Machine Learning Algorithms Highlight tRNA Information Content and Chargaff's Second Parity Rule Score as Important Features in Discriminating Probiotics from Non-Probiotics.

Probiotic bacteria are microorganisms with beneficial effects on human health and are currently used in numerous food supplements. However, no selection process is able to effectively distinguish probiotics from non-probiotic organisms on the basis of their genomic characteristics. In the current study, four Machine Learning algorithms were employed to accurately identify probiotic bacteria based on their DNA characteristics. Although the prediction accuracies of all algorithms were excellent, the Neural Network returned the highest scores in all the evaluation metrics, managing to discriminate probiotics from non-probiotics with an accuracy greater than 90%. Interestingly, our analysis also highlighted the information content of the tRNA sequences as the most important feature in distinguishing the two groups of organisms probably because tRNAs have regulatory functions and might have allowed probiotics to evolve faster in the human gut environment. Through the methodology presented here, it was also possible to identify seven promising new probiotics that have a higher information content in their tRNA sequences compared to non-probiotics. In conclusion, we prove for the first time that Machine Learning methods can discriminate human probiotic from non-probiotic organisms underlining information within tRNA sequences as the most important genomic feature in distinguishing them.

Microplastics in Fish and Fishery Products and Risks for Human Health: A Review.

In recent years, plastic waste has become a universally significant environmental problem. Ingestion of food and water contaminated with microplastics is the main route of human exposure. Fishery products are an important source of microplastics in the human diet. Once ingested, microplastics reach the gastrointestinal tract and can be absorbed causing oxidative stress, cytotoxicity, and translocation to other tissues. Furthermore, microplastics can release chemical substances (organic and inorganic) present in their matrix or previously absorbed from the environment and act as carriers of microorganisms. Additives present in microplastics such as polybrominated diphenyl ethers (PBDE), bisphenol A (BPA), nonylphenol (NP), octylphenol (OP), and potentially toxic elements can be harmful for humans. However, to date, the data we have are not sufficient to perform a reliable assessment of the risks to human health. Further studies on the toxicokinetics and toxicity of microplastics in humans are needed.

Undeclared animal species in dry and wet novel and hydrolyzed protein diets for dogs and cats detected by microarray analysis.

BACKGROUND: Although the European Pet Food Industry Federation (FEDIAF) stated that labels must be accurate and provide detailed information on the ingredients, mislabeling of pet food has been documented by several authors. This phenomenon is of particular concern when related to products used as elimination diets for the diagnosis of adverse food reaction (AFR) in dogs and cats because the presence of undeclared ingredients may negatively interfere with the trial and prevent the veterinarian from making an appropriate diagnosis. The aim of this study was to shed light upon the problem of contamination and mislabeling in both dry and wet novel protein diets (NPDs) and hydrolyzed protein diets (HPDs) using a microarray-based commercial kit which tests for the presence of 19 animal species. RESULTS: Of the 40 analyzed products (9 dry NPDs, 22 wet NPDs, 6 dry HPDs and 3 wet HPDs), ten presented a content that correctly matched the label, while five did not contain the declared animal species, twenty-three revealed the presence of undeclared animal species, and two had a vague label that did not allow the evaluation of its accuracy. The most frequently contaminants identified in both dry and wet pet foods were pork, chicken and turkey. The presence of undeclared animal species was higher in dry than wet pet foods; furthermore, a lower number of contaminating animal species was identified in HPDs than NPDs (4 vs 10), and a lower number of contaminated HPDs (6 out of 9, 67%) than contaminated NPDs was detected (24 out of 31, 77%). Thirteen out of 14 brands tested presented at least one mislabeled product. CONCLUSIONS: Mislabeling seems to be a widespread issue in pet foods used as elimination diets. Contamination can occur in all types of products used for the purpose, although dry NPDs are the main issue. Due to the high risk of contamination, particular attention should be given to both the selection of raw material suppliers and the production process.

A Limited Survey of Heavy Metal Concentrations in Fresh and Frozen Cuttlefish Ink and Mantle Used As Food.

Cuttlefish ink is consumed as a delicacy worldwide. The current study is the first assessment of heavy metal concentrations in cuttlefish ink versus mantle under different storage methods. A total of 212 samples (64 of fresh mantle, 42 of frozen mantle, 64 of fresh ink, and 42 of frozen ink) were analyzed for the detection of the following heavy metals: arsenic (As), chromium (Cr), iron (Fe), lead (Pb), mercury (Hg), and cadmium (Cd). The median As concentrations were 12.9 mg/kg for fresh mantle, 8.63 mg/kg for frozen mantle, 10.8 mg/kg for frozen ink, and 0.41 mg/kg for fresh ink. The median Cr concentrations were 0.06 mg/kg for fresh mantle and frozen ink, 0.03 mg/kg for frozen mantle, and below the limit of quantification (LOQ) for fresh ink. The median Fe concentrations were 4.08 mg/kg for frozen ink, 1.51 mg/kg for fresh mantle, 0.73 mg/kg for frozen mantle, and below the LOQ for fresh ink. The median Pb concentrations of almost all samples were below the LOQ; only two frozen ink, one fresh ink, one frozen mantle, and one fresh mantle sample exceeded the limit stipulated by the European Union. The Hg concentrations were statistically similar among the four categories of samples; the median Hg concentrations were below the LOQ, and the maximum concentrations were found in frozen ink, at 1.62 mg/kg. The median Cd concentrations were 0.69 mg/kg for frozen ink and 0.11 mg/kg for frozen mantle, fresh mantle and fresh ink concentrations were below the LOQ, and in 11.3% of the tested samples, Cd concentrations were higher than the European Union limit. The probability of samples having a Cd concentration above the legal limit was 35.75 times higher in frozen than in fresh products. Fresh ink had significantly lower concentrations of As, Cr, Fe, and Cd, but the concentrations of Hg and Pb were not significantly different from those of other products. Frozen ink had significantly higher concentrations of Cd, Cr, and Fe, but concentrations of As were lower than those in fresh mantle, pointing out a possible role for the freezing process and for different fishing zones as risk factors for heavy metal contamination.

Prevalence and quantification of thermophilic Campylobacter spp. in Italian retail poultry meat: Analysis of influencing factors.

Retail poultry meat is a crucial vehicle for consumers' exposure to Campylobacters, but no official controls are currently applied in Italy. The aim of this study was the evaluation of Campylobacter contamination of a wide range of poultry meats marketed in Italy. N. 472 chicken and turkey meat samples (sectioned meats, offal, meat preparations and products) were taken from slaughterhouses, deboning plants and different retailers and submitted to detection/enumeration of Campylobacter spp. The isolates were identified by phenotypic and biomolecular techniques. Campylobacter spp. was detected in 34.1% of the samples, with general low counts. Higher values were observed in offal (especially liver) and sectioned meats, with significantly higher rates in skin-on samples (86.8% vs 32.7%). Minced meat preparations showed lower prevalence (22.4% vs 58.3%) and counts than whole pieces. Decreasing rates were observed among slaughterhouses (80%), deboning plants (49%), butcher's shops (37%) and large scale retailers (25%). Sectioned chicken meats were significantly more contaminated than turkey meats. Almost all the isolates were identified as C. jejuni or C. coli, with similar prevalences (18.4% and 20.5%, respectively); C. jejuni was predominant only in samples from slaughterhouses/deboning plants. For setting future control programs, meat typology should be considered the main critical factor.

Multiple-locus sequence typing and analysis of toxin genes in Bacillus cereus food-borne isolates.

In the present study we characterized 47 food-borne isolates of Bacillus cereus using multilocus sequence typing (MLST). Newly determined sequences were combined with sequences available in public data banks in order to produce the largest data set possible. Phylogenetic analysis was performed on a total of 296 strains for which MLST sequence information is available, and three main lineages--I, II, and III--within the B. cereus complex were identified. With few exceptions, all food-borne isolates were in group I. The occurrence of horizontal gene transfer (HGT) among various strains was analyzed by several statistical methods, providing evidence of widespread lateral gene transfer within B. cereus. We also investigated the occurrence of toxin-encoding genes, focusing on their evolutionary history within B. cereus. Several patterns were identified, indicating a pivotal role of HGT in the evolution of toxin-encoding genes. Our results indicate that HGT is an important element in shaping the population structure of the B. cereus complex. The results presented here also provide strong evidence of reticulate evolution within the B. cereus complex.

Fecal carriage of Escherichia coli O157:H7 and carcass contamination in cattle at slaughter in northern Italy.

Feedlot cattle slaughtered at a large abattoir in northern Italy during 2002 were examined for intestinal carriage and carcass contamination with Escherichia coli O157:H7. Carcass samples were taken following the excision method described in the Decision 471/2001/EC, and fecal material was taken from the colon of the calves after evisceration. Bacteria were isolated and identified according to the MFLP-80 and MFLP-90 procedures (Food Directorate's Health Canada's). Eighty-eight non-sorbitol-fermenting E. coli O157:H7 isolates were obtained from 12 of the 45 calves examined. In particular, E. coli O157:H7 isolates were found in 11 (24%) fecal and five (11%) carcass samples. PCR analysis showed that all 11 fecal samples and five carcass samples carried eae-gamma1-positive E. coli O157:H7 isolates. In addition, genes encoding Shigatoxins were detected in O157:H7 isolates from nine and two of those 11 fecal and five carcasses, respectively. A representative group of 32 E. coli O157:H7 isolates was analyzed by phage typing and DNA macrorestriction fragment analysis (PFGE). Five phage types (PT8, PT32v, PT32, PT54, and PT not typable) and seven (I-VII) distinct restriction patterns of similarity >85% were detected. Up to three different O157:H7 strains in an individual fecal sample and up to four from the same animal could be isolated. These findings provide evidence of the epidemiological importance of subtyping more than one isolate from the same sample. Phage typing together with PFGE proved to be very useful tools to detect cross-contamination among carcasses and should therefore be included in HACCP programs at abattoirs. The results showed that the same PFGE-phage type E. coli O157:H7 profile was detected in the fecal and carcass samples from an animal, and also in two more carcasses corresponding to two animals slaughtered the same day.

Fecal carriage of Escherichia coli O157: H7 and carcass contamination in cattle at slaughter in northern Italy

Feedlot cattle slaughtered at a large abattoir in northern Italy during 2002 were examined for intestinal carriage and carcass contamination with Escherichia coli O157:H7. Carcass samples were taken following the excision method described in the Decision 471/2001/EC, and fecal material was taken from the colon of the calves after evisceration. Bacteria were isolated and identified according to the MFLP-80 and MFLP-90 procedures (Food Directorate's Health Canada's). Eighty-eight non-sorbitol-fermenting E. coli O157:H7 isolates were obtained from 12 of the 45 calves examined. In particular, E. coli O157:H7 isolates were found in 11 (24%) fecal and five (11%) carcass samples. PCR analysis showed that all 11 fecal samples and five carcass samples carried eae-gamma1-positive E. coli O157:H7 isolates. In addition, genes encoding Shigatoxins were detected in O157:H7 isolates from nine and two of those 11 fecal and five carcasses, respectively. A representative group of 32 E. coli O157:H7 isolates was analyzed by phage typing and DNA macrorestriction fragment analysis (PFGE). Five phage types (PT8, PT32v, PT32, PT54, and PT not typable) and seven (I-VII) distinct restriction patterns of similarity >85% were detected. Up to three different O157:H7 strains in an individual fecal sample and up to four from the same animal could be isolated. These findings provide evidence of the epidemiological importance of subtyping more than one isolate from the same sample. Phage typing together with PFGE proved to be very useful tools to detect cross-contamination among carcasses and should therefore be included in HACCP programs at abattoirs. The results showed that the same PFGE-phage type E. coli O157:H7 profile was detected in the fecal and carcass samples from an animal, and also in two more carcasses corresponding to two animals slaughtered the same day (AU)

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