DNA metabarcoding and morphological analysis - Assessment of zooplankton biodiversity in transitional waters

Zooplankton biodiversity assessment is a crucial element in monitoring marine ecosystem processes and community responses to environmental alterations. In order to evaluate the suitability of metabarcoding for zooplankton biodiversity assessment and biomonitoring as a fast and more cost-effective method, seasonal zooplankton sampling was carried out in the Venice Lagoon and the nearby coastal area (Northern Adriatic Sea). The molecular analysis showed higher taxa richness compared to the classical morphological method (224 vs. 88 taxa), discriminating better the meroplanktonic component, morphologically identified only up to order level. Both methods revealed a similar spatio-temporal distribution pattern and the sequence abundances and individual counts were significantly correlated for various taxonomic groups. These results indicate that DNA metabarcoding is an efficient tool for biodiversity assessments in ecosystems with high spatial and temporal variability, where high sampling effort is required as well as fast alert systems for non-native species (NIS)

Insights into the oral bacterial microbiota of sows

The investigation of bacterial microbiota represents a developing research field in veterinary medicine intended to look for correlations between animal health and the balance within bacterial populations. The aim of the present work was to define the bacterial microbiota of the oral cavity of healthy sows, which had not been thoroughly described so far. In total, 22 samples of oral fluid were collected and analyzed by 16S-rRNA gene sequencing. CLC Genomics Workbench 20.0 (QIAGEN Digital Insights, Aarhus, Denmark) was then used to examine the results. The predominant orders were Lactobacillales, Clostridiales, and Corynebacteriales. Lactobacillaceae, Corynebacteriaceae, Moraxellaceae, Aerococcaceae, and Staphylococcaceae were the most represented families. As regards the most abundant genera, Lactobacillus, Corynebacterium, Acinetobacter, Staphylococcus, Rothia, Aerococcus, and Clostridium can be pointed out as the bacterial core microbiota. Sows were also divided into “gestating” and “lactating” groups, and mild differences were found between pregnant and lactating sows. The data herein described represent an original contribution to the knowledge of the porcine bacterial microbiota. Moreover, the choice of sows as experimental animals was strategic for identifying the adult microbial community. These data provide a basis for further studies on the oral bacterial microbiota of pigs

Developmental stages and gut microenvironments influence gut microbiota dynamics in the invasive beetle Popillia japonica Newman (Coleoptera: Scarabaeidae)

Popillia japonica Newman (Coleoptera: Scarabaeidae) is a highly polyphagous invasive beetle originating from Japan. This insect is highly resilient and able to rapidly adapt to new vegetation. Insect?associated microorganisms can play important roles in insect physiology, helping their hosts to adapt to changing conditions and potentially contributing to an insect's invasive potential. Such symbiotic bacteria can be part of a core microbiota that is stably transmitted throughout the host's life cycle or selectively recruited from the environment at each developmental stage. The aim of this study was to investigate the origin, stability and turnover of the bacterial communities associated with an invasive population of P. japonica from Italy. Our results demonstrate that soil microbes represent an important source of gut bacteria for P. japonica larvae, but as the insect develops, its gut microbiota richness and diversity decreased substantially, paralleled by changes in community composition. Notably, only 16.75% of the soil bacteria present in larvae are maintained until the adult stage. We further identified the micro?environments of different gut sections as an important factor shaping microbiota composition in this species, likely due to differences in pH, oxygen availability and redox potential. In addition, P. japonica also harboured a stable bacterial community across all developmental stages, consisting of taxa well known for the degradation of plant material, namely the families Ruminococcacae, Christensenellaceae and Lachnospiraceae. Interestingly, the family Christensenallaceae had so far been observed exclusively in humans. However, the Christensenellaceae operational taxonomic units found in P. japonica belong to different taxonomic clades within this family

Does diet breadth affect the complexity of the phytophagous insect microbiota? The case study of Chrysomelidae

Chrysomelidae is a family of phytophagous insects with a highly variable degree of trophic specialization. The aim of this study is to test whether species feeding on different plants (generalists) harbour more complex microbiotas than those feeding on a few or a single plant species (specialists). The microbiota of representative leaf beetle species was characterized with a metabarcoding approach targeting V1–V2 and V4 regions of the bacterial 16S rRNA. Almost all the analysed species harbour at least one reproductive manipulator bacteria (e.g., Wolbachia, Rickettsia). Two putative primary symbionts, previously isolated only from a single species (Bromius obscurus), have been detected in two species of the same subfamily, suggesting a widespread symbiosis in Eumolpinae. Surprisingly, the well-known aphid symbiont Buchnera is well represented in the microbiota of Orsodacne humeralis. Moreover, in this study, using Hill numbers to dissect the components of the microbiota diversity (abundant and rare bacteria), it has been demonstrated that generalist insect species harbour a more diversified microbiota than specialists. The higher microbiota diversity associated with a wider host-plant spectrum could be seen as an adaptive trait, conferring new metabolic potential useful to expand the diet breath, or as a result of environmental stochastic acquisition conveyed by diet

Analisi genetica dei livelli di acetilazione dell'esopolisaccaride prodotto da Burkholderia cepacia

Introduzione: Le infezioni causate da Burkholderia cepacia complex (Bcc) in pazienti affetti da fibrosi cistica (CF) sono spesso correlate ad un aumento di mortalit\ue0 e l\u2019innata resistenza di questi microrganismi ad un ampio range di antibiotici complica il trattamento di tali pazienti. Uno dei meccanismi che rendono i batteri pi\uf9 resistenti all\u2019azione degli antibiotici \ue8 la capacit\ue0 di produrre biofilm. Metodi: Mediante microdiluizione in brodo e l\u2019utilizzo della tecnologia \u201cCalgary Biofilm Device\u201d sono state valutate le minime concentrazioni di antibiotico in grado di inibire la crescita di un ceppo Bcc cresciuto in forma planctonica (MIC) e all\u2019interno di biofilm (BIC). Sono stati paragonati due isolati indipendenti dello stesso ceppo (BTS-2) che, a distanza di 6 anni (BTS2-00 e BTS2-06), ha notevolmente ridotto la propria capacit\ue0 di produrre biofilm. Risultati: I dati preliminari finora ottenuti indicano che l\u2019isolato BTS2-00, produttore di abbondanti quantit\ue0 di biofilm, presenta valori di BIC significativamente superiori alle MIC per alcuni degli antibiotici saggiati. Tale incremento \ue8 per\uf2 molto meno marcato nel caso dell\u2019isolato BTS2-06, che produce biofilm in quantit\ue0 circa 5 volte inferiore. Le MIC dei due isolati sono comparabili nella maggior parte dei casi (con l\u2019eccezione della ciprofloxacina per la quale si pu\uf2 ipotizzare l\u2019acquisizione di un determinante di resistenza avvenuto nel corso del tempo) mentre le BIC di BTS2-06 sono sempre inferiori rispetto a quelle dell\u2019isolato BTS2-00. Conclusioni: L\u2019osservazione che BTS2 presenti un incremento della resistenza delle forme sessili rispetto a quelle planctoniche nei confronti di alcuni degli antibiotici saggiati, non pi\uf9 evidente quando il ceppo riduce la quantit\ue0 di biofilm prodotto, avvalora l\u2019ipotesi che la matrice del biofilm costituisca una barriera efficace contro il passaggio di alcuni antibiotici e dimostra l\u2019importanza di utilizzare test adeguati per valutare l\u2019efficacia della terapia nei pazienti CF

Influence of the culture medium in the evaluation of biofilm inhibitory concentrations for isolates of Burkholderia cenocepacia

Bacteria belonging to the Burkholderia cepacia complex (Bcc) principally cause chronic pulmonary infections in cystic fibrosis (CF) patients. They are intrinsically resistant to many antibiotics, so therapeutic options are often limited. Moreover, their ability to form biofilms (BF) can retard contact with some antimicrobials, making these infections difficult to eradicate even by drugs that display a Minimal Inhibitory Concentration (MIC) lower than the breakpoint. But the MIC is evaluated on the planktonic forms whereas the higher resistance of the sessile forms (BIC: Biofilm Inhibitory Concentration) towards some antibiotics commonly used in the clinical management of lung infections has been widely described (REF). One variable experimental condition in the evaluation of the BIC is the choice of the medium. Data available till now have been obtained using different media, as no guidelines have been established yet. However, preliminary results suggest that the composition of the BF matrix (protein/EPS ratio) varies depending on the medium used to culture bacteria (Cescutti, personal communication). We evaluated the antibiotic susceptibility of a B. cenocepacia clinical isolate, named BTS2, which has stably colonized a patient for ten years, is a good biofilm producer in the sample taken in 2000 (BTS2-00) while shows a significant reduction in this capacity 9 years later (BTS2-09). We compared the susceptibility of its sessile forms grown inside the biofilm synthesized in three different media: Muller Hinton Broth (MHB), commonly used for antimicrobial susceptibility tests; Yeast Extract Medium (YEM), where Bcc produce large amount of the EPS cepacian (REF); and Synthetic Cystic Fibrosis Medium (SCFM), a synthetic medium that mimics the nutritional composition of CF sputum (REF). A modification of the Calgary Device method was used (REF). Bacteria were initially grown as biofilm using one of the media listed above. Then, the incubation with the antibiotic was always carried on in MHB. Some of the tested drugs showed different activity levels on the BF depending on the culture medium used, but the most important difference was observed after incubation with aztreonam, whose BICs in different media diverged more than 50x even in absence of significant differences of the BF production. So, as it seems difficult to ascribe only to the thickness of the BF matrix the protection against the drug, we are planning to analyse its ability to spread into the different BF matrices following the course of a labelled molecule by confocal microscopy analysis