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Ceccarani C, Gaspari V, Morselli S, Djusse ME, Venturoli S, Camboni T, Severgnini M, Foschi C, Consolandi C, Marangoni A. Chlamydia trachomatis and Neisseria gonorrhoeae rectal infections: Interplay between rectal microbiome, HPV infection and Torquetenovirus. PLoS One 2024; 19:e0301873. [PMID: 38578759 PMCID: PMC10997096 DOI: 10.1371/journal.pone.0301873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/22/2024] [Indexed: 04/07/2024] Open
Abstract
Men having sex with men (MSM) represent a key population, in which sexually transmitted rectal infections (STIs) caused by Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and high-risk HPV (HR-HPV) are very common and linked to significant morbidity. Investigating the anorectal microbiome associated with rectal STIs holds potential for deeper insights into the pathogenesis of these infections and the development of innovative control strategies. In this study, we explored the interplay at the rectal site between C. trachomatis, N. gonorrhoeae, HR-HPV infection, and the anorectal microbiome in a cohort of 92 MSM (47 infected by CT and/or NG vs 45 controls). Moreover, we assessed the presence of Torquetenovirus (TTV), a non-pathogenic endogenous virus, considered as a possible predictor of immune system activation. We found a high prevalence of HR-HPV rectal infections (61%), especially in subjects with a concurrent CT/NG rectal infection (70.2%) and in people living with HIV (84%). In addition, we observed that TTV was more prevalent in subjects with CT/NG rectal infections than in non-infected ones (70.2% vs 46.7%, respectively). The anorectal microbiome of patients infected by CT and/or NG exhibited a reduction in Escherichia, while the presence of TTV was significantly associated with higher levels of Bacteroides. We observed a positive correlation of HR-HPV types with Escherichia and Corynebacterium, and a negative correlation with the Firmicutes phylum, and with Prevotella, Oscillospira, Sutterella. Our findings shed light on some of the dynamics occurring within the rectal environment involving chlamydial/gonococcal infections, HPV, TTV, and the anorectal microbiome. These data could open new perspectives for the control and prevention of STIs in MSM.
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Affiliation(s)
- Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
- National Biodiversity Future Center S.c.a.r.l., Palermo, Italy
| | - Valeria Gaspari
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Sara Morselli
- Department of Medical and Surgical Sciences, Section of Microbiology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
| | - Marielle Ezekielle Djusse
- Department of Medical and Surgical Sciences, Section of Microbiology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
| | - Simona Venturoli
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
- National Biodiversity Future Center S.c.a.r.l., Palermo, Italy
| | - Claudio Foschi
- Department of Medical and Surgical Sciences, Section of Microbiology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
- National Biodiversity Future Center S.c.a.r.l., Palermo, Italy
| | - Antonella Marangoni
- Department of Medical and Surgical Sciences, Section of Microbiology, Alma Mater Studiorum—University of Bologna, Bologna, Italy
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Borghi E, Xynomilakis O, Ottaviano E, Ceccarani C, Viganò I, Tognini P, Vignoli A. Gut microbiota profile in CDKL5 deficiency disorder patients. Sci Rep 2024; 14:7376. [PMID: 38548767 PMCID: PMC10978852 DOI: 10.1038/s41598-024-56989-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
CDKL5 deficiency disorder (CDD) is a neurodevelopmental condition characterized by global developmental delay, early-onset seizures, intellectual disability, visual and motor impairments. Unlike Rett Syndrome (RTT), CDD lacks a clear regression period. Patients with CDD frequently encounter gastrointestinal (GI) disturbances and exhibit signs of subclinical immune dysregulation. However, the underlying causes of these conditions remain elusive. Emerging studies indicate a potential connection between neurological disorders and gut microbiota, an area completely unexplored in CDD. We conducted a pioneering study, analyzing fecal microbiota composition in individuals with CDD (n = 17) and their healthy relatives (n = 17). Notably, differences in intestinal bacterial diversity and composition were identified in CDD patients. In particular, at genus level, CDD microbial communities were characterized by an increase in the relative abundance of Clostridium_AQ, Eggerthella, Streptococcus, and Erysipelatoclostridium, and by a decrease in Eubacterium, Dorea, Odoribacter, Intestinomonas, and Gemmiger, pointing toward a dysbiotic profile. We further investigated microbiota changes based on the severity of GI issues, seizure frequency, sleep disorders, food intake type, impairment in neuro-behavioral features and ambulation capacity. Enrichment in Lachnoclostridium and Enterobacteriaceae was observed in the microbiota of patients with more severe GI symptoms, while Clostridiaceae, Peptostreptococcaceae, Coriobacteriaceae, Erysipelotrichaceae, Christensenellaceae, and Ruminococcaceae were enriched in patients experiencing daily epileptic seizures. Our findings suggest a potential connection between CDD, microbiota and symptom severity. This study marks the first exploration of the gut-microbiota-brain axis in subjects with CDD. It adds to the growing body of research emphasizing the role of the gut microbiota in neurodevelopmental disorders and opens doors to potential interventions that target intestinal microbes with the aim of improving the lives of patients with CDD.
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Affiliation(s)
- Elisa Borghi
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Ornella Xynomilakis
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Dipartimento di Scienze Biomediche e Cliniche, Università Degli Studi di Milano, 20157, Milan, Italy
| | | | - Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Ilaria Viganò
- Epilepsy Center-Child Neuropsychiatric Unit, ASST Santi Paolo e Carlo, Milan, Italy
| | - Paola Tognini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.
- Health Science Interdisciplinary Center, Sant'Anna School of Advanced Studies, Pisa, Italy.
| | - Aglaia Vignoli
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
- Childhood and Adolescence Neurology and Psychiatry Unit, ASST GOM Niguarda, Milan, Italy
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Alvisi S, Ceccarani C, Foschi C, Baldassarre M, Lami A, Severgnini M, Camboni T, Consolandi C, Seracchioli R, Meriggiola MC. Effect of ospemifene on vaginal microbiome in postmenopausal women with vulvovaginal atrophy. Menopause 2023; 30:361-369. [PMID: 36727789 DOI: 10.1097/gme.0000000000002150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVES This study aimed (i) to compare the vaginal microbiome profiles of women suffering from vulvovaginal atrophy with that of healthy postmenopausal women and to (ii) assess the effect of ospemifene and systemic hormone treatment on the composition of the vaginal microbiome. METHODS Sixty-seven postmenopausal women attending the Gynecology Clinic of Azienda Ospedaliero-Universitaria of Bologna (Italy) were enrolled. Of them, 39 received a diagnosis of atrophy and 28 were considered healthy controls. In the group of atrophic women, 20 were prescribed ospemifene and 19 received hormone treatment. The vaginal health index was calculated, and a vaginal swab was collected for the assessment of vaginal maturation index and the analysis of vaginal microbiome through 16S rRNA gene sequencing. Clinical/microbiological analyses were repeated after 3 months of treatment. RESULTS The vaginal microbiome of atrophic women was characterized by a significant reduction of Lactobacillus ( P = 0.002) and an increase of Streptococcus ( P = 0.008) and Sneathia ( P = 0.02). A positive correlation between vaginal health index/vaginal maturation index and Lactobacillus abundance was found ( P = 0.002 and P = 0.035, respectively). Both therapeutic approaches effectively improved vaginal indices. Systemic hormone treatment induced changes in minority bacterial groups of the vaginal microbiome, whereas ospemifene was able to eliminate specific bacterial taxa, such as Staphylococcus ( P = 0.04) and Clostridium ( P = 0.01). Both treatments induced a trend in the increase of bifidobacteria. CONCLUSIONS The vaginal microbiome of atrophic women differs significantly from that of healthy postmenopausal women. Ospemifene may lead to a condition of vaginal health, likely characterized by the reduction of "potentially harmful" bacteria.
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Affiliation(s)
| | - Camilla Ceccarani
- Institute of Biomedical Technologies-National Research Council, Segrate, Milan, Italy
| | | | | | | | - Marco Severgnini
- Institute of Biomedical Technologies-National Research Council, Segrate, Milan, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies-National Research Council, Segrate, Milan, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies-National Research Council, Segrate, Milan, Italy
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Morselli S, Foschi C, Laghi L, Zagonari S, Patuelli G, Camboni T, Ceccarani C, Consolandi C, Djusse ME, Pedna MF, Marangoni A, Severgnini M, Sambri V. Torquetenovirus in pregnancy: Correlation with vaginal microbiome, metabolome and pro-inflammatory cytokines. Front Microbiol 2022; 13:998849. [PMID: 36160242 PMCID: PMC9501707 DOI: 10.3389/fmicb.2022.998849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/20/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Torquetenovirus (TTV) is a negative sense, single-stranded DNA virus present in many body fluids of apparently healthy individuals. At present, it is considered a non-pathogenic endogenous virus. TTV can be detected in the vagina of pregnant women, its abundance being modulated with the extent of immune system activation. Until now, there is only scarce information regarding the association between TTV and the composition of the vaginal environment. Therefore, this study aimed to assess the presence of TTV in the vaginal ecosystem of a cohort of white women with a normal pregnancy (n = 60) at different gestational stages (first, second and third trimester) and in 9 subjects suffering a first trimester miscarriage. For each woman, we determined (i) the presence and titer of TTV, (ii) the vaginal bacterial composition by means of Nugent score and 16S rRNA gene sequencing, (iii) the vaginal metabolic profiles through 1H-NMR spectroscopy, and (iv) the vaginal concentration of two pro-inflammatory cytokines (IL-6 and IL-8). More than one third of women were found negative for TTV at all gestational stages. Although not statistically significant, the positivity for TTV dropped from 53.3% in the first to 36.6% in the third trimester. TTV loads varied greatly among vaginal samples, ranging between 2 × 101 and 2 × 105 copies/reaction. No difference in TTV prevalence and loads was observed between women with normal pregnancies and miscarriages. The presence of TTV was more common in women with a higher vaginal leucocyte count (p = 0.02). The levels of IL-6 (p = 0.02), IL-8 (p = 0.03), propionate (p = 0.001) and cadaverine (p = 0.006) were significantly higher in TTV-positive samples. TTV titer was positively correlated with the concentrations of 4-hydroxyphenyllactate (p < 0.0001), isoleucine (p = 0.01) and phenylalanine (p = 0.04). TTV-positive samples were characterized by a higher relative abundance of Sneathia (p = 0.04) and Shuttleworthia (p = 0.0009). In addition, a trend toward a decrease of Lactobacillus crispatus and Lactobacillus jensenii, and an increase of Lactobacillus iners was observed for TTV-positive samples. In conclusion, we found that TTV is quite common in women with normal pregnancy outcomes, representing a possible predictor of local immune status.
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Affiliation(s)
- Sara Morselli
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Claudio Foschi
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Luca Laghi
- Department of Agricultural and Food Sciences (DISTAL), Centre of Foodomics, University of Bologna, Cesena, Italy
- Interdepartmental Centre for Agri-Food Industrial Research (CIRI Agrifood), University of Bologna, Cesena, Italy
| | | | | | - Tania Camboni
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Marielle Ezekielle Djusse
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Federica Pedna
- Great Romagna Hub Laboratory, Unit of Microbiology, Pievesestina di Cesena, Italy
| | - Antonella Marangoni
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
- *Correspondence: Antonella Marangoni
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Vittorio Sambri
- Microbiology Unit, Department of Specialized, Experimental and Diagnostic Medicine (DIMES), University of Bologna, Bologna, Italy
- Great Romagna Hub Laboratory, Unit of Microbiology, Pievesestina di Cesena, Italy
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Severgnini M, Morselli S, Camboni T, Ceccarani C, Salvo M, Zagonari S, Patuelli G, Pedna MF, Sambri V, Foschi C, Consolandi C, Marangoni A. Gardnerella vaginalis clades in pregnancy: New insights into the interactions with the vaginal microbiome. PLoS One 2022; 17:e0269590. [PMID: 35700195 PMCID: PMC9197028 DOI: 10.1371/journal.pone.0269590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/25/2022] [Indexed: 12/03/2022] Open
Abstract
Gardnerella vaginalis (GV) is an anaerobic bacterial species involved in the pathogenesis of bacterial vaginosis (BV), a condition of vaginal dysbiosis associated with adverse pregnancy outcomes. GV strains are categorized into four clades, characterized by a different ability to produce virulence factors, such as sialidase. We investigated the distribution of GV clades and sialidase genes in the vaginal ecosystem of a cohort of pregnant women, assessing the correlations between GV clades and the whole vaginal microbiome. A total of 61 Caucasian pregnant women were enrolled. Their vaginal swabs, collected both at the first and third trimester of pregnancy, were used for (i) evaluation of the vaginal status by Nugent score, (ii) vaginal microbiome profiling by 16S rRNA sequencing, (iii) detection and quantification of GV clades and sialidase A gene by qPCR assays. DNA of at least one GV clade was detected in most vaginal swabs, with clade 4 being the most common one. GV clade 2, together with the presence of multiple clades (>2 simultaneously), were significantly associated with a BV condition. Significantly higher GV loads and sialidase gene levels were found in BV cases, compared to the healthy status. Clade 2 was related to the major shifts in the vaginal microbial composition, with a decrease in Lactobacillus and an increase in several BV-related taxa. As the number of GV clades detected simultaneously increased, a group of BV-associated bacteria tended to increase as well, while Bifidobacterium tended to decrease. A negative correlation between sialidase gene levels and Lactobacillus, and a positive correlation with Gardnerella, Atopobium, Prevotella, Megasphaera, and Sneathia were observed. Our results added knowledge about the interactions of GV clades with the inhabitants of the vaginal microbiome, possibly helping to predict the severity of BV and opening new perspectives for the prevention of pregnancy-related complications.
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Affiliation(s)
- Marco Severgnini
- Institute of Biomedical Technologies – National Research Council, Segrate, Milan, Italy
| | - Sara Morselli
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies – National Research Council, Segrate, Milan, Italy
| | - Camilla Ceccarani
- Institute of Biomedical Technologies – National Research Council, Segrate, Milan, Italy
| | - Melissa Salvo
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | | | | | - Maria Federica Pedna
- Unit of Microbiology, Greater Romagna Hub Laboratory, Pievesestina di Cesena, Italy
| | - Vittorio Sambri
- Microbiology, DIMES, University of Bologna, Bologna, Italy
- Unit of Microbiology, Greater Romagna Hub Laboratory, Pievesestina di Cesena, Italy
| | - Claudio Foschi
- Microbiology, DIMES, University of Bologna, Bologna, Italy
- * E-mail:
| | - Clarissa Consolandi
- Institute of Biomedical Technologies – National Research Council, Segrate, Milan, Italy
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Severgnini M, Morselli S, Camboni T, Ceccarani C, Laghi L, Zagonari S, Patuelli G, Pedna MF, Sambri V, Foschi C, Consolandi C, Marangoni A. A Deep Look at the Vaginal Environment During Pregnancy and Puerperium. Front Cell Infect Microbiol 2022; 12:838405. [PMID: 35656029 PMCID: PMC9152327 DOI: 10.3389/fcimb.2022.838405] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
A deep comprehension of the vaginal ecosystem may hold promise for unraveling the pathophysiology of pregnancy and may provide novel biomarkers to identify subjects at risk of maternal-fetal complications. In this prospective study, we assessed the characteristics of the vaginal environment in a cohort of pregnant women throughout their different gestational ages and puerperium. Both the vaginal bacterial composition and the vaginal metabolic profiles were analyzed. A total of 63 Caucasian women with a successful pregnancy and 9 subjects who had a first trimester miscarriage were enrolled. For the study, obstetric examinations were scheduled along the three trimester phases (9-13, 20-24, 32-34 gestation weeks) and puerperium (40-55 days after delivery). Two vaginal swabs were collected at each time point, to assess the vaginal microbiome profiling (by Nugent score and 16S rRNA gene sequencing) and the vaginal metabolic composition (1H-NMR spectroscopy). During pregnancy, the vaginal microbiome underwent marked changes, with a significant decrease in overall diversity, and increased stability. Over time, we found a significant increase of Lactobacillus and a decrease of several genera related to bacterial vaginosis (BV), such as Prevotella, Atopobium and Sneathia. It is worth noting that the levels of Bifidobacterium spp. tended to decrease at the end of pregnancy. At the puerperium, a significantly lower content of Lactobacillus and higher levels of Gardnerella, Prevotella, Atopobium, and Streptococcus were observed. Women receiving an intrapartum antibiotic prophylaxis for Group B Streptococcus (GBS) were characterized by a vaginal abundance of Prevotella compared to untreated women. Analysis of bacterial relative abundances highlighted an increased abundance of Fusobacterium in women suffering a first trimester abortion, at all taxonomic levels. Lactobacillus abundance was strongly correlated with higher levels of lactate, sarcosine, and many amino acids (i.e., isoleucine, leucine, phenylalanine, valine, threonine, tryptophan). Conversely, BV-associated genera, such as Gardnerella, Atopobium, and Sneathia, were related to amines (e.g., putrescine, methylamine), formate, acetate, alcohols, and short-chain fatty-acids (i.e., butyrate, propionate).
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Affiliation(s)
- Marco Severgnini
- Institute of Biomedical Technologies – National Research Council, Milan, Italy
| | - Sara Morselli
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies – National Research Council, Milan, Italy
| | - Camilla Ceccarani
- Institute of Biomedical Technologies – National Research Council, Milan, Italy
| | - Luca Laghi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | | | | | | | - Vittorio Sambri
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Unit of Microbiology, Greater Romagna Hub Laboratory, Cesena, Italy
| | - Claudio Foschi
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies – National Research Council, Milan, Italy
| | - Antonella Marangoni
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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Montanari C, Ceccarani C, Corsello A, Zuvadelli J, Ottaviano E, Dei Cas M, Banderali G, Zuccotti G, Borghi E, Verduci E. Glycomacropeptide Safety and Its Effect on Gut Microbiota in Patients with Phenylketonuria: A Pilot Study. Nutrients 2022; 14:nu14091883. [PMID: 35565850 PMCID: PMC9104775 DOI: 10.3390/nu14091883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/23/2022] [Accepted: 04/29/2022] [Indexed: 12/07/2022] Open
Abstract
Glycomacropeptide (GMP) represents a good alternative protein source in Phenylketonuria (PKU). In a mouse model, it has been suggested to exert a prebiotic role on beneficial gut bacteria. In this study, we performed the 16S rRNA sequencing to evaluate the effect of 6 months of GMP supplementation on the gut microbiota of nine PKU patients, comparing their bacterial composition and clinical parameters before and after the intervention. GMP seems to be safe from both the microbiological and the clinical point of view. Indeed, we did not observe dramatic changes in the gut microbiota but a specific prebiotic effect on the butyrate-producer Agathobacter spp. and, to a lesser extent, of Subdoligranulum. Clinically, GMP intake did not show a significant impact on both metabolic control, as phenylalanine values were kept below the age target and nutritional parameters. On the other hand, an amelioration of calcium phosphate homeostasis was observed, with an increase in plasmatic vitamin D and a decrease in alkaline phosphatase. Our results suggest GMP as a safe alternative in the PKU diet and its possible prebiotic role on specific taxa without causing dramatic changes in the commensal microbiota.
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Affiliation(s)
- Chiara Montanari
- Department of Pediatrics, Vittore Buzzi Children’s Hospital, University of Milan, 20154 Milan, Italy; (C.M.); (A.C.); (G.Z.); (E.V.)
| | - Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Italy;
| | - Antonio Corsello
- Department of Pediatrics, Vittore Buzzi Children’s Hospital, University of Milan, 20154 Milan, Italy; (C.M.); (A.C.); (G.Z.); (E.V.)
| | - Juri Zuvadelli
- Clinical Department of Pediatrics, ASST Santi Paolo e Carlo, San Paolo Hospital, University of Milan, 20142 Milan, Italy; (J.Z.); (G.B.)
| | - Emerenziana Ottaviano
- Department of Health Science, University of Milan, 20142 Milan, Italy; (E.O.); (M.D.C.)
| | - Michele Dei Cas
- Department of Health Science, University of Milan, 20142 Milan, Italy; (E.O.); (M.D.C.)
| | - Giuseppe Banderali
- Clinical Department of Pediatrics, ASST Santi Paolo e Carlo, San Paolo Hospital, University of Milan, 20142 Milan, Italy; (J.Z.); (G.B.)
| | - Gianvincenzo Zuccotti
- Department of Pediatrics, Vittore Buzzi Children’s Hospital, University of Milan, 20154 Milan, Italy; (C.M.); (A.C.); (G.Z.); (E.V.)
| | - Elisa Borghi
- Department of Health Science, University of Milan, 20142 Milan, Italy; (E.O.); (M.D.C.)
- Correspondence: ; Tel.: +39-0250323240
| | - Elvira Verduci
- Department of Pediatrics, Vittore Buzzi Children’s Hospital, University of Milan, 20154 Milan, Italy; (C.M.); (A.C.); (G.Z.); (E.V.)
- Department of Health Science, University of Milan, 20142 Milan, Italy; (E.O.); (M.D.C.)
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Ceccarani C, Viganò I, Ottaviano E, Redaelli MG, Severgnini M, Vignoli A, Borghi E. Is Gut Microbiota a Key Player in Epilepsy Onset? A Longitudinal Study in Drug-Naive Children. Front Cell Infect Microbiol 2021; 11:749509. [PMID: 34926315 PMCID: PMC8677705 DOI: 10.3389/fcimb.2021.749509] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Microbiota alterations have been recently investigated in individuals with epilepsy and in other neurological diseases as environmental factors that play a role, by acting through the gut-brain axis, in the pathological process. Most studies focus on the contribution of bacterial communities in refractory epilepsy and suggest a beneficial role of ketogenic diet in modulating the gut microbiota and seizure occurrence. However, they do not evaluate whether epilepsy itself alters the gut microbiota in these patients or if the gut microbial communities could contribute as a seizure trigger. In this pilot study, we performed 16S rRNA sequencing and investigated the gut microbial communities of eight children at their seizure onset and after anti-seizure was started (one year follow-up) and we compared microbial data with seven healthy children, age- and sex-matched. In drug-naive subjects, we observed a microbial signature that shared several features with those reported in refractory epilepsy, such as an increased abundance in Akkermansia spp. and Proteobacteria and a decreased relative abundance in Faecalibacterium spp.We suggest that a bacterial-mediated proinflammatory milieu could contribute to seizure occurrence in children with new onset of epilepsy, as already reported for individuals with drug-resistant epilepsy, and that it could vary during treatment in those who are drug-responsive.
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Affiliation(s)
- Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Ilaria Viganò
- Epilepsy Centre, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo Carlo, University of Milan, Milan, Italy
| | | | - Maria Gaia Redaelli
- Epilepsy Centre, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo Carlo, University of Milan, Milan, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Aglaia Vignoli
- Department of Health Sciences, University of Milan, Milan, Italy.,Child Neurology and Psychiatry Unit, Azienda Socio Sanitaria Territoriale Grande Ospedale Metropolitano (ASST GOM) Niguarda, Milan, Italy
| | - Elisa Borghi
- Department of Health Sciences, University of Milan, Milan, Italy
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Severgnini M, Camboni T, Ceccarani C, Morselli S, Cantiani A, Zagonari S, Patuelli G, Pedna MF, Sambri V, Foschi C, Consolandi C, Marangoni A. Distribution of ermB, ermF, tet(W), and tet(M) Resistance Genes in the Vaginal Ecosystem of Women during Pregnancy and Puerperium. Pathogens 2021; 10:pathogens10121546. [PMID: 34959501 PMCID: PMC8705968 DOI: 10.3390/pathogens10121546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/22/2021] [Revised: 11/17/2021] [Accepted: 11/25/2021] [Indexed: 01/02/2023] Open
Abstract
The inhabitants of the vaginal ecosystem can harbor genetic determinants conferring antimicrobial resistance. However, detailed data about the distribution of resistance genes in the vaginal microbiome of pregnant women are still lacking. Therefore, we assessed the presence of macrolide (i.e., erm genes) and tetracycline (i.e., tet genes) resistance markers in the vaginal environment of Caucasian women at different gestational ages. Furthermore, the detection of resistance genes was related to the composition of the vaginal microbiota. A total of 228 vaginal samples, collected at different trimesters of pregnancy or during the puerperium, were tested for the presence of ermB, ermF, tet(W), and tet(M) by in-house end-point PCR assays. The composition of the vaginal microbiota was assessed through a microscopic evaluation (i.e., Nugent score) and by means of sequencing V3–V4 hypervariable regions of the bacterial 16 rRNA gene. Overall, the most detected resistance gene was tet(M) (76.7%), followed by ermB (55.2%). In 17% of women, mainly with a ‘normal’ vaginal microbiota, no resistance genes were found. Except for tet(W), a significant correlation between the positivity of resistance genes and a dysbiotic vaginal status (i.e., bacterial vaginosis (BV)) was noticed. Indeed, samples positive for at least one resistance determinant were characterized by a decrease in Lactobacillus spp. and an increase of BV-related genera (Prevotella, Gardnerella, Atopobium, Sneathia). A high predominance of vaginal Lactobacillus spp. (>85%) was associated with a lower risk of tet(W) gene detection, whereas the presence of Megasphaera (>1%) increased the risk of positivity for all analyzed genes. Different types of vaginal microbiota are associated with peculiar resistance profiles, being a lactobacilli-dominated ecosystem poor in or free of resistance genes. These data could open new perspectives for promoting maternal and neonatal health.
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Affiliation(s)
- Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, 20054 Segrate, Italy; (M.S.); (T.C.); (C.C.); (C.C.)
| | - Tania Camboni
- Institute of Biomedical Technologies, National Research Council, 20054 Segrate, Italy; (M.S.); (T.C.); (C.C.); (C.C.)
| | - Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, 20054 Segrate, Italy; (M.S.); (T.C.); (C.C.); (C.C.)
| | - Sara Morselli
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40128 Bologna, Italy; (S.M.); (A.C.); (V.S.); (A.M.)
| | - Alessia Cantiani
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40128 Bologna, Italy; (S.M.); (A.C.); (V.S.); (A.M.)
| | - Sara Zagonari
- Family Advisory Health Centres, 48121 Ravenna, Italy; (S.Z.); (G.P.)
| | - Giulia Patuelli
- Family Advisory Health Centres, 48121 Ravenna, Italy; (S.Z.); (G.P.)
| | | | - Vittorio Sambri
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40128 Bologna, Italy; (S.M.); (A.C.); (V.S.); (A.M.)
- Unit of Microbiology, Greater Romagna Hub Laboratory, 47023 Cesena, Italy;
| | - Claudio Foschi
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40128 Bologna, Italy; (S.M.); (A.C.); (V.S.); (A.M.)
- Correspondence: ; Tel.: +39-0512144513
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council, 20054 Segrate, Italy; (M.S.); (T.C.); (C.C.); (C.C.)
| | - Antonella Marangoni
- Microbiology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40128 Bologna, Italy; (S.M.); (A.C.); (V.S.); (A.M.)
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10
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Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG, Schluter J, Xavier JB. Author Correction: Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Sci Data 2021; 8:119. [PMID: 33893321 PMCID: PMC8065137 DOI: 10.1038/s41597-021-00903-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s41597-021-00903-0.
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Affiliation(s)
- Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Bradford P Taylor
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Camilla Ceccarani
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Emily Fontana
- Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Luigi A Amoretti
- Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Roberta J Wright
- Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Antonio L C Gomes
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Jonathan U Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Ying Taur
- Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Eric Littmann
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Jonas Schluter
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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11
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Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG, Schluter J, Xavier JB. Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Sci Data 2021; 8:71. [PMID: 33654104 PMCID: PMC7925583 DOI: 10.1038/s41597-021-00860-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 10/12/2020] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
The impact of the gut microbiota in human health is affected by several factors including its composition, drug administrations, therapeutic interventions and underlying diseases. Unfortunately, many human microbiota datasets available publicly were collected to study the impact of single variables, and typically consist of outpatients in cross-sectional studies, have small sample numbers and/or lack metadata to account for confounders. These limitations can complicate reusing the data for questions outside their original focus. Here, we provide comprehensive longitudinal patient dataset that overcomes those limitations: a collection of fecal microbiota compositions (>10,000 microbiota samples from >1,000 patients) and a rich description of the "hospitalome" experienced by the hosts, i.e., their drug exposures and other metadata from patients with cancer, hospitalized to receive allogeneic hematopoietic cell transplantation (allo-HCT) at a large cancer center in the United States. We present five examples of how to apply these data to address clinical and scientific questions on host-associated microbial communities.
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Affiliation(s)
- Chen Liao
- grid.51462.340000 0001 2171 9952Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY USA
| | - Bradford P. Taylor
- grid.51462.340000 0001 2171 9952Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY USA
| | - Camilla Ceccarani
- grid.51462.340000 0001 2171 9952Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY USA ,grid.4708.b0000 0004 1757 2822Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Emily Fontana
- grid.51462.340000 0001 2171 9952Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY USA
| | - Luigi A. Amoretti
- grid.51462.340000 0001 2171 9952Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY USA
| | - Roberta J. Wright
- grid.51462.340000 0001 2171 9952Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY USA
| | - Antonio L. C. Gomes
- grid.51462.340000 0001 2171 9952Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY USA
| | - Jonathan U. Peled
- grid.51462.340000 0001 2171 9952Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA
| | - Ying Taur
- grid.51462.340000 0001 2171 9952Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY USA
| | - Miguel-Angel Perales
- grid.51462.340000 0001 2171 9952Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA
| | - Marcel R. M. van den Brink
- grid.51462.340000 0001 2171 9952Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA
| | - Eric Littmann
- grid.170205.10000 0004 1936 7822Duchossois Family Institute, University of Chicago, Chicago, IL USA
| | - Eric G. Pamer
- grid.170205.10000 0004 1936 7822Duchossois Family Institute, University of Chicago, Chicago, IL USA
| | - Jonas Schluter
- grid.51462.340000 0001 2171 9952Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY USA
| | - Joao B. Xavier
- grid.51462.340000 0001 2171 9952Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY USA
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12
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Cremonesi P, Morandi S, Ceccarani C, Battelli G, Castiglioni B, Cologna N, Goss A, Severgnini M, Mazzucchi M, Partel E, Tamburini A, Zanini L, Brasca M. Raw Milk Microbiota Modifications as Affected by Chlorine Usage for Cleaning Procedures: The Trentingrana PDO Case. Front Microbiol 2020; 11:564749. [PMID: 33123103 PMCID: PMC7573252 DOI: 10.3389/fmicb.2020.564749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/22/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
Abstract
Milk microbiota represents a key point in raw milk cheese production and contributes to the development of typical flavor and texture for each type of cheese. The aim of the present study was to evaluate the influence of chlorine products usage for cleaning and sanitizing the milking equipment on (i) raw milk microbiota; (ii) the deriving whey-starter microbiota; and (iii) Trentingrana Protected Designation of Origin (PDO) cheese microbiota and volatilome. Milk samples from three farms affiliated to a Trentingrana PDO cheese factory were collected three times per week during a 6-weeks period in which a sodium hypochlorite detergent (period C) was used and during a subsequent 6-weeks period of non-chlorine detergent usage (period NC). Samples were subjected to microbiological [Standard Plate Count; coliforms; coagulase-positive staphylococci; and lactic acid bacteria (LAB)] and metagenomic analysis (amplification of V3-V4 regions of 16S rRNA gene performed on Illumina MiSeq platform). In addition, cheese volatilome was determined by SPME-GC-MS. In the transition from period C to period NC, higher SPC and LAB counts in milk were recorded. Milk metagenomic analysis showed a peculiar distinctive microbiota composition for the three farms during the whole experimental period. Moreover, differences were highlighted comparing C and NC periods in each farm. A difference in microbial population related to chlorine usage in bulk milk and vat samples was evidenced. Moreover, chlorine utilization at farm level was found to affect the whey-starter population: the usually predominant Lactobacillus helveticus was significantly reduced during NC period, whereas Lactobacillus delbrueckii had the exact opposite trend. Alpha- and beta-diversity revealed a separation between the two treatment periods with a higher presence of L. helveticus, L. delbrueckii, and Streptococcus thermophilus in cheese samples after NC detergent period. Cheese volatilome analysis showed a slight decrease in lipolysis during C period in the inner part of the cheese wheel. Although preliminary, these results suggest a profound influence on milk and cheese microbiota, as well as on raw milk cheese production and quality, due to the use of chlorine. However, further studies will be needed to better understand the complex relationship between chlorine and microbiota along all the cheese production steps.
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Affiliation(s)
- Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council, Lodi, Italy
| | - Stefano Morandi
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Camilla Ceccarani
- Institute of Biomedical Technologies, Italian National Research Council, Segrate, Italy.,Department of Health Sciences, San Paolo Hospital Medical School, University of Milan, Milan, Italy
| | - Giovanna Battelli
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council, Lodi, Italy
| | - Nicola Cologna
- Trentingrana-Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Andrea Goss
- Trentingrana-Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, Italian National Research Council, Segrate, Italy
| | | | - Erika Partel
- Technology Transfer Center, Edmund Mach Foundation, Trento, Italy
| | - Alberto Tamburini
- Department of Agricultural and Environmental Sciences, Faculty of Agricultural and Food Sciences, University of Milan, Milan, Italy
| | | | - Milena Brasca
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
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13
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Marangoni A, Ceccarani C, Camboni T, Consolandi C, Foschi C, Salvo M, Gaspari V, D’Antuono A, Belletti M, Re MC, Severgnini M. Pharyngeal microbiome alterations during Neisseria gonorrhoeae infection. PLoS One 2020; 15:e0227985. [PMID: 31945133 PMCID: PMC6984747 DOI: 10.1371/journal.pone.0227985] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 01/04/2020] [Indexed: 11/25/2022] Open
Abstract
Pharyngeal gonorrhoea is a common sexually transmitted infection among ‘men having sex with other men’ (MSM). Neisseria gonorrhoeae (NG) pharyngeal infections are usually characterized by the absence of symptoms, acting as an important reservoir for their further spread. To the best of our knowledge, no information about the composition of the pharyngeal microbiome during an ongoing NG infection is currently available. Therefore, in this study, we characterized the pharyngeal bacterial community profiles associated with NG infection in a well-selected cohort of HIV-negative MSM reporting unsafe oral intercourse. A total of 70 pharyngeal swabs were considered, comparing non-infected subjects (n = 45) versus patients with pharyngeal gonorrhoea (n = 25) whose microbiota composition was analyzed from pharyngeal swabs through sequencing of hypervariable V3-V4 regions of the 16S rRNA gene. The pharyngeal microbiome of all subjects was dominated by Prevotellaceae, Veillonellaceae and Streptococcaceae families. Patients with pharyngeal gonorrhoea harboured a pharyngeal microbiome quite similar to negative subjects. Nevertheless, when looking to less-represented bacterial species (relative abundance approximately 1% or less), an imbalance between aerobe and anaerobe microorganisms was observed in NG-infected patients. In particular, the pharyngeal microbiome of NG-positive individuals was richer in several anaerobes (e.g. Treponema, Parvimonas, Peptococcus, Catonella, Filifactor) and poorer in various aerobe genera (i.e. Pseudomonas, Escherichia), compared to non-infected controls. No significant differences were noticed in the distribution of commensal Neisseria species of the oropharynx between NG-positive and negative subjects. Metabolic variations induced by changes in the microbiome abundance were assessed by a functional prediction of the bacterial metabolic pathways: a more abundant involvement of D-glutamine and D-glutamate metabolism, carbohydrate metabolism, as well as a greater activation of the energy metabolism was observed in patients with pharyngeal gonorrhoea compared to non-infected individuals. Information about the bacterial composition of the pharyngeal microbiome in case of gonorrhoea could shed light on the pathogenesis of the infection and open new perspectives for the prevention and control of this condition.
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Affiliation(s)
| | - Camilla Ceccarani
- Institute of Biomedical Technologies–National Research Council, Segrate, Milan, Italy
- Department of Health Sciences, University of Milan, Milan, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies–National Research Council, Segrate, Milan, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies–National Research Council, Segrate, Milan, Italy
| | - Claudio Foschi
- Microbiology, DIMES, University of Bologna, Bologna, Italy
- * E-mail:
| | - Melissa Salvo
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | | | | | | | - Maria Carla Re
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies–National Research Council, Segrate, Milan, Italy
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14
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Ceccarani C, Marangoni A, Severgnini M, Camboni T, Laghi L, Gaspari V, D'Antuono A, Foschi C, Re MC, Consolandi C. Rectal Microbiota Associated With Chlamydia trachomatis and Neisseria gonorrhoeae Infections in Men Having Sex With Other Men. Front Cell Infect Microbiol 2019; 9:358. [PMID: 31681634 PMCID: PMC6813206 DOI: 10.3389/fcimb.2019.00358] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 06/06/2019] [Accepted: 10/02/2019] [Indexed: 01/02/2023] Open
Abstract
Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) represent the most common agents of sexually transmitted rectal infections among men having sex with other men (MSM). In this study, we assessed the bacterial composition of the rectal microbiota associated with CT and/or NG infections in a cohort of men reporting unsafe rectal intercourse. A total of 125 rectal swabs were collected and four groups were compared: non-infected subjects (n = 53), patients with CT (n = 37), or NG rectal infection (n = 17) and patients with contemporary positivity for CT/NG (n = 18). CT and NG infections were detected by a real-time commercial test and the rectal microbiota composition was analyzed from rectal swabs through sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene. The rectal microbiota of all subgroups was dominated by Prevotellaceae, Enterobacteriaceae, and Ruminococcaceae families. Irrespective of the analyzed subgroup, we found that the rectal environment of all the enrolled MSM was rich in Prevotella and Escherichia genera. Moreover, a shift in the bacterial composition between patients with sexually transmitted rectal infections and controls was noticed: infected patients were characterized by a depletion of Escherichia species, associated with an increase of anaerobic genera, including Peptoniphilus, Peptostreptococcus, and Parvimonas. Overall, the presence of rectal symptoms did not significantly modify the rectal microbiota profiles among the four groups of analyzed patients. We confirmed that HIV-positive patients are characterized by a lower bacterial richness than HIV-negative subjects. However, we found that the presence of HIV has a different impact on bacterial rectal communities compared to CT and NG infections, modifying the relative abundance of several genera, including Gardnerella, Lactobacillus, Corynebacterium, and Sutterella. Information about the rectal microbiota composition in CT and NG infections could shed light on the pathogenesis of these conditions and could contribute to the onset of new strategies for their control.
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Affiliation(s)
- Camilla Ceccarani
- National Research Council, Institute of Biomedical Technologies, Milan, Italy.,Department of Health Sciences, University of Milan, Milan, Italy
| | | | - Marco Severgnini
- National Research Council, Institute of Biomedical Technologies, Milan, Italy
| | - Tania Camboni
- National Research Council, Institute of Biomedical Technologies, Milan, Italy
| | - Luca Laghi
- Department of Agro-Food Science and Technology, Centre of Foodomics, University of Bologna, Cesena, Italy
| | | | | | - Claudio Foschi
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - Maria Carla Re
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - Clarissa Consolandi
- National Research Council, Institute of Biomedical Technologies, Milan, Italy
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15
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Ceccarani C, Foschi C, Parolin C, D'Antuono A, Gaspari V, Consolandi C, Laghi L, Camboni T, Vitali B, Severgnini M, Marangoni A. Diversity of vaginal microbiome and metabolome during genital infections. Sci Rep 2019; 9:14095. [PMID: 31575935 PMCID: PMC6773718 DOI: 10.1038/s41598-019-50410-x] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [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: 05/05/2019] [Accepted: 09/06/2019] [Indexed: 12/30/2022] Open
Abstract
We characterized the vaginal ecosystem during common infections of the female genital tract, as vulvovaginal candidiasis (VVC, n = 18) and Chlamydia trachomatis infection (CT, n = 20), recruiting healthy (HC, n = 21) and bacterial vaginosis-affected (BV, n = 20) women as references of eubiosis and dysbiosis. The profiles of the vaginal microbiome and metabolome were studied in 79 reproductive-aged women, by means of next generation sequencing and proton based-nuclear magnetic resonance spectroscopy. Lactobacillus genus was profoundly depleted in all the genital infections herein considered, and species-level analysis revealed that healthy vaginal microbiome was dominated by L. crispatus. In the shift from HC to CT, VVC, and BV, L. crispatus was progressively replaced by L. iners. CT infection and VVC, as well as BV condition, were mainly characterised by anaerobe genera, e.g. Gardnerella, Prevotella, Megasphaera, Roseburia and Atopobium. The changes in the bacterial communities occurring during the genital infections resulted in significant alterations in the vaginal metabolites composition, being the decrease of lactate a common marker of all the pathological conditions. In conclusion, according to the taxonomic and metabolomics analysis, we found that each of the four conditions is characterized by a peculiar vaginal microbiome/metabolome fingerprint.
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Affiliation(s)
- Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy.,Department of Health Sciences, San Paolo Hospital Medical School, University of Milan, Milan, Italy
| | - Claudio Foschi
- Microbiology, Experimental Diagnostic and Specialty Department (DIMES), University of Bologna, Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy.
| | | | | | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Luca Laghi
- Centre of Foodomics, Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Antonella Marangoni
- Microbiology, Experimental Diagnostic and Specialty Department (DIMES), University of Bologna, Bologna, Italy
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16
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Bassanini G, Ceccarani C, Borgo F, Severgnini M, Rovelli V, Morace G, Verduci E, Borghi E. Phenylketonuria Diet Promotes Shifts in Firmicutes Populations. Front Cell Infect Microbiol 2019; 9:101. [PMID: 31058098 PMCID: PMC6477998 DOI: 10.3389/fcimb.2019.00101] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 02/08/2019] [Accepted: 03/25/2019] [Indexed: 12/21/2022] Open
Abstract
Low-phenylalanine diet, the mainstay of treatment for phenylketonuria (PKU), has been shown to increase glycemic index and glycemic load, affecting the availability of substrates for microbial fermentation. Indeed, changes in the PKU gut microbiota compared with healthy controls have been previously reported. In this study we compared the gut microbial communities of children with PKU and with mild hyperphenylalaninemia (MHP, unrestricted diet). For each group, we enrolled 21 children (4–18 years old), for a total dataset of 42 subjects. We assessed dietary intake and performed gut microbiota analysis by sequencing the V3–V4 hypervariable regions of the 16S rRNA gene. Short chain fatty acids (SCFAs) were quantified by gas chromatographic analysis. While alpha-diversity analysis showed no significant differences between PKU and MHP groups, microbial community analysis highlighted a significant separation of the gut microbiota according to both unweighted (p = 0.008) and weighted Unifrac distances (p = 0.033). Major differences were seen within the Firmicutes phylum. Indeed, PKU children were depleted in Faecalibacterium spp. and enriched in Blautia spp. and Clostridium spp (family Lachnospiraceae). We found a divergent response of members of the Firmicutes phylum with respect to daily glycemic index, higher in PKU children. Faecalibacterium prausnitzii, unclassified Ruminococcaceae and, to a lesser extent Roseburia spp. negatively correlated with glycemic index, whereas unclassified Lachnospiraceae were positively associated. Indicator species analysis suggested F. prausnitzii be related to MHP status and Ruminococcus bromii to be associated with PKU. Despite PKU children having a higher vegetable and fiber intake, resembling a vegan diet, their gut microbial profile is different from the microbiota reported in the literature for individuals consuming a high-fiber/low-protein diet. Indeed, beneficial microorganisms, such as F. prausnitzii, considered a biomarker for a healthy status and one of the main butyrate producers, are depleted in PKU gut microbiota. We suggest that both the quality and quantity of carbohydrates ingested participate in determining the observed Firmicutes shifts on the PKU population.
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Affiliation(s)
- Giulia Bassanini
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Camilla Ceccarani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Francesca Borgo
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Valentina Rovelli
- Department of Pediatrics, San Paolo Hospital, Università degli Studi di Milano, Milan, Italy
| | - Giulia Morace
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elvira Verduci
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,Department of Pediatrics, San Paolo Hospital, Università degli Studi di Milano, Milan, Italy
| | - Elisa Borghi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
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17
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Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C, Pezzoli G. Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism. Mov Disord 2018; 34:396-405. [PMID: 30576008 DOI: 10.1002/mds.27581] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Although several studies have suggested that abnormalities in gut microbiota may play a critical role in the pathogenesis of PD, data are still extremely heterogeneous. METHODS 16S gene ribosomal RNA sequencing was performed on fecal samples of 350 individuals, subdivided into idiopathic PD (n = 193, of whom 39 were drug naïve) stratified by disease duration, PSP (n = 22), MSA (n = 22), and healthy controls (HC; n = 113). Several confounders were taken into account, including dietary habits. RESULTS Despite the fact that unadjusted comparison of PD and HC showed several differences in relative taxa abundances, the significant results were greatly reduced after adjusting for confounders. Although most of these differences were associated with disease duration, lower abundance in Lachnospiraceae was the only difference between de novo PD and HC (remaining lower across almost all PD duration strata). Decreased Lachnospiraceae and increased Lactobacillaceae and Christensenellaceae were associated with a worse clinical profile, including higher frequencies of cognitive impairment, gait disturbances, and postural instability. When compared with HC, MSA and PSP patients shared the changes in PD, with a few exceptions: in MSA, Lachnospiraceae were not lower, and Prevotellaceae were reduced; in PSP, Lactobacillaceae were similar, and Streptococcaceae were reduced. CONCLUSIONS Gut microbiota may be an environmental modulator of the pathogenesis of PD and contribute to the interindividual variability of clinical features. Data are influenced by PD duration and several confounders that need to be taken into account in future studies. Prospective studies in de novo PD patients are needed to elucidate the net effect of dysbiosis on the progression of the disease. © 2018 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Michela Barichella
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies (IBT), Italian National Research Council (CNR), Milan, Italy
| | - Roberto Cilia
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy
| | - Erica Cassani
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy
| | - Carlotta Bolliri
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy
| | - Serena Caronni
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy
| | - Valentina Ferri
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy
| | - Raffaella Cancello
- IRCCS Istituto Auxologico Italiano, Obesity Research Laboratory, Milan, Italy
| | - Camilla Ceccarani
- Institute of Biomedical Technologies (IBT), Italian National Research Council (CNR), Milan, Italy.,Department of Health Sciences, San Paolo Hospital Medical School, University of Milan, Milan, Italy
| | - Samanta Faierman
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy
| | - Giovanna Pinelli
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy.,Department of Parkinson Disease Rehabilitation, Moriggia-Pelascini Hospital, Gravedona ed Uniti, Fondazione Europea Ricerca Biomedica (FERB), Gravedona, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies (IBT), Italian National Research Council (CNR), Milan, Italy
| | - Luigi Zecca
- Institute of Biomedical Technologies (IBT), Italian National Research Council (CNR), Milan, Italy.,Department of Psychiatry, Columbia University Medical Center, New York State Psychiatric Institute, New York, NY USA
| | - Emanuele Cereda
- Clinical Nutrition and Dietetics Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies (IBT), Italian National Research Council (CNR), Milan, Italy
| | - Gianni Pezzoli
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini-CTO, Milan, Italy
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18
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Cremonesi P, Ceccarani C, Curone G, Severgnini M, Pollera C, Bronzo V, Riva F, Addis MF, Filipe J, Amadori M, Trevisi E, Vigo D, Moroni P, Castiglioni B. Milk microbiome diversity and bacterial group prevalence in a comparison between healthy Holstein Friesian and Rendena cows. PLoS One 2018; 13:e0205054. [PMID: 30356246 PMCID: PMC6200206 DOI: 10.1371/journal.pone.0205054] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023] Open
Abstract
Dry and early lactation periods represent the most critical phases for udder health in cattle, especially in highly productive breeds, such as the Holstein Friesian (HF). On the other hand, some autochthonous cattle breeds, such as the Rendena (REN), have a lower prevalence of mastitis and other transition-related diseases. In this study, milk microbiota of 6 HF and 3 REN cows, all raised on the same farm under the same conditions, was compared. A special focus was placed on the transition period to define bacterial groups’ prevalence with a plausible effect on mammary gland health. Four time points (dry-off, 1 d, 7–10 d and 30 d after calving) were considered. Through 16S rRNA sequencing, we characterized the microbiota composition for 117 out of the 144 milk samples initially collected, keeping only the healthy quarters, in order to focus on physiological microbiome changes and avoid shifts due to suspected diseases. Microbial populations were very different in the two breeds along all the time points, with REN milk showing a significantly lower microbial biodiversity. The taxonomic profiles of both cosmopolitan and local breeds were dominated by Firmicutes, mostly represented by the Streptococcus genus, although in very different proportions (HF 27.5%, REN 68.6%). Large differences in HF and REN cows were, also, evident from the metabolic predictive analysis from microbiome data. Finally, only HF milk displayed significant changes in the microbial composition along the transition period, while REN maintained a more stable microbiota. In conclusion, in addition to the influence on the final characteristics of dairy products obtained from milk of the two breeds, differences in the milk microbiome might, also, have an impact on their mammary gland health.
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Affiliation(s)
- Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Lodi, Italy
- * E-mail:
| | - Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, (CNR), Segrate, Milan, Italy
- Dipartimento di Scienze della Salute, San Paolo Hospital Medical School, Università degli Studi di Milano, Milan, Italy
| | - Giulio Curone
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, (CNR), Segrate, Milan, Italy
| | - Claudia Pollera
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Valerio Bronzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Federica Riva
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Maria Filippa Addis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Joel Filipe
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Massimo Amadori
- Laboratory of Cellular Immunology, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Erminio Trevisi
- Department of Animal Sciences, Food and Nutrition (DIANA), Facoltà di Scienze Agrarie, Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Daniele Vigo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, United States of America
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Lodi, Italy
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