Publications by authors named "Marco Ventura"

286 Publications

Creating an atlas to visualize the biodiversity of the mammalian gut microbiota.

Curr Opin Biotechnol 2021 Jul 16;73:28-33. Epub 2021 Jul 16.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy; Microbiome Research Hub, University of Parma, Parma, Italy. Electronic address:

Given the fundamental role played by the intestinal microbial community in influencing host health, it is not surprising that recent decades have been marked by increased efforts to determine the taxonomic composition of the human gut microbiota and its associated functions. Despite their generally accepted importance, these large-scale human-centered studies prevent an exhaustive overview of those mechanisms and factors that contribute to the mammalian gut microbiota assembly. However, Next-Generation Sequencing techniques and associated bioinformatic tools provide an exciting opportunity to rapidly expand our knowledge on the intestinal microbial communities associated with members of the Mammalia class. These non-human-focused studies established that dietary, host phylogeny, host physiology and anthropogenic influences represent the main factors driving the selection of a specific gut microbial consortium in mammals. The current review is aimed at providing a comprehensive overview on the impact that the above-mentioned factors exert on the assembly of the mammalian gut microbiota.
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http://dx.doi.org/10.1016/j.copbio.2021.06.028DOI Listing
July 2021

Exopolysaccharide Blocks Dendritic Cell Maturation and Activation of CD4 T Cells.

Front Microbiol 2021 16;12:653587. Epub 2021 Jun 16.

APC Microbiome Ireland, University College Cork, Cork, Ireland.

Exopolysaccharide (EPS) is a bacterial extracellular carbohydrate moiety which has been associated with immunomodulatory activity and host protective effects of several gut commensal bacteria. are early colonizers of the human gastrointestinal tract (GIT) but the role of EPS in mediating their effects on the host has not been investigated for many strains. Here, we characterized EPS production by a panel of human isolates and investigated the effect of EPS status on host immune responses using human and murine cell culture-based assay systems. We report that EPS production is heterogenous across strains and that immune responses in human THP-1 monocytes are strain-specific, but not EPS status-specific. Using wild type and isogenic EPS deficient mutants of strains UCC2003 and JCM7017 we show that EPS had strain-specific divergent effects on cytokine responses from murine bone marrow derived macrophages (BMDMs) and dendritic cells (BMDCs). The UCC2003 EPS negative (EPS) strain increased expression of cytokine genes (, and ) relative to untreated BMDCs and BMDCs treated with wild type strain. UCC2003 and JCM7017 EPS strains increased expression of dendritic cell (DC) activation and maturation marker genes (, and ) relative to untreated BMDCs. Consistent with this, BMDCs co-cultured with UCC2003 and JCM7017 EPS strains engineered to express OVA antigen activated OVA-specific OT-II CD4 T-cells in a co-culture antigen-presentation assay while EPS proficient strains did not. Collectively, these data indicate that EPS proficient strains use EPS to prevent maturation of DCs and activation of antigen specific CD4 T cells responses to . This study identifies a new immunomodulatory role for EPS and suggests it may be important for immune evasion of adaptive immunity by and contribute to host-microbe mutualism.
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http://dx.doi.org/10.3389/fmicb.2021.653587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8242212PMC
June 2021

Phylogenomic Reconstruction and Metabolic Potential of the Genus .

Microorganisms 2021 Jun 19;9(6). Epub 2021 Jun 19.

Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.

Bacteria belonging to the genus are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of LMG 26462 and the presence of unclassified strains. Here, we determined the genome sequence of LMG 26462 and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus . Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified strains belong to valid species or are putative new species. Since some members of the genus can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only LMG 26462 contains a symbiosis island implicated in nodulation and nitrogen fixation.
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http://dx.doi.org/10.3390/microorganisms9061332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8235418PMC
June 2021

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses.

mSystems 2021 Jun 29:e0058321. Epub 2021 Jun 29.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parmagrid.10383.39, Parma, Italy.

The use of bioinformatic tools for read-based taxonomic and functional analyses of metagenomic data sets, including their assembly and management, is rather fragmentary due to the absence of an accepted gold standard. Moreover, most currently available software tools need input of millions of reads and rely on approximations in data analysis in order to reduce computing times. These issues result in suboptimal results in terms of accuracy, sensitivity, and specificity when used either for the reconstruction of taxonomic or functional profiles through read analysis or analysis of genomes reconstructed by metagenomic assembly. Moreover, the recent introduction of novel DNA sequencing technologies that generate long reads, such as Nanopore and PacBio, represent a valuable data resource that still suffers from a lack of dedicated tools to perform integrated hybrid analysis alongside short read data. In order to overcome these limitations, here we describe a comprehensive bioinformatic platform, METAnnotatorX2, aimed at providing an optimized user-friendly resource which maximizes output quality, while also allowing user-specific adaptation of the pipeline and straightforward integrated analysis of both short and long read data. To further improve performance quality and accuracy of taxonomic assignment of reads and contigs, custom preprocessed and taxonomically revised genomic databases for viruses, prokaryotes, and various eukaryotes were developed. The performance of METAnnotatorX2 was tested by analysis of artificial data sets encompassing viral, archaeal, bacterial, and eukaryotic (fungal) sequence reads that simulate different biological matrices. Moreover, real biological samples were employed to validate results. We developed a novel tool, i.e., METAnnotatorX2, that includes a number of new advanced features for analysis of deep and shallow metagenomic data sets and is accompanied by (regularly updated) customized databases for archaea, bacteria, fungi, protists, and viruses. Both software and databases were developed so as to maximize sensitivity and specificity while including support for shallow metagenomic data sets. Through extensive tests performed on Illumina and Nanopore artificial data sets, we demonstrated the high performance of the software to not only extract taxonomic and functional information from sequence reads but also to assemble and process genomes from metagenomic data. The robustness of these functionalities was validated using "real-life" data sets obtained from Illumina and Nanopore sequencing of biological samples. Furthermore, the performance of METAnnotatorX2 was compared to other available software tools for analysis of shotgun metagenomics data.
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http://dx.doi.org/10.1128/mSystems.00583-21DOI Listing
June 2021

Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire.

Environ Microbiol Rep 2021 Jun 21. Epub 2021 Jun 21.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

In recent decades, infants' gut microbiota has aroused constant scientific interest, primarily due to early- and long-term repercussions on the host health. In this context, nutritional challenges such as those found in less developed countries can influence infants' gut microbiota development, thus generating potentially critical health outcomes. However, comprehensive investigations regarding species-level differences in the infant gut microbiota's composition between urbanized and rural countries are still missing. In this study, 16S rRNA and Shallow Shotgun metagenomics sequencing were exploited to dissect the microbial community's species-level composition of 11 faecal samples collected from infants living in a semi-urban area of Sub-Saharan Africa, i.e. Côte d'Ivoire. Moreover, the generated data were coupled with those retrieved from public available metagenomic repositories, including two rural communities and 13 urban communities of industrialized countries. The meta-analysis led to the identification of Infant Species Community States Type (ISCSTs) and microbial species covariances, which were exploited to reveal key signatures of infants living in rural and semi-urban societies. Remarkably, analysis of rural and semi-urban datasets revealed shifts from ISCSTs prevalent in urbanized populations with putative health implications. Thus, indicating the need for population-wide investigations aimed to define the factors determining such potentially harmful gut microbial communities' signatures.
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http://dx.doi.org/10.1111/1758-2229.12960DOI Listing
June 2021

Gastric microbiota composition in patients with corpus atrophic gastritis.

Dig Liver Dis 2021 Jun 8. Epub 2021 Jun 8.

Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant'Andrea Hospital, University Sapienza, Rome, Italy. Electronic address:

Background: In corpus atrophic gastritis (CAG), hypochlorhydria makes plausible the overgrowth of intragastric bacteria, whose role in gastric carcinogenesis is under debate.

Aims: To characterize the antrum/corpus composition of the gastric bacterial microbiota in CAG patients compared to controls without CAG.

Methods: A cross-sectional monocentric study on consecutive patients with known histological diagnosis of CAG undergoing gastroscopy for gastric cancer surveillance and patients without CAG undergoing gastroscopy for dyspepsia or anemia (108 biopsies from 55 patients, median age 61.5). Genomic DNA from one antral and one corpus biopsy from each case (n = 23) and control (n = 32) was extracted. Gastric microbiota was assessed by sequencing hypervariable regions of the 16SrRNA gene.

Results: Bacterial abundance and diversity were significantly lower in CAG cases than in controls (p < 0.001). Firmicutes were more frequent in cases, Bacteroidetes and Fusobacteria in controls (p < 0.0001). Streptococcaceae were more abundant in cases (p < 0.0001), Prevotellaceae in controls (p < 0.0001). The genus Streptococcus was positively correlated with severe OLGA/OLGIM stages linked to a higher risk of gastric cancer.

Conclusion: Gastric bacterial microbiota in CAG showed a reduced abundance and complexity but was characterized by higher colonization of Firmicutes, in particular Streptococcus, increased in subjects with severe atrophy/metaplasia stages at higher risk of gastric cancer.
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http://dx.doi.org/10.1016/j.dld.2021.05.005DOI Listing
June 2021

Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction.

Environ Microbiol 2021 Jun 19;23(6):3294-3305. Epub 2021 May 19.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, 43124, Italy.

Whole metagenomic shotgun (WMS) sequencing has dramatically enhanced our ability to study microbial genomics. The possibility to unveil the genetic makeup of bacteria that cannot be easily isolated has significantly expanded our microbiological horizon. Here, we report an approach aimed at uncovering novel bacterial species by the use of targeted WMS sequencing. Employing in silico data retrieved from metabolic modelling to formulate a chemically defined medium (CDM), we were able to isolate and subsequently sequence the genomes of six putative novel species of bacteria from the gut of non-human primates.
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http://dx.doi.org/10.1111/1462-2920.15559DOI Listing
June 2021

Draft Genome Sequence and Polyhydroxyalkanoate Biosynthetic Potential of Jeongeupia naejangsanensis Type Strain DSM 24253.

Microbiol Resour Announc 2021 Apr 15;10(15). Epub 2021 Apr 15.

Department of Science, Roma Tre University, Rome, Italy

is a Gram-negative, cellulose-degrading betaproteobacterium. Here, we report the draft genome sequence of the type strain DSM 24253 and identify the genes implicated in the biosynthesis of polyhydroxyalkanoate bioplastic polymers.
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http://dx.doi.org/10.1128/MRA.00167-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8050969PMC
April 2021

Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hördt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005).

Syst Appl Microbiol 2021 May 26;44(3):126199. Epub 2021 Mar 26.

Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy. Electronic address:

The monotypic carboxydophilic genus Carbophilus has recently been transferred to the genus Aminobacter within the family Phyllobacteriaceae, and Carbophilus carboxidus was renamed Aminobacter carboxidus (comb. nov.) [Hördt et al. 2020]. Due to the poor resolution of the 16S rRNA gene-based phylogeny, an extensive phylogenomic analysis of the family Phyllobacteriaceae was conducted, with particular focus on the genus Aminobacter. Whole genome-based analyses of Phyllobacteriaceae type strains provided evidenced that the genus Aminobacter forms a monophyletic cluster, clearly demarcated from all other members of the family. Close relatedness between A. carboxidus DSM 1086 and A. lissarensis DSM 17454 was inferred from core proteome phylogeny, shared gene content, and multilocus sequence analyses. ANI and GGDC provided genetic similarity values above the species demarcating threshold for these two type strains. Metabolic profiling and cell morphology analysis corroborated the phenotypic identity between A. carboxidus DSM 1086 and A. lissarensis DSM 17454. Search for the presence of carbon monoxide dehydrogenase (CODH) genes in Phyllobacteriaceae genomes revealed that the form II CODH is widespread in the family, whereas form I CODH was detected in few Mesorhizobium type strains, and in both A. carboxidus DSM 1086 and A. lissarensis DSM 17454. Results of phylogenomic, chemotaxonomic, and morphological investigations, combined with the presence of similarly arranged CODH genes, indicate that A. carboxidus DSM 1086 and A. lissarensis DSM 17454 are distinct strains of the same species. Hence A. carboxidus is a later subjective heterotypic synonym of A. lissarensis.
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http://dx.doi.org/10.1016/j.syapm.2021.126199DOI Listing
May 2021

Early-Life Development of the Bifidobacterial Community in the Infant Gut.

Int J Mol Sci 2021 Mar 25;22(7). Epub 2021 Mar 25.

Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain.

The establishment of the gut microbiota poses implications for short and long-term health. is an important taxon in early life, being one of the most abundant genera in the infant intestinal microbiota and carrying out key functions for maintaining host-homeostasis. Recent metagenomic studies have shown that different factors, such as gestational age, delivery mode, or feeding habits, affect the gut microbiota establishment at high phylogenetic levels. However, their impact on the specific bifidobacterial populations is not yet well understood. Here we studied the impact of these factors on the different species and subspecies at both the quantitative and qualitative levels. Fecal samples were taken from 85 neonates at 2, 10, 30, 90 days of life, and the relative proportions of the different bifidobacterial populations were assessed by 16S rRNA-23S rRNA internal transcribed spacer (ITS) region sequencing. Absolute levels of the main species were determined by q-PCR. Our results showed that the bifidobacterial population establishment is affected by gestational age, delivery mode, and infant feeding, as it is evidenced by qualitative and quantitative changes. These data underline the need for understanding the impact of perinatal factors on the gut microbiota also at low taxonomic levels, especially in the case of relevant microbial populations such as . The data obtained provide indications for the selection of the species best suited for the development of bifidobacteria-based products for different groups of neonates and will help to develop rational strategies for favoring a healthy early microbiota development when this process is challenged.
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http://dx.doi.org/10.3390/ijms22073382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8036440PMC
March 2021

The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host.

Comput Struct Biotechnol J 2021 9;19:1472-1487. Epub 2021 Mar 9.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

Members of the genus are dominant and symbiotic inhabitants of the mammalian gastrointestinal tract. Being vertically transmitted, bifidobacterial host colonization commences immediately after birth and leads to a phase of host infancy during which bifidobacteria are highly prevalent and abundant to then transit to a reduced, yet stable abundance phase during host adulthood. However, in order to reach and stably colonize their elective niche, i.e. the large intestine, bifidobacteria have to cope with a multitude of oxidative, osmotic and bile salt/acid stress challenges that occur along the gastrointestinal tract (GIT). Concurrently, bifidobacteria not only have to compete with the myriad of other gut commensals for nutrient acquisition, but they also require protection against bacterial viruses. In this context, Next-Generation Sequencing (NGS) techniques, allowing large-scale comparative and functional genome analyses have helped to identify the genetic strategies that bifidobacteria have developed in order to colonize, survive and adopt to the highly competitive mammalian gastrointestinal environment. The current review is aimed at providing a comprehensive overview concerning the molecular strategies on which bifidobacteria rely to stably and successfully colonize the mammalian gut.
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http://dx.doi.org/10.1016/j.csbj.2021.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7979991PMC
March 2021

Phageome Analysis of Bifidobacteria-Rich Samples.

Methods Mol Biol 2021 ;2278:71-85

School of Microbiology & APC Microbiome Ireland, Univeristy College Cork, Cork, Ireland.

Bifidobacteria are important early colonizers of the human intestinal tract. The relative abundance of bifidobacterial species may be modulated, in part, by bacteriophage activity. Metagenomic studies of these populations is a crucial step in understanding this important interaction. This chapter outlines the technical instructions required to analyze the virome of a bifidobacteria-rich sample, for example, an infant fecal sample.
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http://dx.doi.org/10.1007/978-1-0716-1274-3_7DOI Listing
April 2021

Protocol to Select Bifidobacteria from Fecal and Environmental Samples.

Methods Mol Biol 2021 ;2278:61-70

School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland.

Bifidobacteria are commensal microorganisms able to colonize several ecological niches. Since their discovery, culture-dependent methods combined with the most modern next-generation sequencing techniques have contributed to shed light on the ecological, functional and genomic features of bifidobacteria, purporting them as microorganisms with probiotic traits. Thanks to their acclaimed health-promoting effects, several members of the Bifidobacterium genus have been included in a variety of functional foods and drugs. In this context, the functional relevance of bifidobacteria in the gut explains ongoing efforts to isolate novel and potentially beneficial strains. For this purpose, development of effective and selective isolation protocols in concert with knowledge on the physiological characteristics of bifidobacterial are fundamental requirements for their recovery and discovery from their natural environments, in particular from fecal samples.
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http://dx.doi.org/10.1007/978-1-0716-1274-3_6DOI Listing
April 2021

Vaginotypes of the human vaginal microbiome.

Environ Microbiol 2021 Mar 28;23(3):1780-1792. Epub 2021 Feb 28.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.

The human vaginal environment harbours a community of bacteria that plays an important role in maintaining vaginal health and in protecting this environment from various urogenital infections. This bacterial population, also known as vaginal microbiota, has been demonstrated to be dominated by members of the Lactobacillus genus. Several studies employing 16S rRNA gene-based amplicon sequencing have classified the vaginal microbiota into five distinct community state types (CSTs) or vaginotypes. To deepen our understanding of the vaginal microbiota we performed an in-depth meta-analysis of 1312 publicly available datasets concerning healthy vaginal microbiome information obtained by metagenomics sequencing. The analysis confirmed the predominance of taxa belonging to the Lactobacillus genus, followed by members of the genera Gardnerella, Vibrio and Atopobium. Moreover, the statistical robustness offered by this meta-analysis allowed us to disentangle the species-level composition of dominant and accessory taxa constituting each vaginotype and to revisit and refine the previously proposed CST classification. In addition, a functional characterization of the metagenomic datasets revealed particular genetic features associated with each assigned vaginotype.
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http://dx.doi.org/10.1111/1462-2920.15441DOI Listing
March 2021

Comparative genome analyses of isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment.

Appl Environ Microbiol 2021 Feb 12. Epub 2021 Feb 12.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy

Vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the vaginal microbiota is dominated by members of the genus, whose relative abundance and microbial taxa composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 healthy vaginal microbiome samples through shotgun metagenomics analyses. Based on our results we observed that was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated fifteen strains from different environments in which this species is abounding, ranging from vaginal swabs of healthy women to chicken fecal samples. The genomes of these strains were decoded and their genetic content was analyzed and correlated with their physiological features. An extensive comparative genomic analysis encompassing all publicly available genome sequences of and combined with those decoded in this study, revealed a genetic adaptation of strains to their ecological niche. In addition, growth experiments involving all isolated strains together with a synthetic vaginal microbiota reveal how this species is able to modulate the composition of the vaginal microbial consortia at strain level. Overall, our findings suggest that plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria. The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the high prevalence of species is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 public healthy vaginal samples through shotgun metagenomics analyses. Results showed that was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genome of new strains from different environments and the comparative genomics analysis revealed a genetic adaptation of strains to their ecological niche. In addition, in-vitro growth experiments display the capability of this species to modulate the composition of the vaginal microbial consortia. Overall, our findings suggest an ecological role exploited by in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.
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http://dx.doi.org/10.1128/AEM.02899-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8091109PMC
February 2021

Amoxicillin-Clavulanic Acid Resistance in the Genus .

Appl Environ Microbiol 2021 03 11;87(7). Epub 2021 Mar 11.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy

Amoxicillin-clavulanic acid (AMC) is one of the most frequently prescribed antibiotic formulations in the Western world. Extensive oral use of this antimicrobial combination influences the gut microbiota. One of the most abundant early colonizers of the human gut microbiota is represented by different taxa of the genus, which include many members that are considered to bestow beneficial effects upon their host. In the current study, we investigated the impact of AMC administration on the gut microbiota composition, comparing the gut microbiota of 23 children that had undergone AMC antibiotic therapy to that of 19 children that had not been treated with antibiotics during the preceding 6 months. Moreover, we evaluated AMC sensitivity by MIC test of 261 bifidobacterial strains, including reference strains for the currently recognized 64 bifidobacterial (sub)species, as well as 197 bifidobacterial isolates of human origin. These assessments allowed the identification of four bifidobacterial strains that exhibit a high level of AMC insensitivity, which were subjected to genomic and transcriptomic analyses to identify the putative genetic determinants responsible for this AMC insensitivity. Furthermore, we investigated the ecological role of AMC-resistant bifidobacterial strains by batch cultures. Based on our results, we observed a drastic reduction in gut microbiota diversity of children treated with antibiotics, which also affected the abundance of , a bacterial genus commonly found in the infant gut. MIC experiments revealed that more than 98% of bifidobacterial strains tested were shown to be inhibited by the AMC antibiotic. Isolation of four insensitive strains and sequencing of their genomes revealed the identity of possible genes involved in AMC resistance mechanisms. Moreover, gut-simulating experiments revealed that one strain, i.e., PRL2020, is able to persist in the presence of a complex microbiota combined with AMC antibiotic.
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http://dx.doi.org/10.1128/AEM.03137-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8091617PMC
March 2021

Draft Genome Sequence and Secondary Metabolite Biosynthetic Potential of the Lysobacter niastensis Type Strain DSM 18481.

Microbiol Resour Announc 2021 Jan 7;10(1). Epub 2021 Jan 7.

Department of Science, Roma Tre University, Rome, Italy

belongs to a group of bacterial predators that produce a number of bioactive small molecules endowed with lytic properties toward other microorganisms. Here, we report the draft genome sequence of the type strain DSM 18481 and the identification of gene clusters implicated in the biosynthesis of secondary metabolites.
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http://dx.doi.org/10.1128/MRA.01296-20DOI Listing
January 2021

Probiogenomics Analysis of 97 Strains as a Tool for the Identification of Promising Next-Generation Probiotics.

Microorganisms 2020 Dec 30;9(1). Epub 2020 Dec 30.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy.

Members of the genus represent the most common colonizers of the human vagina and are well-known for preserving vaginal health and contrasting the colonization of opportunistic pathogens. Remarkably, high abundance of in the vaginal environment has been linked to vaginal health, leading to the widespread use of many strains as probiotics. Nevertheless, despite the scientific and industrial relevance of this species, a comprehensive investigation of the genomics of taxon is still missing. For this reason, we have performed a comparative genomics analysis of 97 strains, encompassing 16 strains sequenced in the framework of this study alongside 81 additional publicly available genome sequences. Thus, allowing the dissection of the pan-genome and core-genome followed by a comprehensive phylogenetic analysis based on the predicted core genes that revealed clustering based on ecological origin. Subsequently, a genomics-targeted approach, i.e., probiogenomics analysis, was applied for in-depth analysis of the eight strains of human origin sequenced in this study. In detail their genetic repertoire was screened for strain-specific genes responsible for phenotypic features that may guide the identification of optimal candidates for next-generation probiotics. The latter includes bacteriocin production, carbohydrates transport and metabolism, as well as a range of features that may be responsible for improved ecological fitness. In silico results regarding the genetic repertoire involved in carbohydrate metabolism were also validated by growth assays on a range of sugars, leading to the selection of putative novel probiotic strains.
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http://dx.doi.org/10.3390/microorganisms9010073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824148PMC
December 2020

Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut.

Microorganisms 2020 Dec 22;9(1). Epub 2020 Dec 22.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.

The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host-microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.
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http://dx.doi.org/10.3390/microorganisms9010008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822027PMC
December 2020

The Gut-Muscle Axis in Older Subjects with Low Muscle Mass and Performance: A Proof of Concept Study Exploring Fecal Microbiota Composition and Function with Shotgun Metagenomics Sequencing.

Int J Mol Sci 2020 Nov 25;21(23). Epub 2020 Nov 25.

Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Via Antonio Gramsci 14, 43126 Parma, Italy.

The gut microbiota could influence the pathophysiology of age-related sarcopenia through multiple mechanisms implying modulation of chronic inflammation and anabolic resistance. The aim of this study was to compare the fecal microbiota composition and functionality, assessed by shotgun metagenomics sequencing, between two groups of elderly outpatients, differing only for the presence of primary sarcopenia. Five sarcopenic elderly subjects and twelve non-sarcopenic controls, classified according to lower limb function and bioimpedance-derived skeletal muscle index, provided a stool sample, which was analyzed with shotgun metagenomics approaches, to determine the overall microbiota composition, the representation of bacteria at the species level, and the prediction of bacterial genes involved in functional metabolic pathways. Sarcopenic subjects displayed different fecal microbiota compositions at the species level, with significant depletion of two species known for their metabolic capacity of producing short-chain fatty acids (SCFAs), and , and of . Additionally, their fecal metagenome had different representation of genes belonging to 108 metabolic pathways, namely, depletion of genes involved in SCFA synthesis, carotenoid and isoflavone biotransformation, and amino acid interconversion. These results support the hypothesis of an association between microbiota and sarcopenia, indicating novel possible mediators, whose clinical relevance should be investigated in future studies.
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http://dx.doi.org/10.3390/ijms21238946DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728056PMC
November 2020

Five novel bifidobacterial species isolated from faeces of primates in two Czech zoos: sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov.

Int J Syst Evol Microbiol 2021 Jan 23;71(1). Epub 2020 Nov 23.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

Five strains, VB23, VB24, VB25, VB26 and VB31, were isolated from chimpanzee (), cotton-top tamarin (), Goeldi's marmoset (), moustached tamarin () and patas monkey (), respectively, which were kept in two Czech zoos. These strains were isolated from faecal samples and were Gram-positive, non-motile, non-sporulating, anaerobic and fructose-6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA revealed close relatedness between VB23 and LMG 11039 (96.0 %), VB24 and subsp. DSM 20433 (96.1 %), VB25 and LMG 30939 (96.5 %), VB26 and LMG 30297 (98.1 %), and VB31 and . LMG 11039 (99.40 %). Internal transcribed spacer profiling revealed that VB23, VB24, VB25, VB26 and VB31 had highest similarity to LMG 13208 (77.2 %), subsp. ATCC 15697 (85.8 %), DSM 23969 (76.9 %), LMG 13208 (81.2 %) and LMG 11039 (88.2 %), respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses with their closest neighbours supported the independent phylogenetic positions of the strains with values between 86.3 and 94.3 % for ANI and 25.8 and 54.9 % for dDDH. These genomic and phylogenetic analyses suggested that the evaluated strains were novel species named sp. nov. (VB31=DSM 109960=CCUG 73843), sp. nov. (VB25=DSM 109958=CCUG 73842), sp. nov. (VB24=DSM 109957=CCUG 73932), sp. nov. (VB26=DSM 109959=CCUG 73845) and sp. nov. (VB23=DSM 109963=CCUG 73840).
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http://dx.doi.org/10.1099/ijsem.0.004573DOI Listing
January 2021

Draft Genome Sequence of the Carboxydotrophic Alphaproteobacterium Aminobacter carboxidus Type Strain DSM 1086.

Microbiol Resour Announc 2020 Nov 5;9(45). Epub 2020 Nov 5.

Department of Science, Roma Tre University, Rome, Italy

is a soil Gram-negative alphaproteobacterium belonging to the physiological group of carboxydobacteria which aerobically oxidize CO to CO Here, we report the draft genome sequence of the DSM 1086 type strain and the identification of both form I and form II CO dehydrogenase systems in this strain.
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http://dx.doi.org/10.1128/MRA.01170-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645674PMC
November 2020

Decoding the Genomic Variability among Members of the Species.

Microorganisms 2020 Nov 3;8(11). Epub 2020 Nov 3.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy.

Members of the 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 strains collected from fecal samples of several primate species and an . Thus, we investigated the genomic variability and metabolic abilities of the new 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 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.
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http://dx.doi.org/10.3390/microorganisms8111720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693768PMC
November 2020

Lysogenization of a Lactococcal Host with Three Distinct Temperate Phages Provides Homologous and Heterologous Phage Resistance.

Microorganisms 2020 Oct 29;8(11). Epub 2020 Oct 29.

School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland.

is the most widely exploited microorganism in global dairy fermentations. Lactococcal strains are described as typically harboring a number of prophages in their chromosomes. The presence of such prophages may provide both advantages and disadvantages to the carrying host. Here, we describe the deliberate generation of three distinct lysogens of the model lactococcal strain 3107 and the impact of additional prophage carriage on phage-resistance and anti-microbial susceptibility. Lysogen-specific responses were observed, highlighting the unique relationship and impact of each lysogenic phage on its host. Both homologous and heterologous phage-resistance profiles were observed, highlighting the presence of possible prophage-encoded phage-resistance factors. Superinfection exclusion was among the most notable causes of heterologous phage-resistance profiles with resistance observed against members of the , P335, P087, and 949 lactococcal phage groups. Through these analyses, it is now possible to identify phages that may pursue similar DNA injection pathways. The generated lysogenic strains exhibited increased sensitivity to the antimicrobial compounds, nisin and lysozyme, relative to the parent strain, although it is noteworthy that the degree of sensitivity was specific to the individual (pro)phages. Overall, the findings highlight the unique impact of each prophage on a given strain and the requirement for strain-level analysis when considering the implications of lysogeny.
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http://dx.doi.org/10.3390/microorganisms8111685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693887PMC
October 2020

Special Issue "Bifidobacteria: Insights from Ecology to Genomics of a Key Microbial Group of the Mammalian Gut Microbiota".

Microorganisms 2020 Oct 27;8(11). Epub 2020 Oct 27.

APC Microbiome Ireland and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.

In recent years, substantial efforts have been made to dissect the composition of microbial communities that are present in the human gut, and to investigate their interactions with their host [...].
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http://dx.doi.org/10.3390/microorganisms8111660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693948PMC
October 2020

Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications.

Appl Environ Microbiol 2020 12 17;87(1). Epub 2020 Dec 17.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy

is described as a common anaerobic vaginal bacterium whose presence may correlate with vaginal dysbiotic conditions. In the current study, we performed phylogenomic analyses of 72 genome sequences, revealing noteworthy genome differences underlying a polyphyletic organization of this taxon. Particularly, the genomic survey revealed that this species may actually include nine distinct genotypes (GGtype1 to GGtype9). Furthermore, the observed link between sialidase and phylogenomic grouping provided clues of a connection between virulence potential and the evolutionary history of this microbial taxon. Specifically, based on the outcomes of these analyses, GGtype3, GGtype7, GGtype8, and GGtype9 appear to have virulence potential since they exhibited the sialidase gene in their genomes. Notably, the analysis of 34 publicly available vaginal metagenomic samples allowed us to trace the distribution of the nine genotypes identified in this study among the human population, highlighting how differences in genetic makeup could be related to specific ecological properties. Furthermore, comparative genomic analyses provided details about the pan- and core genome contents, including putative genetic elements involved in the adaptation to the ecological niche as well as many putative virulence factors. Among these putative virulence factors, particularly noteworthy genes identified were the gene encoding cholesterol-dependent cytolysin (CDC) toxin vaginolysin and genes related to microbial biofilm formation, iron uptake, adhesion to the vaginal epithelium, as well as macrolide antibiotic resistance. The identification of nine different genotypes among members of allowed us to distinguish an uneven distribution of virulence-associated genetic traits within this taxon and thus suggest the potential occurrence of putative pathogen and commensal strains. These findings, coupled with metagenomics microbial profiling of human vaginal microbiota, permitted us to get insights into the distribution of the genotypes among the human population, highlighting the presence of different structural communities in terms of genotypes.
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http://dx.doi.org/10.1128/AEM.02188-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755242PMC
December 2020

Microbiota and Cancer: The Emerging Beneficial Role of Bifidobacteria in Cancer Immunotherapy.

Front Microbiol 2020 8;11:575072. Epub 2020 Sep 8.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

Many intestinal bacteria are believed to be involved in various inflammatory and immune processes that influence tumor etiology because of their metabolic properties and their ability to alter the microbiota homeostasis. Although many functions of the microbiota are still unclear, there is compelling experimental evidence showing that the intestinal microbiota is able to modulate carcinogenesis and the response to anticancer therapies, both in the intestinal tract and other body sites. Among the wide variety of gut-colonizing microorganisms, various species belonging to the genus are believed to elicit beneficial effects on human physiology and on the host-immune system. Recent findings, based on preclinical mouse models and on human clinical trials, have demonstrated the impact of gut commensals including bifidobacteria on the efficacy of tumor-targeting immunotherapy. Although the underlying molecular mechanisms remain obscure, bifidobacteria and other microorganisms have become a promising aid to immunotherapeutic procedures that are currently applied to treat cancer. The present review focuses on strategies to recruit the microbiome in order to enhance anticancer responses and develop therapies aimed at fighting the onset and progression of malignancies.
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http://dx.doi.org/10.3389/fmicb.2020.575072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7507897PMC
September 2020

Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs).

Comput Struct Biotechnol J 2020 15;18:2480-2493. Epub 2020 Sep 15.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.

Appropriate development of the intestinal microbiota during infancy is known to be important for human health. In fact, aberrant alterations of the microbial composition during childhood may cause short- and/or long-term negative health effects. Many factors influence the initial assembly and subsequent progression of the gut microbiota of a neonate, such as feeding type, delivery mode, gestational age, maternal metabolic status and antibiotic exposure. In the current study, the composition of the infant gut core-microbiota was explored, revealing particular variations of this core-microbiota during the first three years as influenced by delivery mode and feeding type. A multi-population cohort meta-analysis was performed by selecting 15 publicly available datasets pertaining to taxonomic profiles of 1035 fecal samples of healthy infants, as obtained by means of a 16S rRNA gene-based profiling approach. Interestingly, this multi-population cohort meta-analysis revealed great microbial complexity and specific taxonomic shifts in children older than six months, suggesting a major impact by the introduction of solid foods which prompts progression of infant gut microbiota towards that typical of adults. The taxonomic data sets employed in this multi-population cohort meta-analysis possess the statistical robustness to allow the identification of infant community state types (ICSTs). Our analysis therefore reveals the existence of specific taxonomic patterns that correspond to particular nutritional and developmental stages of early life, and that had previously been obscured by the high variability typical of such infant gut microbiota.
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http://dx.doi.org/10.1016/j.csbj.2020.08.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7516180PMC
September 2020

Envisioning emerging frontiers on human gut microbiota and its applications.

Microb Biotechnol 2021 01 24;14(1):12-17. Epub 2020 Sep 24.

APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.

The human gut microbiota is involved in multiple health-influencing host interactions during the host's entire life span. Microbes colonize the infant gut instantaneously after birth and subsequently the founding and interactive progress of this early gut microbiota is considered to be driven and modulated by different host- and microbe-associated forces. A rising number of studies propose that the composition of the human gut microbiota in the early stages of life impact on the human health conditions at later stages of life. This notion has powered research aimed at detailed investigations of the infant gut microbiota composition. Nevertheless, the molecular mechanisms supporting the gut microbiome functionality and the interaction of the early gut microbes with the human host remain largely unknown.
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http://dx.doi.org/10.1111/1751-7915.13671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7888449PMC
January 2021

Impact of Extreme Obesity and Diet-Induced Weight Loss on the Fecal Metabolome and Gut Microbiota.

Mol Nutr Food Res 2021 03 7;65(5):e2000030. Epub 2020 Oct 7.

Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, 33300, Spain.

Scope: A limited number of human studies have characterized fecal microbiota and metabolome in extreme obesity and after diet-induced weight loss.

Methods And Results: Fecal samples from normal-weight and extremely obese adults and from obese participants before and after moderate diet-induced weight loss are evaluated for their interaction with the intestinal adenocarcinoma cell line HT29 using an impedance-based in vitro model, which reveals variations in the interaction between the gut microbiota and host linked to obesity status. Microbiota composition, short chain fatty acids, and other intestinal metabolites are further analyzed to assess the interplay among diet, gut microbiota, and host in extreme obesity. Microbiota profiles are distinct between normal-weight and obese participants and are accompanied by fecal signatures in the metabolism of biliary compounds and catecholamines. Moderate diet-induced weight loss promotes shifts in the gut microbiota, and the primary fecal metabolomics features are associated with diet and the gut-liver and gut-brain axes.

Conclusions: Analyses of the fecal microbiota and metabolome enable assessment of the impact of diet on gut microbiota composition and activity, supporting the potential use of certain fecal metabolites or members of the gut microbiota as biomarkers for the efficacy of weight loss in extreme obesity.
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http://dx.doi.org/10.1002/mnfr.202000030DOI Listing
March 2021
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