggplant fermentation), three types of popular traditional fermented vegetables of Vietnamese origin. To this end a polyphasic approach combining matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and pheS gene sequence analysis was used. In addition, denaturing gradient gel electrophoresis was performed as a culture-independent method to complement the observed culturable diversity data. A total of 881 LAB isolates were recovered from 21 different samples. Predominant LAB associated with 'dua muoi' and 'ca muoi' were identified as Lactobacillus fermentum (56.6%), Lactobacillus pentosus (24.4%) and Lactobacillus plantarum (17.1%). Less abundant species were Pediococcus pentosaceus (1.0%) and Lactobacillus brevis (0.5%). Species present less than 0.1% included Lactobacillus paracasei, Lactobacillus pantheris and Pediococcus acidilactici. In contrast to fermented mustard and beet with the highest prevalence of L. fermentum, the species most recovered from fermented eggplant samples was L. pentosus. In addition, an important degree of genetic variability within the different predominant species was observed and strain dependency correlating with the type of fermented vegetable or location of production could be demonstrated using multivariate statistics. This research gives an extensive and detailed inventory of the LAB diversity associated with the production of diverse Vietnamese fermented vegetables and demonstrates the influence of type of raw material and/or production location and conditions on this diversity.


Assuntos
Fermentação , Microbiologia de Alimentos , Lactobacillaceae/fisiologia , Verduras/microbiologia , Biodiversidade , Lactobacillaceae/genética , Lactobacillaceae/isolamento & purificação , Pediococcus/classificação , Pediococcus/genética , Pediococcus/isolamento & purificação , Vietnã
14.
Syst Appl Microbiol ; 36(1): 1-10, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23219252

RESUMO

The phenotypic and genotypic characteristics of fourteen human clinical Achromobacter strains representing four genogroups which were delineated by sequence analysis of nusA, eno, rpoB, gltB, lepA, nuoL and nrdA loci, demonstrated that they represent four novel Achromobacter species. The present study also characterized and provided two additional reference strains for Achromobacter ruhlandii and Achromobacter marplatensis, species for which, thus far, only single strains are publicly available, and further validated the use of 2.1% concatenated nusA, eno, rpoB, gltB, lepA, nuoL and nrdA sequence divergence as a threshold value for species delineation in this genus. Finally, although most Achromobacter species can be distinguished by biochemical characteristics, the present study also highlighted considerable phenotypic intraspecies variability and demonstrated that the type strains may be phenotypically poor representatives of the species. We propose to classify the fourteen human clinical strains as Achromobacter mucicolens sp. nov. (with strain LMG 26685(T) [=CCUG 61961(T)] as the type strain), Achromobacter animicus sp. nov. (with strain LMG 26690(T) [=CCUG 61966(T)] as the type strain), Achromobacter spiritinus sp. nov. (with strain LMG 26692(T) [=CCUG 61968(T)] as the type strain), and Achromobacter pulmonis sp. nov. (with strain LMG 26696(T) [=CCUG 61972(T)] as the type strain).


Assuntos
Achromobacter/classificação , Achromobacter/isolamento & purificação , Infecções por Bactérias Gram-Negativas/microbiologia , Achromobacter/genética , Proteínas de Bactérias/genética , Técnicas de Tipagem Bacteriana , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , Humanos , Dados de Sequência Molecular , Tipagem de Sequências Multilocus , Filogenia
15.
Syst Appl Microbiol ; 35(3): 175-82, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-22361568

RESUMO

The aim of the present study was to identify a collection of 35 Cupriavidus isolates at the species level and to examine their capacity to nodulate and fix N(2). These isolates were previously obtained from the root nodules of two promiscuous trap species, Phaseolus vulgaris and Leucaena leucocephala, inoculated with soil samples collected near Sesbania virgata plants growing in Minas Gerais (Brazil) pastures. Phenotypic and genotypic methods applied for this study were SDS-PAGE of whole-cell proteins, and 16S rRNA and gyrB gene sequencing. To confirm the ability to nodulate and fix N(2), the presence of the nodC and nifH genes was also determined, and an experiment was carried out with two representative isolates in order to authenticate them as legume nodule symbionts. All 35 isolates belonged to the betaproteobacterium Cupriavidus necator, they possessed the nodC and nifH genes, and two representative isolates were able to nodulate five different promiscuous legume species: Mimosa caesalpiniaefolia, L. leucocephala, Macroptilium atropurpureum, P. vulgaris and Vigna unguiculata. This is the first study to demonstrate that C. necator can nodulate legume species.


Assuntos
Betaproteobacteria/classificação , Betaproteobacteria/isolamento & purificação , Cupriavidus necator/fisiologia , Fabaceae/microbiologia , Fixação de Nitrogênio , Simbiose , Proteínas de Bactérias/análise , Proteínas de Bactérias/genética , Betaproteobacteria/genética , Betaproteobacteria/fisiologia , Brasil , Análise por Conglomerados , Cupriavidus necator/crescimento & desenvolvimento , Cupriavidus necator/metabolismo , DNA Girase/genética , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Eletroforese em Gel de Poliacrilamida , Fabaceae/fisiologia , Dados de Sequência Molecular , N-Acetilglucosaminiltransferases/genética , Oxirredutases/genética , Filogenia , Proteoma/análise , RNA Ribossômico 16S/genética , Nódulos Radiculares de Plantas , Análise de Sequência de DNA
16.
Syst Appl Microbiol ; 35(4): 253-62, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22609342

RESUMO

Forty-eight Burkholderia isolates from different land use systems in the Amazon region were compared to type strains of Burkholderia species for phenotypic and functional characteristics that can be used to promote plant growth. Most of these isolates (n=46) were obtained by using siratro (Macroptilium atropurpureum - 44) and common bean (Phaseolus vulgaris - 2) as the trap plant species; two isolates were obtained from nodules collected in the field from Indigofera suffruticosa and Pithecellobium sp. The evaluated characteristics were the following: colony characterisation on "79" medium, assimilation of different carbon sources, enzymatic activities, solubilisation of phosphates, nitrogenase activity and antifungal activity against Fusarium oxysporium f. sp. phaseoli. Whole cell protein profiles, 16S rRNA, gyrB, and recA gene sequencing and multilocus sequence typing were used to identify the isolates. The isolates showed different cultural and biochemical characteristics depending on the legume species from which they were obtained. Except for one isolate from I. suffruticosa, all isolates were able to solubilise calcium phosphate and present nitrogenase activity under free-living conditions. Only one isolate from common beans, showed antifungal activity. The forty four isolates from siratro nodules were identified as B. fungorum; isolates UFLA02-27 and UFLA02-28, obtained from common bean plants, were identified as B. contaminans; isolate INPA89A, isolated from Indigofera suffruticosa, was a close relative of B. caribensis but could not be assigned to an established species; isolate INPA42B, isolated from Pithecellobium sp., was identified as B. lata. This is the first report of nitrogenase activity in B. fungorum, B. lata and B. contaminans.


Assuntos
Biodiversidade , Burkholderia/classificação , Burkholderia/metabolismo , Variação Genética , Fixação de Nitrogênio , Plantas/microbiologia , Microbiologia do Solo , Proteínas de Bactérias/análise , Proteínas de Bactérias/genética , Técnicas de Tipagem Bacteriana , Brasil , Burkholderia/genética , Burkholderia/isolamento & purificação , Análise por Conglomerados , DNA Girase/genética , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Dados de Sequência Molecular , Tipagem de Sequências Multilocus , Filogenia , RNA Ribossômico 16S/genética , Recombinases Rec A/genética , Rizosfera , Análise de Sequência de DNA
17.
Int J Syst Evol Microbiol ; 60(Pt 5): 1108-1112, 2010 May.
Artigo em Inglês | MEDLINE | ID: mdl-19666785

RESUMO

Four butyrate-producing isolates were obtained from the caecal content of a 4-week-old broiler chicken. The 16S rRNA gene sequences were determined and confirmed the close relatedness of the four isolates, which suggested that they were derived from a single bacterial clone. Phylogenetic analysis based on 16S rRNA gene sequences showed that its closest relatives were members of cluster XIVa of the Clostridium subphylum of Gram-positive bacteria and that the closest related type strain was Anaerostipes caccae L1-92(T) (94.5 % similarity). Similarity levels of 96-98 % with sequences from uncultured bacteria from human stool samples were observed. On the basis of morphological, biochemical and phylogenetic characteristics, this strain is assigned to a novel species in the genus Anaerostipes, for which the name Anaerostipes butyraticus sp. nov. is proposed. The type strain is 35-7(T) (=LMG 24724(T) =DSM 22094(T)). An emended description of the genus Anaerostipes is also provided.


Assuntos
Butiratos/metabolismo , Ceco/microbiologia , Galinhas/microbiologia , Bacilos Gram-Positivos Asporogênicos/classificação , Bacilos Gram-Positivos Asporogênicos/isolamento & purificação , Anaerobiose , Animais , Técnicas de Tipagem Bacteriana , Bélgica , DNA Bacteriano/análise , DNA Ribossômico/análise , Genes de RNAr , Genótipo , Bacilos Gram-Positivos Asporogênicos/genética , Bacilos Gram-Positivos Asporogênicos/fisiologia , Dados de Sequência Molecular , Fenótipo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie
18.
Int J Syst Evol Microbiol ; 59(Pt 5): 1126-32, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19406805

RESUMO

A polyphasic study was undertaken to clarify the taxonomic position of Campylobacter lari-like strains isolated from shellfish and humans. The diversity within the strain collection was initially screened by means of fluorescent amplified fragment length polymorphism analysis and whole-cell protein electrophoresis, revealing the existence of two clusters distinct from C. lari and other Campylobacter species. The divergence of these clusters was confirmed by phenotypic analysis and by 16S rRNA and hsp60 gene sequence analysis. Phylogenetic analysis identified C. lari, Campylobacter jejuni, Campylobacter coli and Campylobacter insulaenigrae as the closest phylogenetic neighbours of both taxa. DNA-DNA hybridizations revealed that one cluster, comprising 10 strains, represented a novel Campylobacter species, for which the name Campylobacter peloridis sp. nov. is proposed, with 2314BVA(T) (=LMG 23910(T) =CCUG 55787(T)) as the type strain. The second cluster, comprising six strains, represents a novel subspecies within the species C. lari, for which the name Campylobacter lari subsp. concheus subsp. nov. is proposed, with 2897R(T) (=LMG 21009(T) =CCUG 55786(T)) as the type strain. The description of C. lari subsp. concheus has the effect of automatically creating the subspecies Campylobacter lari subsp. lari subsp. nov. (type strain LMG 8846(T)=NCTC 11352(T)).


Assuntos
Bivalves/microbiologia , Infecções por Campylobacter/microbiologia , Campylobacter lari/classificação , Campylobacter/classificação , Frutos do Mar/microbiologia , Animais , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Técnicas de Tipagem Bacteriana , Campylobacter/genética , Campylobacter/isolamento & purificação , Campylobacter/fisiologia , Campylobacter lari/genética , Campylobacter lari/isolamento & purificação , Campylobacter lari/fisiologia , DNA Bacteriano/análise , DNA Ribossômico/análise , Diarreia/microbiologia , Genes de RNAr , Proteínas de Choque Térmico/genética , Humanos , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Fenótipo , Filogenia , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie
19.
Int J Syst Evol Microbiol ; 59(Pt 1): 102-11, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19126732

RESUMO

The aim of the present study was to re-examine the taxonomic position and structure of taxon K (also known as group K) within the Burkholderia cepacia complex (Bcc). For this purpose, a representative set of strains was examined by a traditional polyphasic taxonomic approach, by multilocus sequence typing (MLST) analysis and by analysis of available whole-genome sequences. Analysis of the recA gene sequence revealed three different lineages, designated recA-I, recA-II and recA-III. DNA-DNA hybridization experiments demonstrated that recA-I and recA-II isolates each represented a single novel species. However, DNA-DNA hybridization values of recA-II strains towards recA-III strains and among recA-III strains were at the threshold level for species delineation. By MLST, recA-I isolates were clearly distinguished from the others and represented a distinct lineage referred to as MLST-I, whereas recA-II and recA-III isolates formed a second MLST lineage referred to as MLST-II. A divergence value of 3.5 % was obtained when MLST-I was compared with MLST-II. The internal level of concatenated sequence divergence within MLST-I and MLST-II was 1.4 and 2.7 %, respectively; by comparison with the level of concatenated sequence divergence in established Bcc species, these data demonstrate that the MLST-I and MLST-II lineages represent two distinct species within the Bcc. The latter conclusion was supported by comparison of the whole-genome average nucleotide identity (ANI) level of MLST-I and MLST-II strains with strains of established Bcc species and by a whole-genome-based phylogenetic analysis. We formally propose to classify taxon K bacteria from the MLST-I and MLST-II lineages as Burkholderia contaminans sp. nov. (with strain J2956T =LMG 23361T =CCUG 55526T as the type strain) and Burkholderia lata sp. nov. (with strain 383T =ATCC 17760T =LMG 22485T =CCUG 55525T as the type strain), respectively. The MLST approach was confirmed as a valuable instrument in polyphasic taxonomic studies; more importantly, the cumulative data for about 1000 Bcc isolates analysed demonstrate that the 3 % concatenated sequence divergence level correlates with the 70 % DNA-DNA hybridization or 95 % whole-genome ANI threshold levels for species delineation.


Assuntos
Complexo Burkholderia cepacia/classificação , Complexo Burkholderia cepacia/isolamento & purificação , Fibrose Cística/microbiologia , Mastite/veterinária , Doenças dos Ovinos/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Infecções por Burkholderia/microbiologia , Infecções por Burkholderia/veterinária , Complexo Burkholderia cepacia/genética , Complexo Burkholderia cepacia/fisiologia , DNA Bacteriano/análise , DNA Ribossômico/análise , Feminino , Genoma Bacteriano , Humanos , Mastite/microbiologia , Hibridização de Ácido Nucleico , Filogenia , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética , Recombinases Rec A/genética , Análise de Sequência de DNA , Ovinos , Especificidade da Espécie
20.
Int J Syst Evol Microbiol ; 58(Pt 2): 420-3, 2008 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-18218942

RESUMO

A Gram-negative, rod-shaped, aerobic bacterium, designated strain RP007(T), was isolated from a polycyclic aromatic hydrocarbon-contaminated soil in New Zealand. Two additional strains were recovered from a compost heap in Belgium (LMG 18808) and from the rhizosphere of maize in the Netherlands (LMG 24204). The three strains had virtually identical 16S rRNA gene sequences and whole-cell protein profiles, and they were identified as members of the genus Burkholderia, with Burkholderia phenazinium as their closest relative. Strain RP007(T) had a DNA G+C content of 63.5 mol% and could be distinguished from B. phenazinium based on a range of biochemical characteristics. Strain RP007(T) showed levels of DNA-DNA relatedness towards the type strain of B. phenazinium and those of other recognized Burkholderia species of less than 30 %. The results of 16S rRNA gene sequence analysis, DNA-DNA hybridization experiments and physiological and biochemical tests allowed the differentiation of strain RP007(T) from all recognized species of the genus Burkholderia. Strains RP007(T), LMG 18808 and LMG 24204 are therefore considered to represent a single novel species of the genus Burkholderia, for which the name Burkholderia sartisoli sp. nov. is proposed. The type strain is RP007(T) (=LMG 24000(T) =CCUG 53604(T) =ICMP 13529(T)).


Assuntos
Burkholderia/classificação , Burkholderia/isolamento & purificação , Hidrocarbonetos Policíclicos Aromáticos , Microbiologia do Solo , Poluentes do Solo , Proteínas de Bactérias/análise , Técnicas de Tipagem Bacteriana , Composição de Bases , Burkholderia/genética , Burkholderia/fisiologia , DNA Bacteriano/análise , Ácidos Graxos/análise , Genes de RNAr , Dados de Sequência Molecular , Nova Zelândia , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie
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