Gabriele Andrea Lugli

University of Parma

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Co-Authors

Marco Ventura

University of Parma

187

Christian Milani

University of Parma

136

Douwe van Sinderen

University College Cork

134

Francesca Turroni

University of Parma

131

Leonardo Mancabelli

University of Parma

121

Alice Viappiani

University of Parma

Sabrina Duranti

University of Parma

Giulia Alessandri

University of Siena

Chiara Tarracchini

University of Parma

Federico Fontana

University of Parma

Cooperative Institutions

University of Parma

University College Cork

APC Microbiome Institute

University of Milan

National University of Ireland

Istituti di Ricovero e Cura a Carattere Scientifico

Politecnico di Milano

Industriale Chimica (Italy)

Consejo Superior de Investigaciones Científicas

University of Trento

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5627119 Catalytic system and process for the production of poydiolefins

Journal of Molecular Catalysis A Chemical (1997)

Paolo Biagini Gabriele Andrea Lugli F. Garbassi Piero Andreussi

10.1016/s1381-1169(98)80083-6

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Citations (2)

High 1,4‐cis‐polybutadiene by uranium catalysts, 1. Tris(π‐allyl)uranium halide catalysts

Die Makromolekulare Chemie (1974)

Gabriele Andrea Lugli A. Mazzei Sergio Poggio

Abstract The synthesis of tris(π‐allyl)uranium halides ( 2a–c ) and their behaviour in the stereospecific polymerization of butadiene are reported. Independently from the nature of the halogen bound to uranium, very high 1,4‐ cis ‐polymer with a fairly good yield is obtained. The catalytic activity of allyluranium derivatives is very much improved when a Lewis acid is added as a co‐catalyst. It is characteristic of the polymer to show a cis ‐content up to 99% and an exceptionally high chain regularity at least for long chain sequencies.

Stereospecificity

10.1002/macp.1974.021750706

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Citations (51)

Brussowvirus SW13 Requires a Cell Surface-Associated Polysaccharide To Recognize Its Streptococcus thermophilus Host

Applied and Environmental Microbiology (2022)

Katherine Lavelle Irina Sadovskaya Evgeny Vinogradov Philip Kelleher Gabriele Andrea Lugli

Four bacteriophage-insensitive mutants (BIMs) of the dairy starter bacterium Streptococcus thermophilus UCCSt50 were isolated following challenge with Brussowvirus SW13. The BIMs displayed an altered sedimentation phenotype. Whole-genome sequencing and comparative genomic analysis of the BIMs uncovered mutations within a family 2 glycosyltransferase-encoding gene (orf06955UCCSt50) located within the variable region of the cell wall-associated rhamnose-glucose polymer (Rgp) biosynthesis locus (designated the rgp gene cluster here). Complementation of a representative BIM, S. thermophilus B1, with native orf06955UCCSt50 restored phage sensitivity comparable to that of the parent strain. Detailed bioinformatic analysis of the gene product of orf06955UCCSt50 identified it as a functional homolog of the Lactococcus lactis polysaccharide pellicle (PSP) initiator WpsA. Biochemical analysis of cell wall fractions of strains UCCSt50 and B1 determined that mutations within orf06955UCCSt50 result in the loss of the side chain decoration from the Rgp backbone structure. Furthermore, it was demonstrated that the intact Rgp structure incorporating the side chain structure is essential for phage binding through fluorescence labeling studies. Overall, this study confirms that the rgp gene cluster of S. thermophilus encodes the biosynthetic machinery for a cell surface-associated polysaccharide that is essential for binding and subsequent infection by Brussowviruses, thus enhancing our understanding of S. thermophilus phage-host dynamics. IMPORTANCE Streptococcus thermophilus is an important starter culture bacterium in global dairy fermentation processes, where it is used for the production of various cheeses and yogurt. Bacteriophage predation of the species can result in substandard product quality and, in rare cases, complete fermentation collapse. To mitigate these risks, it is necessary to understand the phage-host interaction process, which commences with the recognition of, and adsorption to, specific host-encoded cell surface receptors by bacteriophage(s). As new groups of S. thermophilus phages are being discovered, the importance of underpinning the genomic elements that specify the surface receptor(s) is apparent. Our research identifies a single gene that is critical for the biosynthesis of a saccharidic moiety required for phage adsorption to its S. thermophilus host. The acquired knowledge provides novel insights into phage-host interactions for this economically important starter species.

Gene cluster

10.1128/aem.01723-21

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Citations (9)

Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi‐omics approach

Environmental Microbiology (2022)

Federico Fontana Giulia Alessandri Chiara Tarracchini Massimiliano G. Bianchi Sonia Mirjam Rizzo

Abstract The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi‐omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species‐representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross‐laboratory reproducibility and relevance of research findings.

Identification

Strain (injury)

10.1111/1462-2920.16205

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Citations (10)

Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

Microorganisms (2020)

Gabriele Andrea Lugli Chiara Tarracchini Giulia Alessandri Christian Milani Leonardo Mancabelli

Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR–Cas and restriction–modification systems may be responsible for the high genome synteny identified among members of this taxon.

Synteny

10.3390/microorganisms8111720

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Citations (21)

Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection

Microbiology Spectrum (2023)

Leonardo Mancabelli Giuseppe Taurino Andrea Ticinesi Tecla Ciociola Federica Vacondio

The human organism is inhabited by trillions of microorganisms, known as microbiota, which are considered to exploit a pivotal role in the regulation of host health and immunity. Recent investigations have suggested a relationship between the composition of the human microbiota and COVID-19 infection, highlighting a possible role of bacterial communities in the modulation of the disease severity. In this study, we performed a shotgun metagenomics analysis to explore and compare the nasopharyngeal microbiota of 38 hospitalized Italian patients with and without COVID-19 infection during the third and fourth pandemic waves. In detail, the metagenomic analysis combined with specific correlation analyses suggested a positive association of several microbial species, such as S. parasanguinis and P. melaninogenica, with the severity of COVID-19 infection. Furthermore, the comparison of the microbiota composition between the nasopharyngeal and their respective fecal samples highlighted an association between these different compartments represented by a sharing of several bacterial species. Additionally, lipidomic and deep-shotgun functional analyses of the fecal samples suggested a metabolic impact of the microbiome on the host's immune response, indicating the presence of key metabolic compounds in COVID-19 patients, such as lipid oxidation end products, potentially related to the inflammatory state. Conversely, the patients without COVID-19 displayed enzymatic patterns associated with the biosynthesis and degradation of specific compounds like lysine (synthesis) and phenylalanine (degradation) that could positively impact disease severity and contribute to modulating COVID-19 infection. IMPORTANCE The human microbiota is reported to play a major role in the regulation of host health and immunity, suggesting a possible impact on the severity of COVID-19 disease. This preliminary study investigated the possible correlation between nasopharyngeal microbiota and COVID-19 infection. In detail, the analysis of the nasopharyngeal microbiota of hospitalized Italian patients with and without COVID-19 infection suggested a positive association of several microbial species with the severity of the disease and highlighted a sharing of several bacteria species with the respective fecal samples. Moreover, the metabolic analyses suggested a possible impact of the microbiome on the host's immune response and the disease severity.

Human Microbiome Project

10.1128/spectrum.02194-23

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Citations (3)

Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium

PLoS ONE (2015)

Alexandra E. Briner Gabriele Andrea Lugli Christian Milani Sabrina Duranti Francesca Turroni

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.

Prophage

Trans-activating crRNA

10.1371/journal.pone.0133661

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Citations (76)

The Genome Sequence of Bifidobacterium moukalabense DSM 27321 Highlights the Close Phylogenetic Relatedness with the Bifidobacterium dentium Taxon

Genome Announcements (2014)

Gabriele Andrea Lugli Sabrina Duranti Christian Milani Francesca Turroni Alice Viappiani

Bifidobacterium moukalabense DSM 27321 is the reference strain for a recently described new bifidobacterial species that has been isolated from a wild west lowland gorilla. Here, we report the whole-genome sequence of DSM 27321, which supports very close phylogenetic relatedness with members of the Bifidobacterium adolescentis phylogenetic group and, in particular, the Bifidobacterium dentium taxon.

Strain (injury)

Phylogenetic relationship

Phylogenetic nomenclature

10.1128/genomea.00048-14

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Citations (7)

Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota

Frontiers in Microbiology (2024)

Chiara Argentini Gabriele Andrea Lugli Chiara Tarracchini Federico Fontana Leonardo Mancabelli

Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.

Bifidobacterium breve

Human gastrointestinal tract

Commensalism

Gut microbiome

Strain (injury)

10.3389/fmicb.2024.1349391

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Citations (4)

The Probiotic Identity Card: A Novel “Probiogenomics” Approach to Investigate Probiotic Supplements

Frontiers in Microbiology (2022)

Gabriele Andrea Lugli Giulia Longhi Giulia Alessandri Leonardo Mancabelli Chiara Tarracchini

Probiotic bacteria are widely administered as dietary supplements and incorporated as active ingredients in a variety of functional foods due to their purported health-promoting features. Currently available probiotic products may have issues with regards to their formulation, such as insufficient levels of viable probiotic bacteria, complete lack of probiotic strains that are stated to be present in the product, and the presence of microbial contaminants. To avoid the distribution of such unsuitable or misleading products, we propose here a novel approach named Probiotic Identity Card (PIC), involving a combination of shotgun metagenomic sequencing and bacterial cell enumeration by flow cytometry. PIC was tested on 12 commercial probiotic supplements revealing several inconsistencies in the formulation of five such products based on their stated microbial composition and viability.

Health Benefits

10.3389/fmicb.2021.790881

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Citations (18)