Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy

Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy

The complex microbial community of withered berries of cv. Corvina as revealed by metagenomic analysis

Corvina is the most important of Verona\u2019s red grape varieties and forms the basis for the production of unique wines, such as Amarone and Recioto of the Valpolicella area (Italy). The distinctive features of such wines are linked to the peculiar winemaking techniques and especially to the post-harvest grape withering process, when the grapes are partially dried in attics for three/four months to concentrate sugars up to about 27% (w/v). Dehydratation increases the concentration of constituent substances in berries, determining also specific expression of grape genes. During this process, grapes are colonized with a complex microbiota to an extent which depends on environmental temperature and humidity. In this study, a whole metagenome sequencing (WMS) approach was used to analyse the microbial consortia present on Corvina berries at the end of the withering process performed in two different conditions (\u201ctraditional\u201d or \u201cfast\u201d). Representative berry samples were collected and washed to avoid grapevine DNA contamination. Bioinformatic analyses, performed on reads and scaffolds, revealed that traditionally withered berries were dominated by Clostridiales and Pseudomonadales, while the fast procedure determined the presence of Enterobacteriales and Lactobacillales. On the contrary, few consistent differences characterized the eukaryotic fraction, dominated by Aspergillus and Penicillium for both samples. Interestingly, the \u201cbinning\u201d procedure revealed 15 most abundant genomes characterizing the two conditions. These results provide insights into the microbial community of Corvina withered berries and reveal relevant variations attributable to environmental withering conditions. Further studies will be performed to determine whether the different microbial compositions could lead to significant chemical variations of the musts, with an impact on the organoleptic properties of wine. This study underlines how novel technologies, like WMS, could open novel perspectives in the knowledge and management of traditional processes as the withering process of Corvina, with an impact on the winemaking of important Italian wines

A synthesis of bacterial and archaeal phenotypic trait data

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients

Geo-archaeological study of the territory of Burnum\u2019s Roman site (Croatia) through LANDSAT multi-temporal satellite images and high resolution GeoEye.

Archaeologists can increasingly profit fromdigital elevationmodels for study and analysis of the actual landscape, which can contain signs of the past or mirror the ancient landscapes. From among the techniques available for such analyses, a photogrammetric method was chosen here that used images acquired by an unmanned aerial vehicle and involved structure-from-motion algorithms during the process. These methods were selected because as the state-of-the-art of the discipline they are in the initial stages and are under continuous evolution. Furthermore, they provided us with the possibility of rapid, highly automated, and also low-cost, production of high-resolution three-dimensional data. This test was carried out on the Roman site of Burnum (Croatia). It focused on the comparison between the digital surface model created using an unmanned aerial vehicle with a structure-from-motion approach, and the digital terrain model already built through a kinematic Global Navigation Satellite System survey. The results of the validation provided a final vertical accuracy of about 10 cm,which was achieved in specific areas where there were no trees, bushes and high grass. Through the resulting digital terrain models, archaeologists can provide vital support for important hypothesis regarding the ancient environment

Effects of bioprotective cultures on the microbial community during storage of Italian fresh filled pasta

Filled pasta is a typical Italian product consisting in a thin dough stuffed with dairy, meat or vegetable ingredients. When industrially produced, its microbial stability relies on thermal treatment, proper storage temperature and modified atmosphere packaging. Since these processes can strongly affect the traditional features of pasta (mainly flavor and texture), alternative strategies have been investigated. In this study, milder heat treatments were applied and combined with the addition of bioprotective cultures (Lactobacillus rhamnosus and Lactobacillus paracasei) in the filling of Ricotta based Tortelloni to assure microbial quality and safety. Their effects on microbiological patterns during storage at 6 \ub0C was studied through culture dependent and independent methods; in addition, the influence on organoleptic profile (through SPME-GC-MS and sensory evaluation) was also assessed. The results demonstrated that bioprotective cultures had a relevant quantitative and qualitative effect on the microbiota of Tortelloni during storage: although they were not dominant, their presence reduced the initial microbiota associated with raw materials and gave a competitive advantage to safer or organoleptically acceptable LAB species, such as leuconostocs. Although these LAB cultures influenced the aroma profile of filled pasta (i.e. increase of alcohols, esters and acids), the sensory evaluation confirmed the overall acceptability of the product. The addition of bioprotective cultures can therefore be considered a helpful strategy to reduce thermal treatments and to better maintain the traditional textural and flavor characteristics of this product