In the 1990s several biocontrol agents on that contained Burkholderia strains were registered by the United States Environmental Protection Agency (EPA). After risk assessment these products were ...withdrawn from the market and a moratorium was placed on the registration of Burkholderia-containing products, as these strains may pose a risk to human health. However, over the past few years the number of novel Burkholderia species that exhibit plant-beneficial properties and are normally not isolated from infected patients has increased tremendously. In this commentary we wish to summarize recent efforts that aim at discerning pathogenic from beneficial Burkholderia strains.
The
Burkholderia cepacia complex is a group of closely related species with conflicting biological properties. Triggered by the devastating effect of pulmonary infections in cystic fibrosis patients, ...the scientific community generated an unusually large amount of taxonomic data for these bacteria during the past 15 years. This review presents the polyphasic, multilocus and genomic methodology used for the classification and identification of these bacteria. The current state-of-the-art demonstrates that present day taxonomists can replace traditional DNA–DNA hybridizations for species level demarcation and 16S rRNA sequence analysis for studying phylogeny by superior whole genome sequence-based parameters within the framework of polyphasic taxonomic studies.
Six endospore-forming, Gram-stain-positive or variable, motile, rod-shaped, aerobic or facultatively anaerobic bacteria with different MALDI-TOF mass spectra (MS) were isolated from the phyllosphere ...of
plants grown in plant chambers after inoculation of surface sterilized seeds with a top soil microbial cell suspension. They were identified as members of the genus
through comparison with a commercial MALDI-TOF MS database and comparative 16S rRNA gene sequencing. Their genome sequences comprised multiple biosynthetic gene clusters and suggested they have unexplored biotechnological potential. Analyses of average nucleotide identity values between these strains and the type strains of their nearest neighbour species demonstrated that they represented a novel
species each. A detailed phenotypic comparison yielded distinctive biochemical characteristics for each of these novel species. We therefore propose to classify that these isolates into six novel species within genus
, for which we propose the names
sp. nov.,
sp. nov.,
sp. nov.,
sp. nov.,
sp. nov. and
sp. nov., with strains LMG 31456
(=R-74617
=CECT 30138
), LMG 31459
(=R-74621
=CECT 30135
), LMG 31461
(=R-74618
=CECT 30133
), LMG 31457
(=R-74619
=CECT 30137
), LMG 31458
(=R-74620
=CECT 30136
) and LMG 31460
(=R-74622
=CECT 30134
) as the type strains, respectively.
The genus
comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of
and
on the basis of whole genome ...sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus
into 25 genera including the emended genus
, which includes host-adapted organisms that have been referred to as the
group,
and 23 novel genera for which the names
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
and
are proposed. We also propose to emend the description of the family
to include all genera that were previously included in families
and
. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as
until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus
encompassing species adapted to vertebrates (such as
,
,
,
,
and
) or invertebrates (such as
and
).
Summary
Members of the genus Burkholderia are versatile organisms that occupy a surprisingly wide range of ecological niches. These bacteria are exploited for biocontrol, bioremediation and plant ...growth promotion purposes, but safety issues regarding human infections, especially in cystic fibrosis patients, have not been solved. This minireview gives an overview of the taxonomic and ecological diversity of the genus with particular emphasis on strains belonging to the Burkholderia cepacia complex and addresses the important question whether ‘good’ and ‘bad’ strains are actually the same.
The present study combined high-throughput culture-dependent plating and culture-independent amplicon sequencing with a metabolite target analysis to systematically dissect the identity, evolution, ...and role of the microorganisms, substrates, and metabolites during the four-phase fermentation and maturation process of lambic beer production. This led to the following new insights. The changing physicochemical parameters and substrate and metabolite compositions of the fermenting wort and maturing lambic beer provoked several transitions between microbial species and explained the four-step production process. Manual wort acidification with lactic acid shortened the enterobacterial phase and thus kept biogenic amine formation by enterobacteria present during the early stages of fermentation at a minimum. Growth advantages during the alcoholic fermentation phase caused a transition from the prevalence by
and
species to that by
and later on
, due to changing environmental parameters. During the acidification phase,
was prevalent and performed a malolactic fermentation.
produced acetic acid and acetoin. Upon maturation,
species appeared, together with
and
, thereby contributing to acetic acid production, depending on the oxygen availability. Moreover, the
species consumed the acetoin produced by the acetic acid bacteria for redox balancing. The breakdown of maltooligosaccharides seemed to be independent of the occurrence of
species and started already early in the fermentation process.
The prokaryotic genus name Verticia Vandamme et al. 2015 is illegitimate because it is a later homonym of the insect genus name Verticia Malloch 1927 Principle 2, Rule 51b(4) of the Prokaryotic Code ...(2008 Revision). This name is therefore not a correct name (Principle 6), and a replacement genus name must be proposed (Rule 54).
Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic ...Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended.
Eight water kefir fermentation series differing in buffer capacity and calcium concentration of the water used for fermentation were studied during eight backslopping steps. High buffer capacities ...resulted in high pH values and high calcium concentrations resulted in low pH values at the end of each backslopping step. When the water buffer capacity and/or calcium concentration were below certain minima, the water kefir grain growth decreased gradually over multiple backsloppings. High water buffer capacities resulted in high concentrations of residual total carbohydrate concentrations and low metabolite concentrations. Further, high water buffer capacities resulted in high ratios of lactic acid bacteria to yeasts, which was reflected in high molar ratios of the concentrations of lactic acid to ethanol and acetic acid to ethanol. The most prevalent microorganisms of the water kefir grain inoculum and grains of all fermentation series at the end of the eighth backslopping step were
,
,
,
,
, and
. These microbial communities were influenced by the water buffer capacity and had an impact on the substrate consumption and metabolite production during water kefir fermentation.
Lambic sour beers are the products of a spontaneous fermentation that lasts for one to three years before bottling. The present study determined the microbiota involved in the fermentation of lambic ...beers by sampling two fermentation batches during two years in the most traditional lambic brewery of Belgium, using culture-dependent and culture-independent methods. From 14 samples per fermentation, over 2000 bacterial and yeast isolates were obtained and identified. Although minor variations in the microbiota between casks and batches and a considerable species diversity were found, a characteristic microbial succession was identified. This succession started with a dominance of Enterobacteriaceae in the first month, which were replaced at 2 months by Pediococcus damnosus and Saccharomyces spp., the latter being replaced by Dekkera bruxellensis at 6 months fermentation duration.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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