Papers by Livio Antonielli
Frontiers in Plant Science, 2016
Genome announcements, 2016
We report here the draft genome sequence of Paenibacillus polymyxa strain CCI-25, which displays ... more We report here the draft genome sequence of Paenibacillus polymyxa strain CCI-25, which displays strong antifungal and antibacterial activities in vitro The genome encompasses nonribosomal peptide synthetases predicted to encode a tridecaptin, polymyxin, fusaricidin, an iturin-like synthetase, a lantibiotic similar to paenicidin A, as well as a type 1 polyketide synthase.
International journal of systematic and evolutionary microbiology, Jan 30, 2016
A Gram-positive, motile, yellow-pigmented and rod-shaped bacterial strain, designated AR33T, was ... more A Gram-positive, motile, yellow-pigmented and rod-shaped bacterial strain, designated AR33T, was isolated from the rhizosphere of Salix caprea L. growing in a former zinc ⁄ lead mining and processing site in Austria. A polyphasic approach was applied to determine its taxonomic position. 16S rRNA gene sequence analysis, morphological and chemotaxonomic properties showed that strain AR33T belongs to the genus Agromyces. Strain AR33T had peptidoglycan type B2γ and the major menaquinones were MK-11, MK-10 and MK-12. The main branched-chain fatty acids were anteiso-C15:0, anteiso-C17:0 and iso-C16:0. Strain AR33T showed catalase and oxidase activity and multiple heavy metal resistances to zinc, lead and cadmium. The DNA G+C content was 70.1 mol%. 16S rRNA gene identity values with closely related recognized Agromyces species ranged between 98 and 99%. However, DNA-DNA hybridization between strain AR33T and other three Agromyces species showed values lower than 42% similarity. Therefore, ...
Food Microbiology, May 1, 2010
Pichia guilliermondii was the only identified yeast in pineapple fruits. Lactobacillus plantarum ... more Pichia guilliermondii was the only identified yeast in pineapple fruits. Lactobacillus plantarum and Lactobacillus rossiae were the main identified species of lactic acid bacteria. Typing of lactic acid bacteria differentiated isolates depending on the layers. L. plantarum 1OR12 and L. rossiae 2MR10 were selected within the lactic acid bacteria isolates based on the kinetics of growth and acidification. Five technological options, including minimal processing, were considered for pineapple: heating at 72 C for 15 s (HP); spontaneous fermentation without (FP) or followed by heating (FHP), and fermentation by selected autochthonous L. plantarum 1OR12 and L. rossiae 2MR10 without (SP) or preceded by heating (HSP). After 30 days of storage at 4 C, HSP and SP had a number of lactic acid bacteria 1000 to 1,000,000 times higher than the other processed pineapples. The number of yeasts was the lowest in HSP and SP. The Community Level Catabolic Profiles of processed pineapples indirectly confirmed the capacity of autochthonous starters to dominate during fermentation. HSP and SP also showed the highest antioxidant activity and firmness, the better preservation of the natural colours and were preferred for odour and overall acceptability.
The Open Applied Informatics Journal, Jul 15, 2011
The problem of species and in particular microbial species is central in biology. An active colla... more The problem of species and in particular microbial species is central in biology. An active collaboration of various specialists such as taxonomists, epistemologists, mathematicians and bioinformatics experts is desirable for its solution.
Background: The increasing number of techniques introduced to describe organisms and taxa produce... more Background: The increasing number of techniques introduced to describe organisms and taxa produce multivariate datasets, often composed of relatively independent descriptors. Handling several descriptors can be laborious and often unnecessary when their information is not congruent to that of other datasets used in the same study. On the other hand, different levels of correlation between single descriptors to a whole dataset may suggest useful scientific hints. The DADI (Distance-based Analysis for (optimal) Descriptor Identification) algorithm is proposed to allow a rapid and complete analysis among descriptors coming from two different datasets with the same number of objects. DADI was employed to select FTIR (Fourier Transform Infrared Spectroscopy) spectral wavelengths according to their correlation with the 26S rDNA sequences of strains belonging to a yeast genus.
Soil Biology and Biochemistry, 2015
Genome Announcements, 2015
Microbacterium spp. isolated from heavy metal (HM)-contaminated environments (soil and plants) ca... more Microbacterium spp. isolated from heavy metal (HM)-contaminated environments (soil and plants) can play a role in mobilization processes and in the phytoextraction of HM. Here, we report the whole-genome sequences and annotation of 10 Microbacterium spp. isolated from both HM-contaminated and -noncontaminated compartments.
PeerJ, 2015
Heterotrophic plate counts (HPC) are routinely determined within the scope of water quality asses... more Heterotrophic plate counts (HPC) are routinely determined within the scope of water quality assessment. However, variable HPC methods with different cultivation parameters (i.e., temperature and media type) are applied, which could lead to significant effects in the outcome of the analysis. Therefore the effect of different HPC methods, according to DIN EN ISO 6222 and EPA, on the culturable microbial community composition was investigated by 16S rRNA gene sequence analysis and statistical evaluation was performed. The culturable community composition revealed significant effects assigned to temperature (p < 0.01), while for media type no statistical significance was observed. However, the abundance of certain detected bacteria was affected. Lower temperature (22 • C) showed the abundance of naturally occurring Pseudomonadaceae and Aeromonadaceae, whereas at high temperature (37 • C) numerous Enterobacteriaceae, Citrobacter spp. and Bacilli were identified. The highest biodiversity was detected at lower temperature, especially on R2A medium. These results indicate that different temperatures (low and high) should be included into HPC measurement and selection of media should, ideally, be adjusted to the monitored water source. Accordingly, it can be inferred that the HPC method is more suitable for continuous monitoring of the same water source than for single assessments of a water sample. Subjects Microbiology, Molecular Biology Keywords Culturable community composition, Temperature, Heterotrophic plate count, Media type, 16S rRNA gene sequence analysis, Microbial water quality assessment How to cite this article Gensberger et al. (2015), Effect of different heterotrophic plate count methods on the estimation of the composition of the culturable microbial community. PeerJ 3:e862; Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59:143-169. Anderson MJ. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecology 26(1):32-46 . Burtscher MM, Zibuschka F, Mach RL, Lindner G, Farnleitner AH. 2009. Heterotrophic plate count vs. in situ bacterial 16S rRNA gene amplicon profiles from drinking water reveal completely different communities with distinct spatial and temporal allocations in a distribution net. Water SA 35(4):495-504. Cáceres M, Legendre P. 2009. Associations between species and groups of sites: indices and statistical inference. Ecology 90:3566-3574 Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7:335-336 . DIN EN ISO 19458. Wasserbeschaffenheit-Probenahme für mikrobiologische. 2006. Untersuchungen: Deutsche Fassung EN ISO. DIN EN ISO 6222. Water quality-enumeration of culturable micro-organisms-colony count by inoculation in a nutrient agar culture media. 1999. Geneva: International Organization for Standardization. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics . Gower JC, Blasius J. 2005. Multivariate prediction with nonlinear principal components analysis: theory. Quality and Quantity 39(4):359-372 DOI 10.1007/s11135-005-3005-1. Hammes F, Berney M, Wang Y, Vital M, Köster O, Egli T. 2008. Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes. Water Research 42:269-277 DOI 10.1016/j.watres.2007.07.009. Hervé M. 2014. RVAideMemoire: diverse basic statistical and graphical functions. R package. version 0.9-40. Available at http://CRAN.R-project.org/package=RVAideMemoire. Inomata A, Chiba T, Hosaka M. 2009. Identification of heterotrophic plate count bacteria isolated from drinking water in Japan by DNA sequencing analysis. . 2013. Package 'vegan.' Available at http://cran. r-project.org, http://vegan.r-forge.r-project.org/. Pavlov D, De Wet CME, Grabow WOK, Ehlers MM. 2004. Potentially pathogenic features of heterotrophic plate count bacteria isolated from treated and untreated drinking water. International Journal of Food Microbiology 92(3):275-287 DOI 10.1016/j.ijfoodmicro.2003.08.018. Reasoner DJ, Geldreich EE. 1985. A new medium for the enumeration and subculture of bacteria from potable water. Applied and Environmental Microbiology 49(1):1-7. Sartory DP, Gu H, Chen CM. 2008. Comparison of a novel MPN method against the yeast extract agar (YEA) pour plate method for the enumeration of heterotrophic bacteria from drinking water.
The lactic acid bacteria and yeast microbiota of eighteen sourdoughs used for the manufacture of ... more The lactic acid bacteria and yeast microbiota of eighteen sourdoughs used for the manufacture of some traditional Italian sweet leavened baked goods were studied through culture-dependent method and pyrosequencing. Flours used for back slopping and sourdoughs were also biochemically characterized. Principal component analysis was applied to explore eventual correlations between process parameters applied during back slopping, some flour nutrients, profile of microbiota, and biochemical characteristics of sourdoughs. The median values of the cell density of lactic acid bacteria and yeasts were 8.05 and 7.03 log CFU/g, respectively. As shown by culture-dependent method, Lactobacillus sanfranciscensis was identified in all the sourdoughs, except for Panaredda and Torcolo di San Costanzo. For eleven sourdoughs, all the lactic acid bacteria isolates were allotted to this species. For Buccellato di Lucca, Mbriagotto, Pandoro, and Nadalin sourdoughs, at least 80% of the isolates was allotted to this species. Other lactic acid bacteria isolated with a relatively high frequence were Lactobacillus plantarum and Leuconostoc citreum. Pyrosequencing confirmed and complemented the culture-dependent approach, detecting L. sanfranciscensis also in Panaredda and Torcolo di San Costanzo sourdoughs. Saccharomyces cerevisiae was identified in all the sourdoughs, except for Mbriagotto, Ciambella di Mosto and Pandolce Genovese. These latter sourdoughs harbored strains of Candida humilis, whereas five sourdoughs combined the presence of both yeast species. Positive correlations were found between time of back slopping and cell density and main metabolites of lactic acid bacteria. Percentage of sourdough used as inoculum was mainly correlated with the cell density of yeasts and the concentration of ethanol. This study provided a comprehensive and comparative approach to highlight the dominant microbiota of Italian sourdoughs, which could be exploited further to guarantee a highly reproducible quality of the Italian sweet goods studied, while preserving their traditional trait.
The Open Applied Informatics Journal, 2007
The R package ESTHER implements two novel algorithms designed to dispose in a reduced space multi... more The R package ESTHER implements two novel algorithms designed to dispose in a reduced space multidimensional objects defined by binary descriptors. The approach is to assign discrete and fix positions to all possible combinations obtained with the descriptors employed. One of the two algorithms, called clock, position objects on a circle at regular intervals, whereas the other, star, maintains the angular position as in clock, but defines the distance of the object from the center of the circle proportionally to the number of descriptor in state"1". Comparisons with Principal Coordinate Analysis (PCoA) showed that the three methods perform differently according to the number of objects and descriptors and to the distance method employed to carry out the PCoA. The algorithm clock produced the best object clustering in a validation carried out with a matrix generated by molecular fingerprint of yeast isolates.
The Open Applied Informatics Journal, 2011
Typology is based on the concept that one individual (the type) can represent the whole group. In... more Typology is based on the concept that one individual (the type) can represent the whole group. In yeast taxonomy the type strain is the representative of the whole species and is considered an important tool for classification. Although the evolutionary, phylogenetic and biological species concepts are in contrast with this approach, the International Codes of nomenclature still use typology, which remains one of the most operative systems. These incongruities demand a multidisciplinary investigation on the nature of the type, its characteristics and the possibility of the type to be defined on the basis of a shareable criterion. In this paper we present an approach to the problem of type centrality based on mathematical demonstrations and numerical examples. This paper intended to show the possibilities offered to bioinformatics research by the implementation of multidisciplinary approaches in biology and in proposing a general approach to the definition of the type representing any sort of set, described with multiple descriptors.
The Open Applied Informatics Journal, 2011
The problem of species and in particular microbial species is central in biology. An active colla... more The problem of species and in particular microbial species is central in biology. An active collaboration of various specialists such as taxonomists, epistemologists, mathematicians and bioinformatics experts is desirable for its solution.
Genome Announcements, 2014
The Ascomycota species Phaeomoniella chlamydospora, in concert with other fungi, is a causal agen... more The Ascomycota species Phaeomoniella chlamydospora, in concert with other fungi, is a causal agent for grapevine trunk diseases. Here, we present the first draft of the P. chlamydospora genome sequence, which comprises 355 scaffolds, with a total length of 26.59 Mb and 7,279 predicted protein-coding genes.
PLoS ONE, 2014
Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evid... more Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evidence regarding functional interaction with the host plant. Microbial communities in plants were recently reported to be influenced by numerous environmental and anthropogenic factors, including soil and pest management. In this study we used automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and pyrosequencing of 16S rDNA to assess the effect of organic production and integrated pest management (IPM) on bacterial endophytic communities in two widespread grapevines cultivars (Merlot and Chardonnay). High levels of the dominant Ralstonia, Burkholderia and Pseudomonas genera were detected in all the samples We found differences in the composition of endophytic communities in grapevines cultivated using organic production and IPM. Operational taxonomic units (OTUs) assigned to the Mesorhizobium, Caulobacter and Staphylococcus genera were relatively more abundant in plants from organic vineyards, while Ralstonia, Burkholderia and Stenotrophomonas were more abundant in grapevines from IPM vineyards. Minor differences in bacterial endophytic communities were also found in the grapevines of the two cultivars.
The Analyst, 2010
Fourier Transform InfraRed (FTIR) spectroscopy is an increasingly used technique in biology, espe... more Fourier Transform InfraRed (FTIR) spectroscopy is an increasingly used technique in biology, especially for whole cell metabolomic fingerprint. The reproducibility of this technique is influenced by a large number of factors such as the physiological state of cells, sample manipulation and growth conditions. Evidence exists suggesting that the cell shape and dimension can be further elements to consider in whole cell FTIR analysis. In this study we aimed to address the effect of cell geometry on the FTIR spectra and to define the extent of variability occurring between machine and biological replicas with a standardized protocol. The yeast species Saccharomyces cerevisiae (large oval-shaped cells) and Debaryomyces hansenii (small round shaped cells) were employed for their different morphology. Thirty machine replicas of each were analyzed separately and after averaging in groups of three, showing a three to four-fold reduction of the variability. Similarly, a two-fold reduction of variability was observed when thirty biological replicas of the two yeast species were analyzed. The optimal number of replicas to average was then estimated with a bootstrap-like procedure in which biological and machine replicas were randomly resampled 2000 times and averaged in groups spanning from 2 to 12 replicas. This simulation has shown that little if any advantage can be obtained by increasing the number of replicas over five and that the variability exhibited by the small regular cells of D. hansenii was always roughly half of that displayed by the large S. cerevisiae cells, confirming the results obtained with standard non-bootstrapped averages.
The Analyst, 2011
Fourier Transform InfraRed spectroscopy (FTIR) is an emerging technique in biology. One of the an... more Fourier Transform InfraRed spectroscopy (FTIR) is an emerging technique in biology. One of the analytical problems inherent with this approach is the extreme variability typical of biological systems. Extrinsic fonts of variations are the growth media and the growth phase of the microbial culture. In order to gain knowledge on the relations between these two factors and the spectral variability, metabolomic changes in Saccharomyces cerevisiae cells during growth were analyzed with FTIR spectroscopy. Spectral variations reflected the changes occurring in all cellular compartments and components during the different growth stages and describe the metabolomic evolution of cell cultures during growth. Three different media were tested. Different mathematical and statistical treatments were used to describe and evaluate the changes occurring during growth. Variations were mainly concentrated in the exponential phase, whereas fewer changes occurred in stationary phase cells. The three different media caused different metabolomic behaviours during growth. The mathematical distance between the peak areas of amide I, amide II and of two distinct peaks in the carbohydrates region could give a synthetic description of growth and produced similar trends in all the conditions tested. The distance between the two carbohydrate peaks could be used to determine the mid exponential phase and the entrance in the stationary phase. Growth phase was shown to influence the sensitivity of a FTIR-based cell stress bioassay. The knowledge of the metabolomic variations during growth could be used in the future to optimize FTIR applications in microbiology.
Molecular Biology and Evolution, 2014
Here, we report the surprising and, to our knowledge, unique example of horizontal interkingdom t... more Here, we report the surprising and, to our knowledge, unique example of horizontal interkingdom transfer of a human opportunistic pathogen (Propionibacterium acnes) to a crop plant (the domesticated grapevine Vitis vinifera L.). Humans, like most organisms, have established a long-lasting cohabitation with a variety of microbes, including pathogens and gutassociated bacteria. Studies which have investigated the dynamics of such associations revealed numerous cases of bacterial host switches from domestic animals to humans. Much less is, however, known about the exchange of microbial symbionts between humans and plants. Fluorescent in situ hybridization localized P. acnes in the bark, in xylem fibers, and, more interestingly, inside pith tissues. Phylogenetic and population genetic analyses suggest that the establishment of the grapevine-associated P. acnes as obligate endophyte is compatible with a recent transfer event, likely during the Neolithic, when grapevine was domesticated.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2012
A novel species of ascomycetous yeast, Candida coquimbonensis sp. nov., from the necrotic tissue ... more A novel species of ascomycetous yeast, Candida coquimbonensis sp. nov., from the necrotic tissue of cacti in Chile and Australia is described. C. coquimbonensis sp. nov. is closely related and phenotypically similar to Phaffomyces opuntiae. There is no overlap in the geographical distribution between C. coquimbonensis and any species in the Phaffomyces clade. However, this is the first member of the clade to be collected in both native (Chile) and non-native (Australia) cactus habitats. The type strain of C. coquimbonensis sp. nov. is TSU 00-206.4B(T) ( = CBS 12348(T) = USCFST 12-103(T)).
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Papers by Livio Antonielli