1
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Alessandri G, Milani C, Mancabelli L, Mangifesta M, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. The impact of human-facilitated selection on the gut microbiota of domesticated mammals. FEMS Microbiol Ecol 2020; 95:5538759. [PMID: 31344227 DOI: 10.1093/femsec/fiz121] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 03/20/2019] [Accepted: 07/19/2019] [Indexed: 12/26/2022] Open
Abstract
Domestication is the process by which anthropogenic forces shape lifestyle and behavior of wild species to accommodate human needs. The impact of domestication on animal physiology and behavior has been extensively studied, whereas its effect on the gut microbiota is still largely unexplored. For this reason, 16S rRNA gene-based and internal transcribed spacer-mediated bifidobacterial profiling, together with shotgun metagenomics, was employed to investigate the taxonomic composition and metabolic repertoire of 146 mammalian fecal samples, corresponding to 12 domesticated-feral dyads. Our results revealed that changes induced by domestication have extensively shaped the taxonomic composition of the mammalian gut microbiota. In this context, the selection of microbial taxa linked to a more efficient feed conversion into body mass and putative horizontal transmission of certain bacterial genera from humans were observed in the fecal microbiota of domesticated animals when compared to their feral relatives and to humans. In addition, profiling of the metabolic arsenal through metagenomics highlighted extensive functional adaptation of the fecal microbial community of domesticated mammals to changes induced by domestication. Remarkably, domesticated animals showed, when compared to their feral relatives, increased abundance of specific glycosyl hydrolases, possibly due to the higher intake of complex plant carbohydrates typical of commercial animal feeds.
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Affiliation(s)
- Giulia Alessandri
- Department of Veterinary Science, University of Parma, Via del Taglio 8, 43100 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Alice Viappiani
- GenProbio srl, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.,Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Maria Cristina Ossiprandi
- Department of Veterinary Science, University of Parma, Via del Taglio 8, 43100 Parma, Italy.,Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.,Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
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2
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Lugli GA, Duranti S, Milani C, Mancabelli L, Turroni F, Alessandri G, Longhi G, Anzalone R, Viappinai A, Tarracchini C, Bernasconi S, Yonemitsu C, Bode L, Goran MI, Ossiprandi MC, van Sinderen D, Ventura M. Investigating bifidobacteria and human milk oligosaccharide composition of lactating mothers. FEMS Microbiol Ecol 2020; 96:5809960. [PMID: 32188978 DOI: 10.1093/femsec/fiaa049] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 11/27/2019] [Accepted: 03/17/2020] [Indexed: 12/19/2022] Open
Abstract
Human milk is known to carry its own microbiota, of which the precise origin remains obscure. Breastfeeding allows mother-to-baby transmission of microorganisms as well as the transfer of many other milk components, such as human milk oligosaccharides (HMOs), which act as metabolizable substrates for particular bacteria, such as bifidobacteria, residing in infant intestinal tract. In the current study, we report the HMO composition of 249 human milk samples, in 163 of which we quantified the abundance of members of the Bifidobacterium genus using a combination of metagenomic and flow cytometric approaches. Metagenomic data allowed us to identify four clusters dominated by Bifidobacterium adolescentis and Bifidobacterium pseudolongum, Bifidobacterium crudilactis or Bifidobacterium dentium, as well as a cluster represented by a heterogeneous mix of bifidobacterial species such as Bifidobacterium breve and Bifidobacterium longum. Furthermore, in vitro growth assays on HMOs coupled with in silico glycobiome analyses allowed us to elucidate that members of the Bifidobacterium bifidum and B. breve species exhibit the greatest ability to degrade and grow on HMOs. Altogether, these findings indicate that the bifidobacterial component of the human milk microbiota is not strictly correlated with their ability to metabolize HMOs.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | | | | | | | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Chloe Yonemitsu
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, CA, USA
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, CA, USA
| | - Michael I Goran
- Department of Pediatrics, Children's Hospital Los Angeles, The University of Southern California, Los Angeles, CA, USA
| | | | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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3
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Duranti S, Lugli GA, Viappiani A, Mancabelli L, Alessandri G, Anzalone R, Longhi G, Milani C, Ossiprandi MC, Turroni F, Ventura M. Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov. Int J Syst Evol Microbiol 2020; 70:2288-2297. [PMID: 32065574 DOI: 10.1099/ijsem.0.004032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 01/16/2023] Open
Abstract
Two Bifidobacterium strains, i.e., 2176BT and 2177BT, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176BT and 2177BT exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139T and Bifidobacterium bifidum LMG 11041T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176BT=LMG 31469T=CCUG 73785T) and Bifidobacterium leontopitheci sp. nov. (2177BT=LMG 31471T=CCUG 73786T are proposed as novel Bifidobacterium species.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | | | | | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Microbiome Research Hub, University of Parma, Parma, Italy.,Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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4
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Turroni F, Milani C, Duranti S, Lugli GA, Bernasconi S, Margolles A, Di Pierro F, van Sinderen D, Ventura M. The infant gut microbiome as a microbial organ influencing host well-being. Ital J Pediatr 2020; 46:16. [PMID: 32024556 PMCID: PMC7003403 DOI: 10.1186/s13052-020-0781-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/29/2020] [Indexed: 12/16/2022] Open
Abstract
Initial establishment of the human gut microbiota is generally believed to occur immediately following birth, involving key gut commensals such as bifidobacteria that are acquired from the mother. The subsequent development of this early gut microbiota is driven and modulated by specific dietary compounds present in human milk that support selective colonization. This represents a very intriguing example of host-microbe co-evolution, where both partners are believed to benefit. In recent years, various publications have focused on dissecting microbial infant gut communities and their interaction with their human host, being a determining factor in host physiology and metabolic activities. Such studies have highlighted a reduction of microbial diversity and/or an aberrant microbiota composition, sometimes referred to as dysbiosis, which may manifest itself during the early stage of life, i.e., in infants, or later stages of life. There are growing experimental data that may explain how the early human gut microbiota affects risk factors related to adult health conditions. This concept has fueled the development of various nutritional strategies, many of which are based on probiotics and/or prebiotics, to shape the infant microbiota. In this review, we will present the current state of the art regarding the infant gut microbiota and the role of key commensal microorganisms like bifidobacteria in the establishment of the first microbial communities in the human gut.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA - CSIC, Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain
| | | | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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5
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Turroni F, Duranti S, Milani C, Lugli GA, van Sinderen D, Ventura M. Bifidobacterium bifidum: A Key Member of the Early Human Gut Microbiota. Microorganisms 2019; 7:microorganisms7110544. [PMID: 31717486 PMCID: PMC6920858 DOI: 10.3390/microorganisms7110544] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [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: 10/02/2019] [Revised: 10/29/2019] [Accepted: 11/07/2019] [Indexed: 12/30/2022] Open
Abstract
Bifidobacteria typically represent the most abundant bacteria of the human gut microbiota in healthy breast-fed infants. Members of the Bifidobacterium bifidum species constitute one of the dominant taxa amongst these bifidobacterial communities and have been shown to display notable physiological and genetic features encompassing adhesion to epithelia as well as metabolism of host-derived glycans. In the current review, we discuss current knowledge concerning particular biological characteristics of the B. bifidum species that support its specific adaptation to the human gut and their implications in terms of supporting host health.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
- Microbiome Research Hub, University of Parma, 43124 Parma, Italy
- Correspondence:
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland;
- APC Microbiome Institute, University College Cork, T12 YT20 Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
- Microbiome Research Hub, University of Parma, 43124 Parma, Italy
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6
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Duranti S, Lugli GA, Milani C, James K, Mancabelli L, Turroni F, Alessandri G, Mangifesta M, Mancino W, Ossiprandi MC, Iori A, Rota C, Gargano G, Bernasconi S, Di Pierro F, Sinderen D, Ventura M. Bifidobacterium bifidum
and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution. Environ Microbiol 2019; 21:3683-3695. [DOI: 10.1111/1462-2920.14705] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 02/07/2023]
Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
| | - Kieran James
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of Ireland Cork Ireland
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
- Microbiome Research HubUniversity of Parma Parma Italy
| | - Giulia Alessandri
- Department of Veterinary Medical ScienceUniversity of Parma Parma Italy
| | | | - Walter Mancino
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of Ireland Cork Ireland
| | - Maria Cristina Ossiprandi
- Microbiome Research HubUniversity of Parma Parma Italy
- Department of Veterinary Medical ScienceUniversity of Parma Parma Italy
| | - Alexandra Iori
- Neonatal Intensive Care Unit, Obstetric and Pediatric Department, IRCCSArcispedale Santa Maria Nuova Reggio Emilia Italy
| | - Claudio Rota
- Neonatal Intensive Care Unit, Obstetric and Pediatric Department, IRCCSArcispedale Santa Maria Nuova Reggio Emilia Italy
| | - Giancarlo Gargano
- Neonatal Intensive Care Unit, Obstetric and Pediatric Department, IRCCSArcispedale Santa Maria Nuova Reggio Emilia Italy
| | | | | | - Douwe Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of Ireland Cork Ireland
- Department of Veterinary Medical ScienceUniversity of Parma Parma Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of Parma Parma Italy
- Microbiome Research HubUniversity of Parma Parma Italy
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7
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Duranti S, Mancabelli L, Mancino W, Anzalone R, Longhi G, Statello R, Carnevali L, Sgoifo A, Bernasconi S, Turroni F, Ventura M. Exploring the effects of COLOSTRONONI on the mammalian gut microbiota composition. PLoS One 2019; 14:e0217609. [PMID: 31150516 PMCID: PMC6544264 DOI: 10.1371/journal.pone.0217609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/07/2018] [Accepted: 05/16/2019] [Indexed: 11/19/2022] Open
Abstract
COLOSTRONONI is a dietary supplement consisting of bovine colostrum and Morinda citrifolia fruit (Noni). In this study, we tested the capability of COLOSTRONONI to influence gut microbiota composition using an in vivo evaluation in rats. Furthermore, we analyzed the effect of COLOSTRONONI on the systemic inflammatory responses as well as on the gut permeability of the animals. Altogether, our analyses supported the concept of COLOSTRONONI as a natural food supplement that doesn't affect (neither negatively nor positively) gut microbiota homeostasis in healthy conditions. Moreover, COLOSTRONONI highlighted a lower effect in the expression of genes coding for IL-10, Il-12 and TNF-α response allowing us to hypothesize an immunomodulatory activity of this dietary supplement.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Walter Mancino
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | | | - Rosario Statello
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Luca Carnevali
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Andrea Sgoifo
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
- * E-mail:
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8
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Lugli GA, Milani C, Duranti S, Alessandri G, Turroni F, Mancabelli L, Tatoni D, Ossiprandi MC, van Sinderen D, Ventura M. Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches. Genome Biol 2019; 20:96. [PMID: 31097033 PMCID: PMC6524291 DOI: 10.1186/s13059-019-1711-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 11/06/2018] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Giulia Alessandri
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Danilo Tatoni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Maria Cristina Ossiprandi
- Department of Veterinary Medical Science, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy. .,Microbiome Research Hub, University of Parma, Parma, Italy.
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9
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Alessandri G, Milani C, Duranti S, Mancabelli L, Ranjanoro T, Modica S, Carnevali L, Statello R, Bottacini F, Turroni F, Ossiprandi MC, Sgoifo A, van Sinderen D, Ventura M. Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota. Sci Rep 2019; 9:5755. [PMID: 30962486 PMCID: PMC6453949 DOI: 10.1038/s41598-019-42257-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 11/27/2018] [Accepted: 03/22/2019] [Indexed: 01/26/2023] Open
Abstract
Chitin-glucan (CG) represents a natural carbohydrate source for certain microbial inhabitants of the human gut and may act as a prebiotic for a number of bacterial taxa. However, the bifidogenic activity of this substrate is still unknown. In the current study, we evaluated the ability of chitin-glucan to influence growth of 100 bifidobacterial strains belonging to those species commonly identified within the bifidobacterial communities residing in the infant and adult human gut. Such analyses were coupled with transcriptome experiments directed to explore the transcriptional effects of CG on Bifidobacterium breve 2L, which was shown to elicit the highest growth performance on this natural polysaccharide. In addition, an in vivo trial involving a rat model revealed how the colonization efficiency of this bifidobacterial strain was enhanced when the animals were fed with a diet containing CG. Altogether our analyses indicate that CG is a valuable novel prebiotic compound that may be added to the human diet in order to re-establish/reinforce bifidobacteria colonization in the mammalian gut.
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Affiliation(s)
- Giulia Alessandri
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | | | - Luca Carnevali
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosario Statello
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Andrea Sgoifo
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Department of Veterinary Medical Science, University of Parma, Parma, Italy.
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10
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Milani C, Duranti S, Napoli S, Alessandri G, Mancabelli L, Anzalone R, Longhi G, Viappiani A, Mangifesta M, Lugli GA, Bernasconi S, Ossiprandi MC, van Sinderen D, Ventura M, Turroni F. Colonization of the human gut by bovine bacteria present in Parmesan cheese. Nat Commun 2019; 10:1286. [PMID: 30894548 PMCID: PMC6426854 DOI: 10.1038/s41467-019-09303-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 08/02/2018] [Accepted: 02/28/2019] [Indexed: 12/21/2022] Open
Abstract
The abilities of certain microorganisms to be transferred across the food production chain, persist in the final product and, potentially, colonize the human gut are poorly understood. Here, we provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese. We characterize the microbial communities in samples taken from five different locations across the Parmesan cheese production chain, confirming that the final product contains microorganisms derived from cattle gut, milk, and the nearby environment. In addition, we carry out a human pilot study showing that Bifidobacterium mongoliense strains from cheese can transiently colonize the human gut, a process that can be enhanced by cow milk consumption. Some microorganisms may be transferred across the food production chain and, potentially, colonize the human gut. Here, Milani et al. provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | | | - Giulia Alessandri
- Department of Veterinary Science, University of Parma, Parma, 43126, Italy
| | | | | | | | | | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy.,GenProbio srl, Parma, 43124, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | | | | | - Douwe van Sinderen
- Department of Veterinary Science, University of Parma, Parma, 43126, Italy.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy. .,Microbiome Research Hub, University of Parma, Parma, 43124, Italy.
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy. .,Microbiome Research Hub, University of Parma, Parma, 43124, Italy.
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11
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Alessandri G, Milani C, Mancabelli L, Mangifesta M, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. Environ Microbiol 2019; 21:1331-1343. [PMID: 30680877 DOI: 10.1111/1462-2920.14540] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/14/2018] [Accepted: 01/22/2019] [Indexed: 01/13/2023]
Abstract
Domestication of dogs from wolves is the oldest known example of ongoing animal selection, responsible for generating more than 300 dog breeds worldwide. In order to investigate the taxonomic and functional evolution of the canine gut microbiota, a multi-omics approach was applied to six wild wolves and 169 dog faecal samples, the latter encompassing 51 breeds, which fully covers currently known canine genetic biodiversity. Specifically, 16S rRNA gene and bifidobacterial Internally Transcribed Spacer (ITS) profiling were employed to reconstruct and then compare the canine core gut microbiota to those of wolves and humans, revealing that artificial selection and subsequent cohabitation of dogs with their owners influenced the microbial population of canine gut through loss and acquisition of specific bacterial taxa. Moreover, comparative analysis of the intestinal bacterial population of dogs fed on Bones and Raw Food (BARF) or commercial food (CF) diet, coupled with shotgun metagenomics, highlighted that both bacterial composition and metabolic repertoire of the canine gut microbiota have evolved to adapt to high-protein or high-carbohydrates intake. Altogether, these data indicate that artificial selection and domestication not only affected the canine genome, but also shaped extensively the bacterial population harboured by the canine gut.
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Affiliation(s)
- Giulia Alessandri
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Maria C Ossiprandi
- Department of Veterinary Medical Science, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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12
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Duranti S, Lugli GA, Napoli S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov. Int J Syst Evol Microbiol 2019; 69:1288-1298. [PMID: 30789326 DOI: 10.1099/ijsem.0.003306] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 01/09/2023] Open
Abstract
Five Bifidobacterium strains, i.e. 2020BT, 2028BT, 2033BT, 2034BT and 2036BT, were isolated from European beaver (Castor fiber), Goeldi's marmoset (Callimicogoeldii), black-capped squirrel monkey (Saimiriboliviensissubsp. peruviensis) and Patagonian mara (Dolichotispatagonum). All of these isolates were shown to be Gram-positive, facultative anaerobic, d-fructose 6-phosphate phosphoketolase-positive, non-motile and non-sporulating. Phylogenetic analyses based on 16S rRNA gene sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2020BT, 2028BT, 2033BT, 2034BT and 2036BT exhibit close phylogenetic relatedness to Bifidobacterium biavatii DSM 23969T, Bifidobacterium bifidum LMG 11041T, Bifidobacterium choerinum LMG 10510T, Bifidobacterium gallicum LMG 11596T, Bifidobacterium imperatoris LMG 30297T, Bifidobacterium italicum LMG 30187T and Bifidobacterium vansinderenii LMG 30126T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium castoris sp. nov. (2020BT=LMG 30937T=CCUG 72816T), Bifidobacterium callimiconis sp. nov. (2028BT=LMG 30938T=CCUG 72814T), Bifidobacterium samirii sp. nov. (2033BT=LMG 30940T=CCUG 72817T), Bifidobacterium goeldii sp. nov. (2034BT=LMG 30939T=CCUG 72815T) and Bifidobacterium dolichotidis sp. nov. (2036BT=LMG 30941T=CCUG 72818T) are proposed as novel Bifidobacterium species.
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Affiliation(s)
- Sabrina Duranti
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stefania Napoli
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosaria Anzalone
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- 2Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | - Francesca Turroni
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Douwe van Sinderen
- 2Department of Veterinary Medical Science, University of Parma, Parma, Italy.,3APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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13
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Ticinesi A, Milani C, Guerra A, Allegri F, Lauretani F, Nouvenne A, Mancabelli L, Lugli GA, Turroni F, Duranti S, Mangifesta M, Viappiani A, Ferrario C, Dodi R, Dall'Asta M, Del Rio D, Ventura M, Meschi T. Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers. Gut 2018; 67:2097-2106. [PMID: 29705728 DOI: 10.1136/gutjnl-2017-315734] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case-control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls. DESIGN Faecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles. RESULTS SFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=-0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=-0.85, p=0.02). CONCLUSIONS Idiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.
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Affiliation(s)
- Andrea Ticinesi
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Angela Guerra
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Franca Allegri
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Fulvio Lauretani
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Antonio Nouvenne
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Microbiome Research Hub, University of Parma, Parma, Italy.,Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio S.r.l., Parma, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rossella Dodi
- Department of Food and Drugs, University of Parma, Parma, Italy
| | | | - Daniele Del Rio
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Veterinary Science, University of Parma, Parma, Italy
| | - Marco Ventura
- Microbiome Research Hub, University of Parma, Parma, Italy.,Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Tiziana Meschi
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
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14
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Duranti S, Vivo V, Zini I, Milani C, Mangifesta M, Anzalone R, Mancabelli L, Viappiani A, Cantoni AM, Barocelli E, van Sinderen D, Bertoni S, Turroni F. Bifidobacterium bifidum PRL2010 alleviates intestinal ischemia/reperfusion injury. PLoS One 2018; 13:e0202670. [PMID: 30161157 PMCID: PMC6116995 DOI: 10.1371/journal.pone.0202670] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 01/26/2018] [Accepted: 08/07/2018] [Indexed: 02/01/2023] Open
Abstract
Mesenteric ischemia/reperfusion is a clinical emergency with high morbidity and mortality due to the transient reduction of blood supply to the bowel. In recent years, the critical contribution of gut microbiome to human health and proper gastrointestinal functions has gradually emerged. In the current study, we investigated the protective effects of five days supplementation with Bifidobacterium bifidum PRL2010 in a murine model of gut ischemia/reperfusion. Our findings indicate that animals pretreated with B. bifidum PRL2010 showed lower neutrophil recruitment in the lungs, remarkably reduced bacterial translocation and decreased transcription levels of TNFalpha and IL-10 both in liver and kidneys, at the same time increasing those of IL-12 in kidneys. Inhibiting the adhesion of pathogenic bacteria and boosting host innate immunity responses are among the possible protective mechanisms enacted by the probiotic. These results demonstrate that short-period treatment with B. bifidum PRL2010 is a potential strategy to dampen remote organ injury due to mesenteric ischemia/reperfusion.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Valentina Vivo
- Food and Drug Department, University of Parma, Parma, Italy
| | - Irene Zini
- Food and Drug Department, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alice Viappiani
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Elisabetta Barocelli
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Simona Bertoni
- Food and Drug Department, University of Parma, Parma, Italy
- * E-mail:
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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15
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Milani C, Casey E, Lugli GA, Moore R, Kaczorowska J, Feehily C, Mangifesta M, Mancabelli L, Duranti S, Turroni F, Bottacini F, Mahony J, Cotter PD, McAuliffe FM, van Sinderen D, Ventura M. Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. Microbiome 2018; 6:145. [PMID: 30126456 PMCID: PMC6102903 DOI: 10.1186/s40168-018-0527-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/09/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a "gold standard" protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data. RESULTS Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and assembled data. Performances of METAnnotatorX were assessed through investigation of seven mother-newborn pairs, leading to the identification of shared phage genotypes, of which two were genomically decoded and characterized. METAnnotatorX was furthermore employed to evaluate a protocol for the identification of contaminant non-viral DNA in sequenced datasets and was exploited to determine the amount of metagenomic data needed for robust evaluation of human adult-derived (fecal) phageomes. CONCLUSIONS Results obtained in this study demonstrate that a comprehensive pipeline for analysis of phageomes will be pivotal for future explorations of the ecology of phages in the gut environment as well as for understanding their impact on the physiology and bacterial community kinetics as players of dysbiosis and homeostasis in the gut microbiota.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Eoghan Casey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Rebecca Moore
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Joanna Kaczorowska
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc, Moorepark Food Research Centre, Fermoy, Co., Cork, Cork, Ireland
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc, Moorepark Food Research Centre, Fermoy, Co., Cork, Cork, Ireland
| | - Fionnuala M McAuliffe
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe van Sinderen
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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16
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Milani C, Duranti S, Mangifesta M, Lugli GA, Turroni F, Mancabelli L, Viappiani A, Anzalone R, Alessandri G, Ossiprandi MC, van Sinderen D, Ventura M. Phylotype-Level Profiling of Lactobacilli in Highly Complex Environments by Means of an Internal Transcribed Spacer-Based Metagenomic Approach. Appl Environ Microbiol 2018; 84:e00706-18. [PMID: 29728382 PMCID: PMC6029092 DOI: 10.1128/aem.00706-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 03/27/2018] [Accepted: 04/27/2018] [Indexed: 12/12/2022] Open
Abstract
The genus Lactobacillus is a widespread taxon, members of which are highly relevant to functional and fermented foods, while they are also commonly present in host-associated gut and vaginal microbiota. Substantial efforts have been undertaken to disclose the genetic repertoire of all members of the genus Lactobacillus, and yet their species-level profiling in complex matrices is still undeveloped due to the poor phylotype resolution of profiling approaches based on the 16S rRNA gene. To overcome this limitation, an internal transcribed spacer (ITS)-based profiling method was developed to accurately profile lactobacilli at the species level. This approach encompasses a genus-specific primer pair combined with a database of ITS sequences retrieved from all available Lactobacillus genomes and a script for the QIIME software suite that performs all required steps to reconstruct a species-level profile. This methodology was applied to several environments, i.e., human gut and vagina and the ceca of free-range chickens, as well as whey and fresh cheese. Interestingly, the data collected confirmed a relevant role of lactobacilli present in functional and fermented foods in defining the population harbored by the human gut, while, unsurprisingly perhaps, the ceca of free-range chickens were observed to be dominated by lactobacilli characterized in birds living in natural environments. Moreover, vaginal swabs confirmed the existence of previously hypothesized community state types, while analysis of whey and fresh cheese revealed a dominant presence of single Lactobacillus species used as starters for cheese production. Furthermore, application of this ITS profiling method to a mock Lactobacillus community allowed a minimal resolution level of <0.006 ng/μl.IMPORTANCE The genus Lactobacillus is a large and ubiquitous taxon of high scientific and commercial relevance. Despite the fact that the genetic repertoire of Lactobacillus species has been extensively characterized, the ecology of this genus has been explored by metataxonomic techniques that are accurate down to the genus or phylogenetic group level only. Thus, the distribution of lactobacilli in environmental or processed food samples is relatively unexplored. The profiling protocol described here relies on the use of the internal transcribed spacer to perform an accurate classification in a target population of lactobacilli with a <0.006-ng/μl sensitivity. This approach was used to analyze five sample types collected from both human and animal host-associated microbiota, as well as from the cheese production chain. The availability of a tool for species-level profiling of lactobacilli may be highly useful for both academic research and a wide range of industrial applications.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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17
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Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata N. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host Microbe 2018; 24:133-145.e5. [PMID: 30001516 PMCID: PMC6716579 DOI: 10.1016/j.chom.2018.06.005] [Citation(s) in RCA: 640] [Impact Index Per Article: 106.7] [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: 01/23/2018] [Revised: 04/17/2018] [Accepted: 06/14/2018] [Indexed: 02/08/2023]
Abstract
The acquisition and development of the infant microbiome are key to establishing a healthy host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role in this process. However, the source and transmission routes of the infant pioneering microbes are poorly understood. To address this, we longitudinally sampled the microbiome of 25 mother-infant pairs across multiple body sites from birth up to 4 months postpartum. Strain-level metagenomic profiling showed a rapid influx of microbes at birth followed by strong selection during the first few days of life. Maternal skin and vaginal strains colonize only transiently, and the infant continues to acquire microbes from distinct maternal sources after birth. Maternal gut strains proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources. Together, these data describe the mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome.
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Affiliation(s)
- Pamela Ferretti
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy; European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Adrian Tett
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesco Asnicar
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | | | - Sabina Fedi
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Federica Armanini
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Duy Tin Truong
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Serena Manara
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesco Beghini
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Roberto Bertorelli
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Veronica De Sanctis
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | | | - Rosarita Canto
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | - Marina Cologna
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Tiziana Crifò
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | | | | | - Caterina Masè
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Daniela Postai
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Daniela Savoi
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; GenProbio srl, 43124 Parma, Italy
| | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | | | - Moran Yassour
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carmen Maria Collado
- Institute of Agrochemistry and Food Technology, National Research Council, Paterna, 46980 Valencia, Spain
| | - Omry Koren
- Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Saverio Tateo
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | | | - Anna Pedrotti
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy.
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18
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Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov. Syst Appl Microbiol 2018; 41:173-183. [PMID: 29395537 DOI: 10.1016/j.syapm.2018.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 08/09/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
Abstract
Six Bifidobacterium strains, i.e., Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B, were isolated from domestic goose (Anser domesticus), European hamster (Cricetus cricetus), European rabbit (Oryctolagus cuniculus), emperor tamarin (Saguinus imperator) and pygmy marmoset (Callithrix pygmaea). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA, ITS-, multilocus- sequences and the core genome revealed that bifidobacterial strains Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B exhibit close phylogenetic relatedness with Bifidobacterium choerinum LMG 10510, Bifidobacterium hapali DSM 100202, Bifidobacterium saguini DSM 23967 and Bifidobacterium stellenboschense DSM 23968. Genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium anseris sp. nov. (Goo31D=LMG 30189T=CCUG 70960T), Bifidobacterium criceti sp. nov. (Ham19E=LMG 30188T=CCUG 70962T), Bifidobacterium imperatoris sp. nov. (Tam1G=LMG 30297T=CCUG 70961T), Bifidobacterium italicum sp. nov. (Rab10A=LMG 30187T=CCUG 70963T), Bifidobacterium margollesii sp. nov. (Uis1B=LMG 30296T=CCUG 70959T) and Bifidobacterium parmae sp. nov. (Uis4E=LMG 30295T=CCUG 70964T) are proposed as novel Bifidobacterium species.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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19
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Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev 2017; 81:e00036-17. [PMID: 29118049 PMCID: PMC5706746 DOI: 10.1128/mmbr.00036-17] [Citation(s) in RCA: 923] [Impact Index Per Article: 131.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Eoghan Casey
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Jennifer Mahony
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Susana Delgado Palacio
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya Montes
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Juan Miguel Rodriguez
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, California, USA
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Bacteriology & Immunology, RPU Immunobiology, University of Helsinki, Helsinki, Finland
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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20
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Ferrario C, Alessandri G, Mancabelli L, Gering E, Mangifesta M, Milani C, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, Hiyashi R, Mackie R, van Sinderen D, Ventura M. Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses. Environ Microbiol 2017; 19:4771-4783. [PMID: 28967204 DOI: 10.1111/1462-2920.13943] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/22/2022]
Abstract
Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture-independent and -dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free-range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Eben Gering
- Kellogg Biological Station, Michigan State University, Department of Zoology, 3700 East Gull Lake Road, Hickory Corners, MI 49060, USA
| | | | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Maria Cristina Ossiprandi
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Medical-Veterinary Science, University of Parma, Parma, Italy
| | - Ricardo Hiyashi
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Roderick Mackie
- Carle R. Woese Institute for Genomic Biology, Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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21
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Duranti S, Mangifesta M, Lugli GA, Turroni F, Anzalone R, Milani C, Mancabelli L, Ossiprandi MC, Ventura M. Bifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2017; 67:3987-3995. [DOI: 10.1099/ijsem.0.002243] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sabrina Duranti
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Gabriele Andrea Lugli
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosaria Anzalone
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Marco Ventura
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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22
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Ferrario C, Statello R, Carnevali L, Mancabelli L, Milani C, Mangifesta M, Duranti S, Lugli GA, Jimenez B, Lodge S, Viappiani A, Alessandri G, Dall'Asta M, Del Rio D, Sgoifo A, van Sinderen D, Ventura M, Turroni F. How to Feed the Mammalian Gut Microbiota: Bacterial and Metabolic Modulation by Dietary Fibers. Front Microbiol 2017; 8:1749. [PMID: 28955319 PMCID: PMC5600934 DOI: 10.3389/fmicb.2017.01749] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [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: 05/08/2017] [Accepted: 08/28/2017] [Indexed: 12/19/2022] Open
Abstract
The composition of the gut microbiota of mammals is greatly influenced by diet. Therefore, evaluation of different food ingredients that may promote changes in the gut microbiota composition is an attractive approach to treat microbiota disturbances. In this study, three dietary fibers, such as inulin (I, 10%), resistant starch (RS, 10%), and citrus pectin (3%), were employed as supplements to normal chow diet of adult male rats for 2 weeks. Fecal microbiota composition and corresponding metabolite profiles were assessed before and after prebiotics supplementation. A general increase in the Bacteroidetes phylum was detected with a concurrent reduction in Firmicutes, in particular for I and RS experiments, while additional changes in the microbiota composition were evident at lower taxonomic levels for all the three substrates. Such modifications in the microbiota composition were correlated with changes in metabolic profiles of animals, in particular changes in acetate and succinate levels. This study represents a first attempt to modulate selectively the abundance and/or metabolic activity of various members of the gut microbiota by means of dietary fiber.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | - Rosario Statello
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | - Luca Carnevali
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | | | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | - Beatriz Jimenez
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College LondonLondon, United Kingdom
| | - Samantha Lodge
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College LondonLondon, United Kingdom
| | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | | | - Daniele Del Rio
- Department of Food and Drug, University of ParmaParma, Italy
| | - Andrea Sgoifo
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of IrelandCork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of ParmaParma, Italy
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23
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Ticinesi A, Milani C, Lauretani F, Nouvenne A, Mancabelli L, Lugli GA, Turroni F, Duranti S, Mangifesta M, Viappiani A, Ferrario C, Maggio M, Ventura M, Meschi T. Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients. Sci Rep 2017; 7:11102. [PMID: 28894183 PMCID: PMC5593887 DOI: 10.1038/s41598-017-10734-y] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/14/2017] [Indexed: 02/07/2023] Open
Abstract
Reduced biodiversity and increased representation of opportunistic pathogens are typical features of gut microbiota composition in aging. Few studies have investigated their correlation with polypharmacy, multimorbidity and frailty. To assess it, we analyzed the fecal microbiota from 76 inpatients, aged 83 ± 8. Microbiome biodiversity (Chao1 index) and relative abundance of individual bacterial taxa were determined by next-generation 16S rRNA microbial profiling. Their correlation with number of drugs, and indexes of multimorbidity and frailty were verified using multivariate linear regression models. The impact of gut microbiota biodiversity on mortality, rehospitalizations and incident sepsis was also assessed after a 2-year follow-up, using Cox regression analysis. We found a significant negative correlation between the number of drugs and Chao1 Index at multivariate analysis. The number of drugs was associated with the average relative abundance of 15 taxa. The drug classes exhibiting the strongest association with single taxa abundance were proton pump inhibitors, antidepressants and antipsychotics. Conversely, frailty and multimorbidity were not significantly associated with gut microbiota biodiversity. Very low Chao1 index was also a significant predictor of mortality, but not of rehospitalizations and sepsis, at follow-up. In aging, polypharmacy may thus represent a determinant of gut microbiota composition, with detrimental clinical consequences.
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Affiliation(s)
- Andrea Ticinesi
- Department of Medicine and Surgery, University of Parma, Parma, Italy. .,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Fulvio Lauretani
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Antonio Nouvenne
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marcello Maggio
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
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24
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Sabbatini R, Galli L, Pignata S, Lo Re G, Valcamonico F, Defferrari C, Spada M, Santini D, Masini C, Ciuffreda L, Ruggeri E, Chioni A, Livi L, Fagnani D, Bonetti A, Giustini L, Duranti S, Procopio G, Caserta C, Cartenì G. Efficacy and safety data in elderly patients (pts) with metastatic renal cell carcinoma (mRCC) included in the nivolumab expanded access program (EAP) in Italy. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx371.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Milani C, Mangifesta M, Mancabelli L, Lugli GA, James K, Duranti S, Turroni F, Ferrario C, Ossiprandi MC, van Sinderen D, Ventura M. Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life. ISME J 2017; 11:2834-2847. [PMID: 28837128 DOI: 10.1038/ismej.2017.138] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/29/2017] [Accepted: 07/14/2017] [Indexed: 02/07/2023]
Abstract
Internally transcribed spacer (ITS) rRNA profiling is a novel tool for detailed analysis of microbial populations at low taxonomic ranks. Here we exploited this approach to explore species-level biogeography of the Bifidobacterium genus across 291 adult mammals. These include humans and 13 other primates, domesticated animals, such as dogs, cats, cows, sheep, goats, horses and pigs, and 46 additional species. The collected profiles revealed the presence of 89 putative novel bifidobacterial taxa in addition to 45 previously described species. Remarkably, in contrast to what is currently known for many gut commensals, we did not observe host-specialization among bifidobacterial species but rather their widespread distribution across mammals. Moreover, ITS rRNA profiling of wild relatives of domesticated dogs, rabbits and pigs clearly indicates that domestication and close contact with humans have impacted on the composition of the fecal bifidobacterial population. These data were complemented by analysis of bifidobacterial communities in milk of eight mammalian families, showing that bifidobacteria represent prototypical early gut microbiota members which are inherited by newborns from their lactating mother. Thus this study highlights the role of bifidobacteria as pioneering gut colonizers of a wide range of mammals.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Kieran James
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Maria C Ossiprandi
- Department of Medical-Veterinary Science, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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26
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Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, Ferrario C, Modesto M, Mattarelli P, Jiří K, van Sinderen D, Ventura M. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. BMC Genomics 2017; 18:568. [PMID: 28764658 PMCID: PMC5540593 DOI: 10.1186/s12864-017-3955-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [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: 04/07/2017] [Accepted: 07/24/2017] [Indexed: 11/26/2022] Open
Abstract
Background Members of the Bifidobacteriaceae family represent both dominant microbial groups that colonize the gut of various animals, especially during the suckling stage of their life, while they also occur as pathogenic bacteria of the urogenital tract. The pan-genome of the genus Bifidobacterium has been explored in detail in recent years, though genomics of the Bifidobacteriaceae family has not yet received much attention. Here, a comparative genomic analyses of 67 Bifidobacteriaceae (sub) species including all currently recognized genera of this family, i.e., Aeriscardovia, Alloscardovia, Bifidobacterium, Bombiscardovia, Gardnerella, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia, was performed. Furthermore, in order to include a representative of each of the 67 (currently recognized) (sub) species belonging to the Bifidobacteriaceae family, we sequenced the genomes of an additional 11 species from this family, accomplishing the most extensive comparative genomic analysis performed within this family so far. Results Phylogenomics-based analyses revealed the deduced evolutionary pathway followed by each member of the Bifidobacteriaceae family, highlighting Aeriscardovia aeriphila LMG 21773 as the deepest branch in the evolutionary tree of this family. Furthermore, functional analyses based on genome content unveil connections between a given member of the family, its carbohydrate utilization abilities and its corresponding host. In this context, bifidobacterial (sub) species isolated from humans and monkeys possess the highest relative number of acquired glycosyl hydrolase-encoding genes, probably in order to enhance their metabolic ability to utilize different carbon sources consumed by the host. Conclusions Within the Bifidobacteriaceae family, genomics of the genus Bifidobacterium has been extensively investigated. In contrast, very little is known about the genomics of members of the other eight genera of this family. In this study, we decoded the genome sequences of each member of the Bifidobacteriaceae family. Thanks to subsequent comparative genomic and phylogenetic analyses, the deduced pan-genome of this family, as well as the predicted evolutionary development of each taxon belonging to this family was assessed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3955-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Killer Jiří
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic.,Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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27
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Duranti S, Lugli GA, Mancabelli L, Armanini F, Turroni F, James K, Ferretti P, Gorfer V, Ferrario C, Milani C, Mangifesta M, Anzalone R, Zolfo M, Viappiani A, Pasolli E, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Fedi S, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Soffiati M, Tateo S, Pedrotti A, Segata N, van Sinderen D, Ventura M. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome 2017; 5:66. [PMID: 28651630 PMCID: PMC5485682 DOI: 10.1186/s40168-017-0282-6] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/05/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS The composition of bifidobacterial communities of 25 mother-infant pairs was investigated based on an internal transcribed spacer (ITS) approach, combined with cultivation-mediated and genomic analyses. We identified bifidobacterial strains/communities that are shared between mothers and their corresponding newborns. Notably, genomic analyses together with growth profiling assays revealed that bifidobacterial strains that had been isolated from human milk are genetically adapted to utilize human milk glycans. In addition, we identified particular bacteriophages specific of bifidobacterial species that are common in the viromes of mother and corresponding child. CONCLUSIONS This study highlights the transmission of bifidobacterial communities from the mother to her child and implies human milk as a potential vehicle to facilitate this acquisition. Furthermore, these data represent the first example of maternal inheritance of bifidobacterial phages, also known as bifidophages in infants following a vertical transmission route.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Kieran James
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Pamela Ferretti
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Rosarita Canto
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Marina Cologna
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Tiziana Crifò
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Sabina Fedi
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | | | - Caterina Masè
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Daniela Postai
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Daniela Savoi
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Saverio Tateo
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Anna Pedrotti
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
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Abstract
It is widely accepted that metabolic disorders, such as obesity, are closely linked to lifestyle and diet. Recently, the central role played by the intestinal microbiota in human metabolism and in progression of metabolic disorders has become evident. In this context, animal studies and human trials have demonstrated that alterations of the intestinal microbiota towards enhanced energy harvest is a characteristic of the obese phenotype. Many publications, involving both animal studies and clinical trials, have reported on the successful exploitation of probiotics and prebiotics to treat obesity. However, the molecular mechanisms underlying these observed anti-obesity effects of probiotics and prebiotic therapies are still obscure. The aim of this mini-review is to discuss the intricate relationship of various factors, including diet, gut microbiota, and host genetics, that are believed to impact on the development of obesity, and to understand how modulation of the gut microbiota with dietary intervention may alleviate obesity-associated symptoms.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
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29
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Ferrario C, Lugli GA, Ossiprandi MC, Turroni F, Milani C, Duranti S, Mancabelli L, Mangifesta M, Alessandri G, van Sinderen D, Ventura M. Next generation sequencing-based multigene panel for high throughput detection of food-borne pathogens. Int J Food Microbiol 2017; 256:20-29. [PMID: 28578266 DOI: 10.1016/j.ijfoodmicro.2017.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 01/20/2023]
Abstract
Contamination of food by chemicals or pathogenic bacteria may cause particular illnesses that are linked to food consumption, commonly referred to as foodborne diseases. Bacteria are present in/on various foods products, such as fruits, vegetables and ready-to-eat products. Bacteria that cause foodborne diseases are known as foodborne pathogens (FBPs). Accurate detection methods that are able to reveal the presence of FBPs in food matrices are in constant demand, in order to ensure safe foods with a minimal risk of causing foodborne diseases. Here, a multiplex PCR-based Illumina sequencing method for FBP detection in food matrices was developed. Starting from 25 bacterial targets and 49 selected PCR primer pairs, a primer collection called foodborne pathogen - panel (FPP) consisting of 12 oligonucleotide pairs was developed. The FPP allows a more rapid and reliable identification of FBPs compared to classical cultivation methods. Furthermore, FPP permits sensitive and specific FBP detection in about two days from food sample acquisition to bioinformatics-based identification. The FPP is able to simultaneously identify eight different bacterial pathogens, i.e. Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Salmonella enterica subsp. enterica serovar enteritidis, Escherichia coli, Shigella sonnei, Staphylococcus aureus and Yersinia enterocolitica, in a given food matrix at a threshold contamination level of 101cell/g. Moreover, this novel detection method may represent an alternative and/or a complementary approach to PCR-based techniques, which are routinely used for FBP detection, and could be implemented in (parts of) the food chain as a quality check.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute, School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
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30
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Lugli GA, Milani C, Mancabelli L, Turroni F, Ferrario C, Duranti S, van Sinderen D, Ventura M. Erratum to: Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age. Microbiome 2017; 5:23. [PMID: 28212659 PMCID: PMC5314606 DOI: 10.1186/s40168-017-0243-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 05/30/2023]
Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
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31
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Lugli GA, Milani C, Mancabelli L, Turroni F, Ferrario C, Duranti S, van Sinderen D, Ventura M. Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age. Microbiome 2017; 5:5. [PMID: 28095919 PMCID: PMC5240250 DOI: 10.1186/s40168-016-0221-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/13/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. RESULTS Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species. Furthermore, in silico analyses allowed the reconstruction of the genome sequences of five ancient bacterial genomes, including apparent pathogenic ancestor strains of Clostridium perfringens and Pseudomonas veronii species present in the gut of the Tyrolean Iceman. CONCLUSIONS Genomic analyses of the reconstructed C. perfringens chromosome clearly support the occurrence of a pathogenic profile consisting of virulence genes already existing in the ancient strain, thereby reinforcing the notion of a very early speciation of this taxon towards a pathogenic phenotype. In contrast, the evolutionary development of P. veronii appears to be characterized by the acquisition of antibiotic resistance genes in more recent times as well as an evolution towards an ecological niche outside of the (human) gastrointestinal tract.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
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32
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Duranti S, Gaiani F, Mancabelli L, Milani C, Grandi A, Bolchi A, Santoni A, Lugli GA, Ferrario C, Mangifesta M, Viappiani A, Bertoni S, Vivo V, Serafini F, Barbaro MR, Fugazza A, Barbara G, Gioiosa L, Palanza P, Cantoni AM, de'Angelis GL, Barocelli E, de'Angelis N, van Sinderen D, Ventura M, Turroni F. Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers. FEMS Microbiol Ecol 2016; 92:fiw191. [PMID: 27604252 DOI: 10.1093/femsec-fiw191] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 09/21/2023] Open
Abstract
Ulcerative colitis (UC) is associated with a substantial alteration of specific gut commensals, some of which may be involved in microbiota-mediated protection. In this study, microbiota cataloging of UC patients by 16S rRNA microbial profiling revealed a marked reduction of bifidobacteria, in particular the Bifidobacterium bifidum species, thus suggesting that this taxon plays a biological role in the aetiology of UC. We investigated this further through an in vivo trial by testing the effects of oral treatment with B. bifidum PRL2010 in a wild-type murine colitis model. TNBS-treated mice receiving 10(9) cells of B. bifidum PRL2010 showed a marked reduction of all colitis-associated histological indices as well as maintenance of mucosal integrity as it was shown by the increase in the expression of many tight junction-encoding genes. The protective role of B. bifidum PRL2010, as well as its sortase-dependent pili, appears to be established through the induction of an innate immune response of the host. These results highlight the importance of B. bifidum as a microbial biomarker for UC, revealing its role in protection against experimentally induced colitis.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Federica Gaiani
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Andrea Grandi
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Angelo Bolchi
- Laboratory of Molecular Biology, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Andrea Santoni
- Laboratory of Molecular Biology, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | | | - Alice Viappiani
- GenProbio srl, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Simona Bertoni
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Valentina Vivo
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Fausta Serafini
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Maria Raffaella Barbaro
- Department of Medical and Surgical Sciences and Center for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Alessandro Fugazza
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences and Center for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Laura Gioiosa
- Department of Neurosciences, University of Parma, 43124 Parma, Italy
| | - Paola Palanza
- Department of Neurosciences, University of Parma, 43124 Parma, Italy
| | - Anna Maria Cantoni
- Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Gian Luigi de'Angelis
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Elisabetta Barocelli
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Nicola de'Angelis
- Unit of Digestive, Hepato-Pancreato-Biliary Surgery and Liver Transplantation, Henri Mondor Hospital, 51 Avenue du Maréchal de Lattre de Tassigny, Créteil 94010, France
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
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Milani C, Ferrario C, Turroni F, Duranti S, Mangifesta M, van Sinderen D, Ventura M. The human gut microbiota and its interactive connections to diet. J Hum Nutr Diet 2016; 29:539-46. [PMID: 27161433 DOI: 10.1111/jhn.12371] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [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: 12/22/2022]
Abstract
The microbiota of the gastrointestinal tract plays an important role in human health. In addition to their metabolic interactions with dietary constituents, gut bacteria may also be involved in more complex host interactions, such as modulation of the immune system. Furthermore, the composition of the gut microbiota may be important in reducing the risk of contracting particular gut infections. Changes in the microbiota during an individual's lifespan are accompanied by modifications in multiple health parameters, and such observations have prompted intense scientific efforts aiming to understand the complex interactions between the microbiota and its human host, as well as how this may be influenced by diet.
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Affiliation(s)
- C Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - C Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - F Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - S Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - D van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - M Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
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Duranti S, Gaiani F, Mancabelli L, Milani C, Grandi A, Bolchi A, Santoni A, Lugli GA, Ferrario C, Mangifesta M, Viappiani A, Bertoni S, Vivo V, Serafini F, Barbaro MR, Fugazza A, Barbara G, Gioiosa L, Palanza P, Cantoni AM, de'Angelis GL, Barocelli E, de'Angelis N, van Sinderen D, Ventura M, Turroni F. Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers. FEMS Microbiol Ecol 2016; 92:fiw191. [PMID: 27604252 DOI: 10.1093/femsec/fiw191] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Ulcerative colitis (UC) is associated with a substantial alteration of specific gut commensals, some of which may be involved in microbiota-mediated protection. In this study, microbiota cataloging of UC patients by 16S rRNA microbial profiling revealed a marked reduction of bifidobacteria, in particular the Bifidobacterium bifidum species, thus suggesting that this taxon plays a biological role in the aetiology of UC. We investigated this further through an in vivo trial by testing the effects of oral treatment with B. bifidum PRL2010 in a wild-type murine colitis model. TNBS-treated mice receiving 10(9) cells of B. bifidum PRL2010 showed a marked reduction of all colitis-associated histological indices as well as maintenance of mucosal integrity as it was shown by the increase in the expression of many tight junction-encoding genes. The protective role of B. bifidum PRL2010, as well as its sortase-dependent pili, appears to be established through the induction of an innate immune response of the host. These results highlight the importance of B. bifidum as a microbial biomarker for UC, revealing its role in protection against experimentally induced colitis.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Federica Gaiani
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Andrea Grandi
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Angelo Bolchi
- Laboratory of Molecular Biology, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Andrea Santoni
- Laboratory of Molecular Biology, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | | | - Alice Viappiani
- GenProbio srl, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Simona Bertoni
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Valentina Vivo
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Fausta Serafini
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Maria Raffaella Barbaro
- Department of Medical and Surgical Sciences and Center for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Alessandro Fugazza
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences and Center for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Laura Gioiosa
- Department of Neurosciences, University of Parma, 43124 Parma, Italy
| | - Paola Palanza
- Department of Neurosciences, University of Parma, 43124 Parma, Italy
| | - Anna Maria Cantoni
- Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Gian Luigi de'Angelis
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Elisabetta Barocelli
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Nicola de'Angelis
- Unit of Digestive, Hepato-Pancreato-Biliary Surgery and Liver Transplantation, Henri Mondor Hospital, 51 Avenue du Maréchal de Lattre de Tassigny, Créteil 94010, France
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
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Magarotto R, Micheloni B, Lunardi G, Duranti S, Inno A, Valerio M, Bustaggi M, Castagna S, Dalle Vedove A, Duma M, Mignolli L, Oliosi L, Platano M, Residori G, Righetti P, Ronconi A, Unguru C, Zivelonghi S, Gori S. Systematic pain evaluation in hospitalized cancer patients in a Medical Oncology Unit: feasibility and utility of pain monitoring by Numeric Rating Scale in cancer pain management. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw344.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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36
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Mancabelli L, Ferrario C, Milani C, Mangifesta M, Turroni F, Duranti S, Lugli GA, Viappiani A, Ossiprandi MC, van Sinderen D, Ventura M. Insights into the biodiversity of the gut microbiota of broiler chickens. Environ Microbiol 2016; 18:4727-4738. [PMID: 27129897 DOI: 10.1111/1462-2920.13363] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/11/2016] [Accepted: 03/17/2016] [Indexed: 02/06/2023]
Abstract
The gastrointestinal tract of poultry is densely populated with microorganisms, which are presumed to interact with the host and ingested feed. Comparison of the gut microbiota of chickens used for large-scale commercial production (Broiler Chicken, BC) and those grown in semi-wild conditions (Free-Range Chicken, FRC) revealed that at phylum level Firmicutes was the dominant phylum of the gut community in BC, while the gut microbiota of FRC contained higher levels of Bacteroidetes and Proteobacteria. Such differences may be due to the diet and/or the intensive use of antibiotics in BC. Indeed, analysis of the resistome of the cecal microbiomes showed a marked richness in BC datasets, with a modulation of the cecal microbiota toward antibiotic resistant bacteria. Functional characterization of the microbiome of FRC samples revealed an increase in gene pathways involved in degradation of complex carbohydrates. Furthermore, in silico analyses of the microbiomes of FRC and BC revealed a higher presence in genes involved in formate production in BC samples. Notably, compared to the BC microbiomes the FRC microbiomes were shown to contain a higher abundance of genes involved in the pathway for acetate production.
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Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | | | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
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Milani C, Ticinesi A, Gerritsen J, Nouvenne A, Lugli GA, Mancabelli L, Turroni F, Duranti S, Mangifesta M, Viappiani A, Ferrario C, Maggio M, Lauretani F, De Vos W, van Sinderen D, Meschi T, Ventura M. Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study. Sci Rep 2016; 6:25945. [PMID: 27166072 PMCID: PMC4863157 DOI: 10.1038/srep25945] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [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: 03/18/2016] [Accepted: 04/22/2016] [Indexed: 12/17/2022] Open
Abstract
The gut microbiota composition of elderly hospitalized patients with Clostridium difficile infection (CDI) exposed to previous antibiotic treatment is still poorly investigated. The aim of this study was to compare the microbiota composition by means of 16S rRNA microbial profiling among three groups of hospitalized elderly patients (age ≥ 65) under standard diet including 25 CDI-positive (CDI group), 29 CDI-negative exposed to antibiotic treatment (AB+ group) and 30 CDI-negative subjects not on antibiotic treatment (AB− group). The functional properties of the gut microbiomes of CDI-positive vs CDI-negative subjects were also assessed by shotgun metagenomics. A significantly lower microbial diversity was detected in CDI samples, whose microbiomes clustered separately from CDI-negative specimens. CDI was associated with a significant under-representation of gut commensals with putative protective functionalities, including Bacteroides, Alistipes, Lachnospira and Barnesiella, and over-representation of opportunistic pathogens. These findings were confirmed by functional shotgun metagenomics analyses, including an in-depth profiling of the Peptostreptococcaceae family. In CDI-negative patients, antibiotic treatment was associated with significant depletion of few commensals like Alistipes, but not with a reduction in species richness. A better understanding of the correlations between CDI and the microbiota in high-risk elderly subjects may contribute to identify therapeutic targets for CDI.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Andrea Ticinesi
- Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.,Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Jacoline Gerritsen
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Antonio Nouvenne
- Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.,Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Marcello Maggio
- Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy.,Geriatric Unit, Parma University Hospital, Parma, Italy
| | - Fulvio Lauretani
- Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy
| | - Willem De Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Tiziana Meschi
- Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.,Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
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Lugli GA, Milani C, Turroni F, Tremblay D, Ferrario C, Mancabelli L, Duranti S, Ward DV, Ossiprandi MC, Moineau S, van Sinderen D, Ventura M. Prophages of the genusBifidobacteriumas modulating agents of the infant gut microbiota. Environ Microbiol 2016; 18:2196-213. [DOI: 10.1111/1462-2920.13154] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics; Department of Life Sciences; University of Parma; Parma Italy
| | - Christian Milani
- Laboratory of Probiogenomics; Department of Life Sciences; University of Parma; Parma Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics; Department of Life Sciences; University of Parma; Parma Italy
| | - Denise Tremblay
- Département de Biochimie, Microbiologie et Bio-Informatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire; Université Laval; Québec City Québec Canada
| | - Chiara Ferrario
- Laboratory of Probiogenomics; Department of Life Sciences; University of Parma; Parma Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics; Department of Life Sciences; University of Parma; Parma Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics; Department of Life Sciences; University of Parma; Parma Italy
| | - Doyle V. Ward
- Broad Institute of MIT and Harvard; Cambridge MA USA
| | | | - Sylvain Moineau
- Département de Biochimie, Microbiologie et Bio-Informatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire; Université Laval; Québec City Québec Canada
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology; National University of Ireland; Cork Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics; Department of Life Sciences; University of Parma; Parma Italy
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Ferrario C, Duranti S, Milani C, Mancabelli L, Lugli GA, Turroni F, Mangifesta M, Viappiani A, Ossiprandi MC, van Sinderen D, Ventura M. Exploring Amino Acid Auxotrophy in Bifidobacterium bifidum PRL2010. Front Microbiol 2015; 6:1331. [PMID: 26635786 PMCID: PMC4656816 DOI: 10.3389/fmicb.2015.01331] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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: 09/17/2015] [Accepted: 11/12/2015] [Indexed: 01/01/2023] Open
Abstract
The acquisition and assimilation strategies followed by members of the infant gut microbiota to retrieve nitrogen from the gut lumen are still largely unknown. In particular, no information on these metabolic processes is available regarding bifidobacteria, which are among the first microbial colonizers of the human intestine. Here, evaluation of amino acid auxotrophy and prototrophy of Bifidobacterium bifidum, with particular emphasis on B. bifidum strain PRL2010 (LMG S-28692), revealed a putative auxotrophy for cysteine. In addition, we hypothesized that cysteine plays a role in the oxidative stress response in B. bifidum. The use of glutathione as an alternative reduced sulfur compound did not alleviate cysteine auxotrophy of this strain, though it was shown to stimulate expression of the genes involved in cysteine biosynthesis, reminiscent of oxidative stress response. When PRL2010 was grown on a medium containing complex substrates, such as whey proteins or casein hydrolysate, we noticed a distinct growth-promoting effect of these compounds. Transcriptional analysis involving B. bifidum PRL2010 cultivated on whey proteins or casein hydrolysate revealed that the biosynthetic pathways for cysteine and methionine are modulated by the presence of casein hydrolysate. Such findings support the notion that certain complex substrates may act as potential prebiotics for bifidobacteria in their ecological niche.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | | | | | - Maria C Ossiprandi
- Department of Medical-Veterinary Science, University of Parma Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, University College Cork, National University of Ireland Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
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Bogina G, Munari E, Marconi M, Bortesi L, Turazza M, Cassandrini P, Cirillo M, Duranti S, Inno A, Magarotto R, Nicodemo M, Picece V, Lunardi G, Gori S. Neuroendocrine differentiation in breast carcinoma: clinicopathological features and outcome. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv348.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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41
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Lunardi G, Magarotto R, Inno A, Cassandrini P, Cirillo M, Duranti S, Nicodemo M, Picece V, Turazza M, Marchetti F, Micheloni B, Valerio M, Zenari L, Gori S. Association between patient reported outcomes and vibratory perception threshold test for measuring neurotoxicity in patients with chemotherapy induced peripheral neuropathy. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv348.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Duranti S, Inno A, Rossi V, Turazza M, Fiorio E, Fabi A, Bisagni G, Foglietta J, Santini D, Pavese I, Zambelli A, Vici P, Leonardi V, Barni S, Saracchini S, Bogina G, Lunardi G, Marchetti F, Montemurro F, Gori S. Clinical and pathological factors predicting long-term disease control with lapatinib and capecitabine for patients with HER2 positive metastastic breast cancer: results from a multicenter retrospective study. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv336.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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43
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Inno A, Lunardi G, Turazza M, Pasetto S, Severi F, Gorgoni G, Bogina G, Bortesi L, Russo A, Alongi F, Fiorentino A, Duranti S, Massocco A, Marchetti F, Valerio M, Salgarello M, Gori S. FDG-PET/CT as a predictor of pathological complete response (pCR) in breast cancer (BC) patients (pts) treated with neoadjuvant chemotherapy (NAC): a single center retrospective study. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv336.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Briner AE, Lugli GA, Milani C, Duranti S, Turroni F, Gueimonde M, Margolles A, van Sinderen D, Ventura M, Barrangou R. Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium. PLoS One 2015; 10:e0133661. [PMID: 26230606 PMCID: PMC4521832 DOI: 10.1371/journal.pone.0133661] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [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: 04/16/2015] [Accepted: 06/30/2015] [Indexed: 12/11/2022] Open
Abstract
CRISPR-Cas systems constitute adaptive immune systems for antiviral defense in bacteria. We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools.
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Affiliation(s)
- Alexandra E. Briner
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Francesca Turroni
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland
| | - Miguel Gueimonde
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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Duranti S, Milani C, Lugli GA, Turroni F, Mancabelli L, Sanchez B, Ferrario C, Viappiani A, Mangifesta M, Mancino W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum. Environ Microbiol 2015; 17:2515-31. [PMID: 25523018 DOI: 10.1111/1462-2920.12743] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/25/2014] [Accepted: 12/03/2014] [Indexed: 11/27/2022]
Abstract
Bifidobacteria are bacterial gut commensals of mammals, birds and social insects that are perceived to influence the metabolism/physiology of their host. In this context, members of the Bifidobacterium bifidum species are believed to significantly contribute to the overall microbiota of the human gut at infant stage. However, the molecular reasons for their adaptation to this environment are poorly understood. In this study, we analysed the pan-genome of B. bifidum species by decoding genomes of 15 B. bifidum strains, which highlighted the existence of a conserved gene uniquely present in this bifidobacterial taxon, underscoring a nutrient acquisition strategy that targets host-derived glycans, such as those present in mucin. Growth experiments and corresponding transcriptomic analyses confirmed the in silico data and supported these intriguing and unique host glycan-specific saccharolytic features. The ubiquity of the genetic features of B. bifidum for the breakdown of host glycans was confirmed by interrogating metagenomic datasets, thereby supporting the notion that metabolic access to host-derived glycans is a potent evolutionary force that has shaped B. bifidum genomes and consequently the ecology of the infant intestinal microbiota.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Francesca Turroni
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Borja Sanchez
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Alice Viappiani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Walter Mancino
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
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Ferrario C, Milani C, Mancabelli L, Lugli GA, Turroni F, Duranti S, Mangifesta M, Viappiani A, Sinderen DV, Ventura M. A genome-based identification approach for members of the genus Bifidobacterium. FEMS Microbiol Ecol 2015; 91:fiv009. [PMID: 25764568 DOI: 10.1093/femsec/fiv009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
During recent years, the significant and increasing interest in novel bifidobacterial strains with health-promoting characteristics has catalyzed the development of methods for efficient and reliable identification of Bifidobacterium strains at (sub) species level. We developed an assay based on recently acquired bifidobacterial genomic data and involving 98 primer pairs, called the Bifidobacterium-ampliseq panel. This panel includes multiplex PCR primers that target both core and variable genes of the pangenome of this genus. Our results demonstrate that the employment of the Bifidobacterium-ampliseq panel allows rapid and specific identification of the so far recognized 48 (sub)species harboring the Bifidobacterium genus, and thus represents a cost- and time-effective bifidobacterial screening methodology.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | - Francesca Turroni
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
| | | | | | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy
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Milani C, Lugli GA, Turroni F, Mancabelli L, Duranti S, Viappiani A, Mangifesta M, Segata N, van Sinderen D, Ventura M. Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol. FEMS Microbiol Ecol 2014; 90:493-503. [PMID: 25117972 DOI: 10.1111/1574-6941.12410] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [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: 07/01/2014] [Revised: 07/29/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022] Open
Abstract
The precise appraisal of the composition of the human gut microbiota still represents a challenging task. The advent of next generation sequencing approaches has opened new ways to dissect the microbial biodiversity of this ecosystem through the use of 16S rRNA gene-based microbiota analysis approaches. However, the detailed representation of specific groups or members of the human gut microbiota, for example Bifidobacteria, may be skewed by the PCR primers employed in the amplification step of the 16S rRNA gene-based microbial profiling pipeline and by the limited resolution of the 16S rRNA gene variable regions. Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hypervariable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus. In addition, we present an optimized protocol for ITS-based profiling utilizing qiime software, allowing accurate and subspecies-specific compositional reconstruction of the bifidobacterial community in the human gut.
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Affiliation(s)
- Christian Milani
- Department of Life Sciences, Laboratory of Probiogenomics, University of Parma, Parma, Italy
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Turroni F, Duranti S, Bottacini F, Guglielmetti S, Van Sinderen D, Ventura M. Bifidobacterium bifidum as an example of a specialized human gut commensal. Front Microbiol 2014; 5:437. [PMID: 25191315 PMCID: PMC4140077 DOI: 10.3389/fmicb.2014.00437] [Citation(s) in RCA: 75] [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] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/01/2014] [Indexed: 12/12/2022] Open
Abstract
Bifidobacteria are considered dominant and for this reason key members of the human gut microbiota, particularly during the first one to two years following birth. A substantial proportion of the bifidobacterial population in the intestine of infants belong to the Bifidobacterium bifidum taxon, whose members have been shown to display remarkable physiological and genetic features involving adhesion to epithelia, as well as utilization of host-derived glycans. Here, we reviewed the current knowledge on the genetic features and associated adaptations of B. bifidum to the human gut.
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Affiliation(s)
- Francesca Turroni
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland Cork, Ireland
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Francesca Bottacini
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland Cork, Ireland
| | - Simone Guglielmetti
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
| | - Douwe Van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
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Bottacini F, O'Connell Motherway M, Kuczynski J, O'Connell KJ, Serafini F, Duranti S, Milani C, Turroni F, Lugli GA, Zomer A, Zhurina D, Riedel C, Ventura M, van Sinderen D. Comparative genomics of the Bifidobacterium breve taxon. BMC Genomics 2014; 15:170. [PMID: 24581150 PMCID: PMC4007704 DOI: 10.1186/1471-2164-15-170] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [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: 09/16/2013] [Accepted: 02/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina. RESULTS In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol. CONCLUSIONS Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Marco Ventura
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.
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50
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Milani C, Hevia A, Foroni E, Duranti S, Turroni F, Lugli GA, Sanchez B, Martín R, Gueimonde M, van Sinderen D, Margolles A, Ventura M. Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One 2013; 8:e68739. [PMID: 23869230 PMCID: PMC3711900 DOI: 10.1371/journal.pone.0068739] [Citation(s) in RCA: 226] [Impact Index Per Article: 20.5] [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: 01/02/2013] [Accepted: 06/03/2013] [Indexed: 01/29/2023] Open
Abstract
Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Arancha Hevia
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA – CSIC, Villaviciosa, Asturias, Spain
| | - Elena Foroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Francesca Turroni
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Borja Sanchez
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA – CSIC, Villaviciosa, Asturias, Spain
| | - Rebeca Martín
- INRA, UMR 1319 MICALIS-Microbiologie de l’Alimentation au Service de la Santé humaine, Pôle Ecosystèmes: Interactions des bactéries commensales et probiotiques avec l’hôte, Domaine de Vilvert, Bât 440 R-2 78352, Jouy en Josas, France
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA – CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA – CSIC, Villaviciosa, Asturias, Spain
- * E-mail: (AM); (MV)
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
- * E-mail: (AM); (MV)
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