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Vernaci G, Savarino EV, Patuzzi I, Facchin S, Zingone F, Massa D, Faggioni G, Giarratano T, Miglietta F, Griguolo G, Fassan M, Lo Mele M, Gasparini E, Bisagni G, Guarneri V, Dieci MV. Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy. Oncologist 2023; 28:e703-e711. [PMID: 36940301 PMCID: PMC10485294 DOI: 10.1093/oncolo/oyad060] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/31/2023] [Indexed: 03/22/2023] Open
Abstract
INTRODUCTION Patients with triple-negative breast cancer (TNBC) achieving a pathological complete response (pCR) after neoadjuvant chemotherapy have a better event-free survival. The role of gut microbiome in early TNBC is underexplored. METHODS Microbiome was analyzed by 16SrRNA sequencing. RESULTS Twenty-five patients with TNBC treated with neoadjuvant anthracycline/taxane-based chemotherapy were included. Fifty-six percent achieved a pCR. Fecal samples were collected before (t0), at 1 (t1), and 8 weeks (t2) from chemotherapy. Overall, 68/75 samples (90.7%) were suitable for microbiome analysis. At t0, pCR group showed a significantly higher α-diversity as compared with no-pCR, (P = .049). The PERMANOVA test on β-diversity highlighted a significant difference in terms of BMI (P = 0.039). Among patients with available matched samples at t0 and t1, no significant variation in microbiome composition was reported over time. CONCLUSIONS Fecal microbiome analysis in early TNBC is feasible and deserves further investigation in order to unravel its complex correlation with immunity and cancer.
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Affiliation(s)
- Grazia Vernaci
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Edoardo Vincenzo Savarino
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
- Gastroenterology Unit, Azienda Ospedale Università di Padova, Padova, Italy
| | | | - Sonia Facchin
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
- Gastroenterology Unit, Azienda Ospedale Università di Padova, Padova, Italy
| | - Fabiana Zingone
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
- Gastroenterology Unit, Azienda Ospedale Università di Padova, Padova, Italy
| | - Davide Massa
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Giovanni Faggioni
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Tommaso Giarratano
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Federica Miglietta
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Gaia Griguolo
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology Unit, University of Padua, Padua, Italy
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Marcello Lo Mele
- Department of Pathology, Azienda Ospedale Università Padova, Padova, Italy
| | - Elisa Gasparini
- Breast Cancer Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Oncology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Giancarlo Bisagni
- Breast Cancer Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Oncology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Valentina Guarneri
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Maria Vittoria Dieci
- Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
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Innocente G, Patuzzi I, Furlanello T, Di Camillo B, Bargelloni L, Giron MC, Facchin S, Savarino E, Azzolin M, Simionati B. Machine Learning and Canine Chronic Enteropathies: A New Approach to Investigate FMT Effects. Vet Sci 2022; 9:vetsci9090502. [PMID: 36136718 PMCID: PMC9505216 DOI: 10.3390/vetsci9090502] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/03/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Fecal microbiota transplantation (FMT) represents a very promising approach to decreasing disease activity in canine chronic enteropathies (CE). However, the relationship between remission mechanisms and microbiome changes has not been elucidated yet. The main objective of this study was to report the clinical effects of oral freeze-dried FMT in CE dogs, comparing the fecal microbiomes of three groups: pre-FMT CE-affected dogs, post-FMT dogs, and healthy dogs. Diversity analysis, differential abundance analysis, and machine learning algorithms were applied to investigate the differences in microbiome composition between healthy and pre-FMT samples, while Canine Chronic Enteropathy Clinical Activity Index (CCECAI) changes and microbial diversity metrics were used to evaluate FMT effects. In the healthy/pre-FMT comparison, significant differences were noted in alpha and beta diversity and a list of differentially abundant taxa was identified, while machine learning algorithms predicted sample categories with 0.97 (random forest) and 0.87 (sPLS-DA) accuracy. Clinical signs of improvement were observed in 74% (20/27) of CE-affected dogs, together with a statistically significant decrease in CCECAI (median value from 5 to 2 median). Alpha and beta diversity variations between pre- and post-FMT were observed for each receiver, with a high heterogeneity in the response. This highlighted the necessity for further research on a larger dataset that could identify different healing patterns of microbiome changes.
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Affiliation(s)
- Giada Innocente
- Research & Development Division, EuBiome S.r.l., 35131 Padova, Italy
| | - Ilaria Patuzzi
- Research & Development Division, EuBiome S.r.l., 35131 Padova, Italy
| | | | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, 35020 Legnaro, Italy
| | - Maria Cecilia Giron
- Department of Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Sonia Facchin
- Department of Surgery, Oncological and Gastrointestinal Science, University of Padova, 35121 Padova, Italy
| | - Edoardo Savarino
- Department of Surgery, Oncological and Gastrointestinal Science, University of Padova, 35121 Padova, Italy
| | - Mirko Azzolin
- Ospedale Veterinario San Francesco, 31038 Castagnole, Italy
| | - Barbara Simionati
- Research & Development Division, EuBiome S.r.l., 35131 Padova, Italy
- Department of Pharmacological Sciences, University of Padova, 35131 Padova, Italy
- Correspondence:
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Morelli G, Patuzzi I, Losasso C, Ricci A, Contiero B, Andrighetto I, Ricci R. Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs. Sci Rep 2022; 12:9199. [PMID: 35655089 PMCID: PMC9163050 DOI: 10.1038/s41598-022-13270-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022] Open
Abstract
Obesity in dogs is an emerging issue that affects canine health and well-being. Its development is ascribed to several factors, including genetic predisposition and dietary management, and recent evidence suggests that intestinal microbiota may be involved as well. Previous works have shown obesity to be linked to significant changes in gut microbiota composition in humans and mice, but only limited information is available on the role played by canine gut microbiota. The aim of this exploratory study was to investigate whether composition of canine faecal microbiota may be influenced by overweight condition and breed. All the enrolled companion dogs were young adults, intact, healthy, and fed commercial extruded pet food; none had received antibiotics, probiotics or immunosuppressant drugs in the previous six months. Labrador Retriever (LR) and Border Collie (BC) were chosen as reference breeds and Body Condition Score (BCS) on a 9-point scale as reference method for evaluating body fat. The faecal microbial communities of 15 lean (BCS 4-5/9; 7 LRs and 8 BCs) and 14 overweight (BCS > 5/9; 8 LRs and 6 BCs) family dogs were analysed using 16S rRNA gene sequencing. Moreover, for each dog, the daily intake of energy (kcal/d) and dietary macronutrients (g/d) were calculated according to an accurate feeding history collection. Firmicutes and Bacteroidetes resulted the predominant phyla (51.5 ± 10.0% and 33.4 ± 8.5%, respectively) in all dogs. Bioinformatic and statistical analysis revealed that no bacterial taxon differed significantly based on body condition, except for genus Allisonella (p < 0.05); BC gut microbiota was richer (p < 0.05) in bacteria belonging to phyla Actinobacteria (family Coriobacteriaceae in particular) and Firmicutes (Allobaculum and Roseburia genera). No remarkable differences were recorded either for diversity indices (i.e., alpha diversity, p > 0.10) or for divergence within the sample set (i.e., beta diversity, p > 0.05). PERMANOVA tests performed on single factors demonstrated the tendency of dietary protein to influence the recruited dogs' microbiota beta-diversity at amplicon sequence variant level (p = 0.08). In conclusion, the faecal microbiota of dogs involved in this exploratory study showed no major variations based on body condition. However, our findings suggested that certain bacterial taxa previously acknowledged in obesity-related studies may be detected in dissimilar amounts depending on canine breed.
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Affiliation(s)
- Giada Morelli
- Department of Animal Medicine, Production and Health, University of Padua, 35020, Legnaro, PD, Italy.
| | - Ilaria Patuzzi
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, PD, Italy
- Research and Development Division, EuBiome S.R.L., 35129, Padua, Italy
| | - Carmen Losasso
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, PD, Italy
| | - Antonia Ricci
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, PD, Italy
| | - Barbara Contiero
- Department of Animal Medicine, Production and Health, University of Padua, 35020, Legnaro, PD, Italy
| | - Igino Andrighetto
- Department of Animal Medicine, Production and Health, University of Padua, 35020, Legnaro, PD, Italy
| | - Rebecca Ricci
- Department of Animal Medicine, Production and Health, University of Padua, 35020, Legnaro, PD, Italy
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Barberio B, Facchin S, Patuzzi I, Ford AC, Massimi D, Valle G, Sattin E, Simionati B, Bertazzo E, Zingone F, Savarino EV. A specific microbiota signature is associated to various degrees of ulcerative colitis as assessed by a machine learning approach. Gut Microbes 2022; 14:2028366. [PMID: 35129058 PMCID: PMC8820804 DOI: 10.1080/19490976.2022.2028366] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Ulcerative colitis (UC) is a complex immune-mediated disease in which the gut microbiota plays a central role, and may determine prognosis and disease progression. We aimed to assess whether a specific microbiota profile, as measured by a machine learning approach, can be associated with disease severity in patients with UC. In this prospective pilot study, consecutive patients with active or inactive UC and healthy controls (HCs) were enrolled. Stool samples were collected for fecal microbiota assessment analysis by 16S rRNA gene sequencing approach. A machine learning approach was used to predict the groups' separation. Thirty-six HCs and forty-six patients with UC (20 active and 26 inactive) were enrolled. Alpha diversity was significantly different between the three groups (Shannon index: p-values: active UC vs HCs = 0.0005; active UC vs inactive UC = 0.0273; HCs vs inactive UC = 0.0260). In particular, patients with active UC showed the lowest values, followed by patients with inactive UC, and HCs. At species level, we found high levels of Bifidobacterium adolescentis and Haemophilus parainfluenzae in inactive UC and active UC, respectively. A specific microbiota profile was found for each group and was confirmed with sparse partial least squares discriminant analysis, a machine learning-supervised approach. The latter allowed us to observe a perfect class prediction and group separation using the complete information (full Operational Taxonomic Unit table), with a minimal loss in performance when using only 5% of features. A machine learning approach to 16S rRNA data identifies a bacterial signature characterizing different degrees of disease activity in UC. Follow-up studies will clarify whether such microbiota profiling are useful for diagnosis and management.
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Affiliation(s)
- Brigida Barberio
- Division of Gastroenterology, Department of Surgery, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
| | - Sonia Facchin
- Division of Gastroenterology, Department of Surgery, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
| | - Ilaria Patuzzi
- Research & Development Division, University of Padova, Padova, Italy
| | - Alexander C. Ford
- Leeds Gastroenterology Institute, St. James’s University Hospital, Leeds, UK,Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Davide Massimi
- Division of Gastroenterology, Department of Surgery, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
| | - Giorgio Valle
- Department of Biology and Cribi Biotechnology Centre, University of Padova, Padova, Italy
| | | | - Barbara Simionati
- Research & Development Division, University of Padova, Padova, Italy
| | - Elena Bertazzo
- Division of Gastroenterology, Department of Surgery, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
| | - Fabiana Zingone
- Division of Gastroenterology, Department of Surgery, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
| | - Edoardo Vincenzo Savarino
- Division of Gastroenterology, Department of Surgery, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy,CONTACT Edoardo Vincenzo Savarino Division of Gastroenterology, Department of Surgery, Oncological and Gastroenterological Sciences, University of Padua, Padua, Italy
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Vernaci GM, Massa D, Patuzzi I, Menichetti A, Giarratano T, Griguolo G, Miglietta F, Fassan M, Savarino E, Conte P, Guarneri V, Dieci MV. Abstract P2-12-04: Characterization of gut microbiome composition in triple negative breast cancer patients treated with neoadjuvant chemotherapy. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p2-12-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Recent evidences showed intestinal microbiota to be implicated in carcinogenesis and response to chemotherapy and immune checkpoint inhibitors in solid tumors. Furthermore, antibiotics are known to deeply influence microbiome composition in healthy people and cancer patients. The role of gut microbiome in triple negative breast cancer (TNBC) is underexplored. Methods: In this pilot prospective study, we characterized the gut microbiome of 30 TNBC patients undergoing neoadjuvant chemotherapy at two Italian Institutions. Fecal samples were collected at 2 timepoints: at the baseline (t0) and at 1 week (t1) from CT. Microbiome was analyzed by 16S rRNA sequencing. Measures of α-diversity expressed by Richness and Simpson evenness were evaluated at the species level. β-diversity was calculated using PERMANOVA test according to UniFrac measures of dissimilarity at the species level.Tumor infiltrating lymphocytes (TILs) were assessed from diagnostic core biopsy and surgical specimen. Results: From September 2017 to March 2020, 30 TNBC patients were enrolled. Median age was 53 years, 43% were premenopausal, 43% were overweight or obese (BMI>25); 97% had a histologic G3 carcinoma, clinical nodal involvements was present in 57%; median TILs at diagnosis was 30%. All patients received anthracycline and taxane-based chemotherapy, including carboplatin in 23 patients (77%). A pCR was achieved in 15 (50%) patients. The overall rate of stool samples collection was 93%. With regards to t0, no differences in terms of α- and β-diversity were found.At t1, α-diversity was significantly higher in pCR group (Simpson evenness index, p=0.016). Considering clinical-pathological features, a BMI <24.9 was associated with higher microbiome richness (p=0.012). Measurements of β-diversity did not differ between groups.As 73% of patients during the treatment phase received antibiotics, with consequent potential microbiome impairment, we repeated analyses at t1 considering fecal samples collected >90 days after the end of antibiotic therapy (N=17). At this analysis, β-diversity evaluated with Unifrac measure was significantly correlated with pCR (p=0.035), with Haemophilus Influentiae being significantly enriched in non-pCR group. Conclusions: Fecal microbiome collection and analysis in this population is feasible and deserves further investigation with regards its association with response to chemotherapy.
Citation Format: Grazia Maria Vernaci, Davide Massa, Ilaria Patuzzi, Alice Menichetti, Tommaso Giarratano, Gaia Griguolo, Federica Miglietta, Matteo Fassan, Edoardo Savarino, PierFranco Conte, Valentina Guarneri, Maria Vittoria Dieci. Characterization of gut microbiome composition in triple negative breast cancer patients treated with neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-12-04.
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Affiliation(s)
- Grazia Maria Vernaci
- Medical Oncology 2 Unit, Istituto Oncologico Veneto; Department of Surgery, Oncology and Gastroenterology University of Padova, Padova, Italy
| | - Davide Massa
- Medical Oncology 2 Unit, Istituto Oncologico Veneto; Department of Surgery, Oncology and Gastroenterology University of Padova, Padova, Italy
| | - Ilaria Patuzzi
- Research & development Division, EuBiome S.r.l., Padova, Italy
| | - Alice Menichetti
- Medical Oncology 2 Unit, Istituto Oncologico Veneto, Padova, Italy
| | | | - Gaia Griguolo
- Medical Oncology 2 Unit, Istituto Oncologico Veneto; Department of Surgery, Oncology and Gastroenterology University of Padova, Padova, Italy
| | - Federica Miglietta
- Medical Oncology 2 Unit, Istituto Oncologico Veneto; Department of Surgery, Oncology and Gastroenterology University of Padova, Padova, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padova, Padova, Italy
| | - Edoardo Savarino
- Department of Surgery, Oncology and Gastroenterology University of Padova, Padova, Italy
| | - PierFranco Conte
- Medical Oncology 2 Unit, Istituto Oncologico Veneto; Department of Surgery, Oncology and Gastroenterology University of Padova, Padova, Italy
| | - Valentina Guarneri
- Medical Oncology 2 Unit, Istituto Oncologico Veneto; Department of Surgery, Oncology and Gastroenterology University of Padova, Padova, Italy
| | - Maria Vittoria Dieci
- Medical Oncology 2 Unit, Istituto Oncologico Veneto; Department of Surgery, Oncology and Gastroenterology University of Padova, Padova, Italy
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Baruzzo G, Patuzzi I, Di Camillo B. Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results. BMC Bioinformatics 2022; 22:618. [PMID: 35130833 PMCID: PMC8822630 DOI: 10.1186/s12859-022-04587-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 16S rRNA-gene sequencing is a valuable approach to characterize the taxonomic content of the whole bacterial population inhabiting a metabolic and spatial niche, providing an important opportunity to study bacteria and their role in many health and environmental mechanisms. The analysis of data produced by amplicon sequencing, however, brings very specific methodological issues that need to be properly addressed to obtain reliable biological conclusions. Among these, 16S count data tend to be very sparse, with many null values reflecting species that are present but got unobserved due to the multiplexing constraints. However, current data workflows do not consider a step in which the information about unobserved species is recovered. RESULTS In this work, we evaluate for the first time the effects of introducing in the 16S data workflow a new preprocessing step, zero-imputation, to recover this lost information. Due to the lack of published zero-imputation methods specifically designed for 16S count data, we considered a set of zero-imputation strategies available for other frameworks, and benchmarked them using in silico 16S count data reflecting different experimental designs. Additionally, we assessed the effect of combining zero-imputation and normalization, i.e. the only preprocessing step in current 16S workflow. Overall, we benchmarked 35 16S preprocessing pipelines assessing their ability to handle data sparsity, identify species presence/absence, recovery sample proportional abundance distributions, and improve typical downstream analyses such as computation of alpha and beta diversity indices and differential abundance analysis. CONCLUSIONS The results clearly show that 16S data analysis greatly benefits from a properly-performed zero-imputation step, despite the choice of the right zero-imputation method having a pivotal role. In addition, we identify a set of best-performing pipelines that could be a valuable indication for data analysts.
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Affiliation(s)
- Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padua, Italy
| | - Ilaria Patuzzi
- Department of Information Engineering, University of Padova, Padua, Italy
- Microbial Ecology Unit, Istituto Zooprofilattico Sperimentale Delle Venezie, Padua, Italy
- Research & Development Division, EuBiome S.R.L., Padua, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padua, Italy.
- CRIBI Biotechnology Centre, University of Padova, Padua, Italy.
- Department of Comparative Biomedicine and Food Science, University of Padova, Padua, Italy.
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Cappellato M, Baruzzo G, Patuzzi I, Di Camillo B. Modeling Microbial Community Networks: Methods and Tools. Curr Genomics 2021; 22:267-290. [PMID: 35273458 PMCID: PMC8822226 DOI: 10.2174/1389202921999200905133146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 11/22/2022] Open
Abstract
:
In the current research landscape, microbiota composition studies are of extreme interest,
since it has been widely shown that resident microorganisms affect and shape the ecological niche
they inhabit. This complex micro-world is characterized by different types of interactions. Understanding
these relationships provides a useful tool for decoding the causes and effects of communities’
organizations. Next-Generation Sequencing technologies allow to reconstruct the internal composition
of the whole microbial community present in a sample. Sequencing data can then be investigated
through statistical and computational method coming from network theory to infer the network of interactions
among microbial species.
:
Since there are several network inference approaches in the literature, in this paper we tried to shed
light on their main characteristics and challenges, providing a useful tool not only to those interested
in using the methods, but also to those who want to develop new ones. In addition, we focused on the
frameworks used to produce synthetic data, starting from the simulation of network structures up to
their integration with abundance models, with the aim of clarifying the key points of the entire generative
process.
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Affiliation(s)
- Marco Cappellato
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padova, Italy
| | | | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy
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Patuzzi I, Orsini M, Cibin V, Petrin S, Mastrorilli E, Tiengo A, Gobbo F, Catania S, Barco L, Ricci A, Losasso C. The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time. Microorganisms 2021; 9:221. [PMID: 33499060 PMCID: PMC7911313 DOI: 10.3390/microorganisms9020221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022] Open
Abstract
Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.
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Affiliation(s)
- Ilaria Patuzzi
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Massimiliano Orsini
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Veronica Cibin
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Sara Petrin
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Eleonora Mastrorilli
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Alessia Tiengo
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Federica Gobbo
- Avian Pathology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (F.G.); (S.C.)
| | - Salvatore Catania
- Avian Pathology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (F.G.); (S.C.)
| | - Lisa Barco
- Experimental Microbiology Department, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy;
| | - Antonia Ricci
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Carmen Losasso
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
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9
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Rota A, Corrò M, Patuzzi I, Milani C, Masia S, Mastrorilli E, Petrin S, Longo A, Del Carro A, Losasso C. Effect of sterilization on the canine vaginal microbiota: a pilot study. BMC Vet Res 2020; 16:455. [PMID: 33228646 PMCID: PMC7684734 DOI: 10.1186/s12917-020-02670-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Surgical sterilization is the most effective method of contraception for dogs. It also prevents pyometra and reduces the risk of mammary tumour development. However, this procedure also has negative effects, such as urinary incontinence. Steroid hormone deprivation following gonadectomy could also affect canine vaginal mucosa conditions and the microbial community colonizing the vaginal tract. This hypothesis was tested by comparing the vaginal cytology and microbial community of two groups of bitches, including 11 in anoestrus and 10 sterilized bitches (post-pubertal sterilization in the last 4 years). Bacteria were identified through metataxonomic analysis, amplifying the V3-V4 regions of 16S rRNA gene, and culturing methods. RESULTS Vaginal mucosa cytology was suggestive of dystrophic conditions in sterilized bitches, whereas a typical anoestrus pattern with parabasal and intermediate cells was appreciable in anoestrous animals. Metataxonomic analysis revealed large inter-individual variability. Salmonella, Mycoplasma and Staphylococcus were present in moderate quantities in almost all the samples in both groups. Mollicutes (class level) and Tenericutes (phylum level) were commonly present in moderate quantities in anoestrus samples, whereas these microbes were present at high levels in a single sample from the sterilized group. Based on culturing, a higher number of different species were isolated from the anoestrous bitches, and Mycoplasma canis was exclusively identified in an anoestrous bitch. Staphylococcus spp. was the most frequently isolated genus in both groups, followed by Streptococcus spp., and, among gram-negative bacteria, Escherichia spp. and Haemophilus spp. A comparison of the numbers of the most frequently isolated genera of bacteria from vaginal cultures of bitches revealed that Pasteurella and Proteus were the most frequently identified in sterilized animals based on metataxonomic analysis (p-value = 0.0497 and 0.0382, respectively), whereas Streptococcus was significantly and most frequently isolated from anoestrous bitches using culture methods (p value = 0.0436). CONCLUSIONS In this preliminary investigation, no global patterns of the vaginal bacteria community were noted that characterized the condition of the bitches; however, cytology suggested local modifications. Sterilization after puberty caused minimal alterations in the vaginal microbial community of bitches within 4 years after surgery.
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Affiliation(s)
- Ada Rota
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2-5, 10095, Grugliasco, Italy.
| | - Michela Corrò
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Ilaria Patuzzi
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Chiara Milani
- Department of Animal Medicine, Production and Health, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Stefania Masia
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Eleonora Mastrorilli
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Sara Petrin
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Alessandra Longo
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Angela Del Carro
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2-5, 10095, Grugliasco, Italy
| | - Carmen Losasso
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
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10
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Baruzzo G, Patuzzi I, Di Camillo B. SPARSim single cell: a count data simulator for scRNA-seq data. Bioinformatics 2020; 36:1468-1475. [PMID: 31598633 DOI: 10.1093/bioinformatics/btz752] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/24/2019] [Accepted: 10/04/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Single cell RNA-seq (scRNA-seq) count data show many differences compared with bulk RNA-seq count data, making the application of many RNA-seq pre-processing/analysis methods not straightforward or even inappropriate. For this reason, the development of new methods for handling scRNA-seq count data is currently one of the most active research fields in bioinformatics. To help the development of such new methods, the availability of simulated data could play a pivotal role. However, only few scRNA-seq count data simulators are available, often showing poor or not demonstrated similarity with real data. RESULTS In this article we present SPARSim, a scRNA-seq count data simulator based on a Gamma-Multivariate Hypergeometric model. We demonstrate that SPARSim allows to generate count data that resemble real data in terms of count intensity, variability and sparsity, performing comparably or better than one of the most used scRNA-seq simulator, Splat. In particular, SPARSim simulated count matrices well resemble the distribution of zeros across different expression intensities observed in real count data. AVAILABILITY AND IMPLEMENTATION SPARSim R package is freely available at http://sysbiobig.dei.unipd.it/? q=SPARSim and at https://gitlab.com/sysbiobig/sparsim. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Ilaria Patuzzi
- Department of Information Engineering, University of Padova, Padova, Italy.,Microbial Ecology Unit, Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy.,CRIBI Innovative Biotechnology Center, University of Padova, Padova, Italy
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11
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Petrin S, Patuzzi I, Di Cesare A, Tiengo A, Sette G, Biancotto G, Corno G, Drigo M, Losasso C, Cibin V. Evaluation and quantification of antimicrobial residues and antimicrobial resistance genes in two Italian swine farms. Environ Pollut 2019; 255:113183. [PMID: 31541814 DOI: 10.1016/j.envpol.2019.113183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/27/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances in bacteria. The occurrence of ARGs in Italian swine farming - which has specific characteristics - was investigated in order to explore resistance spread dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.
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Affiliation(s)
- Sara Petrin
- OU Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Ilaria Patuzzi
- OU Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | | | - Alessia Tiengo
- Food Pathogens and Antimicrobial Resistance Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Giovanni Sette
- Chemistry Department, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Giancarlo Biancotto
- Chemistry Department, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Gianluca Corno
- CNR-IRSA, Corso Tonolli, 50, 28922, Pallanza, Verbania, Italy
| | - Michele Drigo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Carmen Losasso
- OU Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy.
| | - Veronica Cibin
- Food Pathogens and Antimicrobial Resistance Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
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12
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Abstract
BACKGROUND In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable popularity of this technique, an exiguous number of specific tools are currently available for proper 16S rDNA-seq count data preprocessing and simulation. Indeed, the great majority of tools have been developed adapting methodologies previously used for bulk RNA-seq data, with poor assessment of their applicability in the metagenomics field. For such tools and the few ones specifically developed for 16S rDNA-seq data, performance assessment is challenging, mainly due to the complex nature of the data and the lack of realistic simulation models. In fact, to the best of our knowledge, no software thought for data simulation are available to directly obtain synthetic 16S rDNA-seq count tables that properly model heavy sparsity and compositionality typical of these data. RESULTS In this paper we present metaSPARSim, a sparse count matrix simulator intended for usage in development of 16S rDNA-seq metagenomic data processing pipelines. metaSPARSim implements a new generative process that models the sequencing process with a Multivariate Hypergeometric distribution in order to realistically simulate 16S rDNA-seq count table, resembling real experimental data compositionality and sparsity. It provides ready-to-use count matrices and comes with the possibility to reproduce different pre-coded scenarios and to estimate simulation parameters from real experimental data. The tool is made available at http://sysbiobig.dei.unipd.it/?q=Software#metaSPARSimand https://gitlab.com/sysbiobig/metasparsim. CONCLUSION metaSPARSim is able to generate count matrices resembling real 16S rDNA-seq data. The availability of count data simulators is extremely valuable both for methods developers, for which a ground truth for tools validation is needed, and for users who want to assess state of the art analysis tools for choosing the most accurate one. Thus, we believe that metaSPARSim is a valuable tool for researchers involved in developing, testing and using robust and reliable data analysis methods in the context of 16S rRNA gene sequencing.
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Affiliation(s)
- Ilaria Patuzzi
- Department of Information Engineering, University of Padova, via Giovanni Gradenigo, 6, Padova, 35131 Italy
- Microbial Ecology Unit, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro (PD), 35020 Italy
| | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, via Giovanni Gradenigo, 6, Padova, 35131 Italy
| | - Carmen Losasso
- Microbial Ecology Unit, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro (PD), 35020 Italy
| | - Antonia Ricci
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro (PD), 35020 Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, via Giovanni Gradenigo, 6, Padova, 35131 Italy
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13
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Losasso C, Di Cesare A, Mastrorilli E, Patuzzi I, Cibin V, Eckert EM, Fontaneto D, Vanzo A, Ricci A, Corno G. Assessing antimicrobial resistance gene load in vegan, vegetarian and omnivore human gut microbiota. Int J Antimicrob Agents 2018; 52:702-705. [PMID: 30081136 DOI: 10.1016/j.ijantimicag.2018.07.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/16/2018] [Accepted: 07/29/2018] [Indexed: 11/26/2022]
Abstract
Massive antimicrobial use in animal farming is considered as the greatest contributor to the presence of antimicrobial-resistant bacteria (ARB) in food of animal origin. Nevertheless, sewage from treated animals may impact on vegetables grown on fertilised fields, but it is largely unknown whether and to what extent ARB are transferred to vegetables and the human gut. It could be hypothesised that food of animal and vegetal origin have a different role in ARB transfer to the human gut and that different diets could be characterised by different antimicrobial resistance gene (ARG) loads. This study included three groups comprising vegans (n = 26), vegetarians (n = 32) and omnivores (n = 43). Metadata regarding food consumption and anthropometric parameters were collected. Gut microbial communities were investigated by 16S rDNA analysis. Four ARGs (sul2, tetA, blaTEM and strB) were quantified by qPCR. The results showed a lower total load of investigated ARGs in vegan diet (pairwise comparison adjusted results: omnivorous-vegan, P = 0.0119; omnivorous-vegetarian, P = 0.7416; and vegan-vegetarian, P = 0.0119). No significant differences in abundance of each gene separately were found between the three groups. Neither the amount of animal protein nor the occurrence of ARGs was significant in explaining differences in the gut microbial community of individuals, and a large proportion of the differences between community composition (PERMANOVA, 46.87%) was not explained by the analysed variables. The results support the role of omnivorous and vegetarian diets in accumulating ARGs, suggesting a possible role for animal-derived food consumption.
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Affiliation(s)
- Carmen Losasso
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università 10, Legnaro, Italy.
| | - Andrea Di Cesare
- DISTAV, Università degli studi di Genova, Corso Europa 26, Genoa, Italy
| | - Eleonora Mastrorilli
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università 10, Legnaro, Italy
| | - Ilaria Patuzzi
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università 10, Legnaro, Italy; DEI, Università di Padova, Via Gradenigo 6/b, Padua, Italy
| | - Veronica Cibin
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università 10, Legnaro, Italy
| | - Ester M Eckert
- Microbial Ecology Group, CNR-ISE, Corso Tonolli 50, Pallanza, Verbania, Italy
| | - Diego Fontaneto
- Microbial Ecology Group, CNR-ISE, Corso Tonolli 50, Pallanza, Verbania, Italy
| | - Angiola Vanzo
- SIAN, ULSS8 Berica, via IV Novembre 46, Vicenza, Italy
| | - Antonia Ricci
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università 10, Legnaro, Italy
| | - Gianluca Corno
- Microbial Ecology Group, CNR-ISE, Corso Tonolli 50, Pallanza, Verbania, Italy
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14
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Losasso C, Eckert EM, Mastrorilli E, Villiger J, Mancin M, Patuzzi I, Di Cesare A, Cibin V, Barrucci F, Pernthaler J, Corno G, Ricci A. Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study. Front Microbiol 2018; 9:317. [PMID: 29556222 PMCID: PMC5844980 DOI: 10.3389/fmicb.2018.00317] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/09/2018] [Indexed: 12/20/2022] Open
Abstract
Diet and lifestyle have a strong influence on gut microbiota, which in turn has important implications on a variety of health-related aspects. Despite great advances in the field, it remains unclear to which extent the composition of the gut microbiota is modulated by the intake of animal derived products, compared to a vegetable based diet. Here the specific impact of vegan, vegetarian, and omnivore feeding type on the composition of gut microbiota of 101 adults was investigated among groups homogeneous for variables known to have a role in modulating gut microbial composition such as age, anthropometric variables, ethnicity, and geographic area. The results displayed a picture where the three different dietetic profiles could be well distinguished on the basis of participant's dietetic regimen. Regarding the gut microbiota; vegetarians had a significantly greater richness compared to omnivorous. Moreover, counts of Bacteroidetes related operational taxonomic units (OTUs) were greater in vegans and vegetarians compared to omnivores. Interestingly considering the whole bacterial community composition the three cohorts were unexpectedly similar, which is probably due to their common intake in terms of nutrients rather than food, e.g., high fat content and reduced protein and carbohydrate intake. This finding suggests that fundamental nutritional choices such as vegan, vegetarian, or omnivore do influence the microbiota but do not allow to infer conclusions on gut microbial composition, and suggested the possibility for a preferential impact of other variables, probably related to the general life style on shaping human gut microbial community in spite of dietary influence. Consequently, research were individuals are categorized on the basis of their claimed feeding types is of limited use for scientific studies, since it appears to be oversimplified.
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Affiliation(s)
- Carmen Losasso
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Ester M. Eckert
- Microbial Ecology Group, Institute of Ecosystem Study, National Research Council, Verbania, Italy
| | - Eleonora Mastrorilli
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Jorg Villiger
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Marzia Mancin
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Ilaria Patuzzi
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
- Department of Information Engineering, University of Padova, Padova, Itay
| | - Andrea Di Cesare
- Microbial Ecology Group, Institute of Ecosystem Study, National Research Council, Verbania, Italy
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita, University of Genova, Genova, Italy
| | - Veronica Cibin
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Federica Barrucci
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gianluca Corno
- Microbial Ecology Group, Institute of Ecosystem Study, National Research Council, Verbania, Italy
| | - Antonia Ricci
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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15
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Belluco S, Patuzzi I, Ricci A. Bovine meat versus pork in Toxoplasma gondii transmission in Italy: A quantitative risk assessment model. Int J Food Microbiol 2018; 269:1-11. [DOI: 10.1016/j.ijfoodmicro.2017.12.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 11/20/2017] [Accepted: 12/29/2017] [Indexed: 10/18/2022]
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16
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Pezzuto A, Belluco S, Losasso C, Patuzzi I, Bordin P, Piovesana A, Comin D, Mioni R, Ricci A. Effectiveness of Washing Procedures in Reducing Salmonella enterica and Listeria monocytogenes on a Raw Leafy Green Vegetable ( Eruca vesicaria). Front Microbiol 2016; 7:1663. [PMID: 27812356 PMCID: PMC5071777 DOI: 10.3389/fmicb.2016.01663] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/05/2016] [Indexed: 01/24/2023] Open
Abstract
Vegetables are an important source of nutrients, but they can host a large microbial population, particularly bacteria. Foodborne pathogens can contaminate raw vegetables at any stage of their production process with a potential for human infection. Appropriate washing can mitigate the risk of foodborne illness consequent to vegetable consumption by reducing pathogen levels, but few data are available to assess the efficacy of different practices. In the present work, six different washing methods, in the presence or absence of sanitisers (peracetic acid and percitric acid, sodium bicarbonate, sodium hypochlorite) and vinegar, were tested for their effectiveness in reducing Salmonella and Listeria counts after artificial contamination of raw rocket (Eruca vesicaria). Results showed that washing with sodium hypochlorite (200 mg/L) was the only method able to produce a significant 2 Log reduction of Salmonella counts, but only in the case of high initial contamination (7 Log CFU/g), suggesting potential harmful effects for consumers could occur. In the case of Listeria monocytogenes, all the examined washing methods were effective, with 200 mg/L sodium hypochlorite solution and a solution of peracetic and percitric acids displaying the best performances (2 and 1.5 Log reductions, respectively). This highlights the importance of targeting consumers on fit for purpose and safe washing practices to circumvent vegetable contamination by foodborne pathogens.
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Affiliation(s)
- Alessandra Pezzuto
- Optimization and Control of Food Production Laboratory, Istituto Zooprofilattico Sperimentale delle VenezieSan Donà di Piave, Italy
| | - Simone Belluco
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
- Department of Animal Medicine, Production and Health, Università di PadovaPadova, Italy
| | - Carmen Losasso
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
| | - Ilaria Patuzzi
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
- Department of Information Engineering, Università di PadovaPadova, Italy
| | - Paola Bordin
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
| | - Alessia Piovesana
- Optimization and Control of Food Production Laboratory, Istituto Zooprofilattico Sperimentale delle VenezieSan Donà di Piave, Italy
| | - Damiano Comin
- Optimization and Control of Food Production Laboratory, Istituto Zooprofilattico Sperimentale delle VenezieSan Donà di Piave, Italy
| | - Renzo Mioni
- Optimization and Control of Food Production Laboratory, Istituto Zooprofilattico Sperimentale delle VenezieSan Donà di Piave, Italy
| | - Antonia Ricci
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
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Gallocchio F, Cibin V, Biancotto G, Roccato A, Muzzolon O, Carmen L, Simone B, Manodori L, Fabrizi A, Patuzzi I, Ricci A. Testing nano-silver food packaging to evaluate silver migration and food spoilage bacteria on chicken meat. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2016; 33:1063-71. [PMID: 27147130 DOI: 10.1080/19440049.2016.1179794] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Migration of nanomaterials from food containers into food is a matter of concern because of the potential risk for exposed consumers. The aims of this study were to evaluate silver migration from a commercially available food packaging containing silver nanoparticles into a real food matrix (chicken meat) under plausible domestic storage conditions and to test the contribution of such packaging to limit food spoilage bacteria proliferation. Chemical analysis revealed the absence of silver in chicken meatballs under the experimental conditions in compliance with current European Union legislation, which establishes a maximum level of 0.010 mg kg(-1) for the migration of non-authorised substances through a functional barrier (Commission Regulation (EU) No. 10/2011). On the other hand, microbiological tests (total microbial count, Pseudomonas spp. and Enterobacteriaceae) showed no relevant difference in the tested bacteria levels between meatballs stored in silver-nanoparticle plastic bags or control bags. This study shows the importance of testing food packaging not only to verify potential silver migration as an indicator of potential nanoparticle migration, but also to evaluate the benefits in terms of food preservation so as to avoid unjustified usage of silver nanoparticles and possible negative impacts on the environment.
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Affiliation(s)
- Federica Gallocchio
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy
| | - Veronica Cibin
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy
| | - Giancarlo Biancotto
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy
| | - Anna Roccato
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy
| | - Orietta Muzzolon
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy
| | - Losasso Carmen
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy
| | - Belluco Simone
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy.,b Department of Animal Medicine Production and Health , Università di Padova , Legnaro , Italy
| | - Laura Manodori
- c European Centre for the Sustainable Impact of Nanotechnology, Veneto Nanotech S.C.pA , Rovigo , Italy
| | - Alberto Fabrizi
- d Department of Management and Engineering , Università di Padova , Vicenza , Italy
| | - Ilaria Patuzzi
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy
| | - Antonia Ricci
- a Department of Food Safety , Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe) , Legnaro , Italy
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18
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Belluco S, Losasso C, Patuzzi I, Rigo L, Conficoni D, Gallocchio F, Cibin V, Catellani P, Segato S, Ricci A. Silver As Antibacterial toward Listeria monocytogenes. Front Microbiol 2016; 7:307. [PMID: 27014230 PMCID: PMC4779933 DOI: 10.3389/fmicb.2016.00307] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/24/2016] [Indexed: 11/23/2022] Open
Abstract
Listeria monocytogenes is a serious foodborne pathogen that can contaminate food during processing and can grow during food shelf-life. New types of safe and effective food contact materials embedding antimicrobial agents, like silver, can play an important role in the food industry. The present work aimed at evaluating the in vitro growth kinetics of different strains of L. monocytogenes in the presence of silver, both in its ionic and nano form. The antimicrobial effect was determined by assaying the number of culturable bacterial cells, which formed colonies after incubation in the presence of silver nanoparticles (AgNPs) or silver nitrate (AgNO3). Ionic release experiments were performed in parallel. A different reduction of bacterial viability between silver ionic and nano forms was observed, with a time delayed effect exerted by AgNPs. An association between antimicrobial activity and ions concentration was shown by both silver chemical forms, suggesting the major role of ions in the antimicrobial mode of action.
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Affiliation(s)
- Simone Belluco
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
- Department of Animal Medicine, Production and Health, Università di PadovaPadova, Italy
| | - Carmen Losasso
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
| | - Ilaria Patuzzi
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
- Department of Information Engineering, Università di PadovaPadova, Italy
| | - Laura Rigo
- Department of Animal Medicine, Production and Health, Università di PadovaPadova, Italy
| | - Daniele Conficoni
- Department of Animal Medicine, Production and Health, Università di PadovaPadova, Italy
| | - Federica Gallocchio
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
| | - Veronica Cibin
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
| | - Paolo Catellani
- Department of Animal Medicine, Production and Health, Università di PadovaPadova, Italy
| | - Severino Segato
- Department of Animal Medicine, Production and Health, Università di PadovaPadova, Italy
| | - Antonia Ricci
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle VenezieLegnaro, Italy
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19
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Losasso C, Bille L, Patuzzi I, Lorenzetto M, Binato G, Dalla Pozza M, Ferrè N, Ricci A. Possible influence of natural events on heavy metals exposure from shellfish consumption: a case study in the north-East of Italy. Front Public Health 2015; 3:21. [PMID: 25699249 PMCID: PMC4316607 DOI: 10.3389/fpubh.2015.00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/19/2015] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was the estimation of the exposure over time to heavy metals (cadmium, mercury, and lead) due to shellfish consumption in the Veneto Region, Italy. Shellfish consumption was investigated by a food frequency consumption survey. Altogether, 1949 households, stratified into the five most populated areas of the Veneto Region, were involved in the study. Exposure estimation to heavy metals was carried out taking into account the level of metal measured in samples of Manila clams (Ruditapes philippinarum) and grooved carpet shell (Ruditapes decussatus), collected in the frame of the monitoring activities of mollusk production areas of Veneto Region, between January 2007 and December 2012. A general high contribution of the considered shellfish to the Tolerable Weekly Intake was noticed in the case of cadmium, especially in 2011, when a considerable increase in cadmium intake was estimated. This was probably due to a heavy rainfall event that triggered catastrophic flooding with high impact on shellfish capture areas in November 2010. The results strongly emphasize the importance of dealing with food safety in a holistic way, taking into account the potential impact of extraordinary natural events on food chain contamination, in order to identify food hazards at an early stage, before developing into a real risk for consumers.
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Affiliation(s)
- Carmen Losasso
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Laura Bille
- Laboratory of Epidemiology of Water Environment, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Ilaria Patuzzi
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Monica Lorenzetto
- GIS Unit, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Giovanni Binato
- Laboratory of Chemistry, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Manuela Dalla Pozza
- Laboratory of Epidemiology of Water Environment, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Nicola Ferrè
- GIS Unit, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Antonia Ricci
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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