Walter Pirovano
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View article: Preliminary Insights Into the Relationship Between the Gut Microbiome and Host Genome in Posttraumatic Stress Disorder
Preliminary Insights Into the Relationship Between the Gut Microbiome and Host Genome in Posttraumatic Stress Disorder Open
Posttraumatic stress disorder (PTSD) may develop following trauma exposure; however, not all trauma‐exposed individuals develop PTSD, suggesting the presence of susceptibility and resilience factors. The gut microbiome and host genome, whi…
View article: Improved Key Microbial Biomarker Discovery Using Ensemble Statistical Methods
Improved Key Microbial Biomarker Discovery Using Ensemble Statistical Methods Open
In recent years, there has been a growing awareness of the importance of the microbiome in health and disease. Consequently, the number of large microbiome‐related clinical trials has also significantly increased. However, advanced biostat…
View article: Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model
Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model Open
The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little…
View article: Genotyping by sequencing for estimating relative abundances of diatom taxa in mock communities
Genotyping by sequencing for estimating relative abundances of diatom taxa in mock communities Open
View article: Being friendly to the skin microbiome: Experimental assessment
Being friendly to the skin microbiome: Experimental assessment Open
Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc)…
View article: Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity
Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity Open
We carried out a comparative analysis between the bacterial microbiota composition of zoo-housed western lowland gorillas and their wild counterparts through 16S rRNA gene amplicon sequencing. In addition, we characterised the carbohydrate…
View article: The butyrate-producing and spore-forming bacterial genus <i>Coprococcus</i> as a potential biomarker for neurological disorders
The butyrate-producing and spore-forming bacterial genus <i>Coprococcus</i> as a potential biomarker for neurological disorders Open
The host–intestinal microbiome interaction has gained much scientific attention in the past two decades, boosted by advances in DNA sequencing and cultivation techniques. An accumulating amount of evidence shows that gut microbes play cruc…
View article: Additional file 1 of Genotyping by sequencing for estimating relative abundances of diatom taxa in mock communities
Additional file 1 of Genotyping by sequencing for estimating relative abundances of diatom taxa in mock communities Open
Additional file 1: Table S1. The number of reads and clusters processed during the cluster filtering step of the msGBS pipeline. Table S2. Light microscopy counts by the diatom expert based on length, width, and fibula density. Table S3. S…
View article: Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism
Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism Open
View article: Multiomics characterization of the of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity
Multiomics characterization of the of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity Open
We carried out a comparative analysis between the bacterial microbiota composition of zoo-housed western lowland gorillas and their wild counterparts through 16S rRNA gene amplicon sequencing. In addition, we characterized the carbohydrate…
View article: Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism
Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism Open
Distyly is a floral dimorphism associated with a heteromorphic self-incompatibility mechanism that prevents inbreeding and promotes outcrossing in 28 angiosperm families. Distyly is controlled by a cluster of genes, i.e. the S-locus superg…
View article: Genotyping by Sequencing for Estimating Relative Abundances of Diatom Taxa in Mock Communities
Genotyping by Sequencing for Estimating Relative Abundances of Diatom Taxa in Mock Communities Open
Background: Diatoms are present in all waters and are highly sensitive to pollution gradients. Therefore, they are ideal bioindicators for water quality assessment. Current indices used in these applications are based on identifying diatom…
View article: Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex Open
In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse gro…
View article: Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex
Phylotranscriptomics Reveals the Reticulate Evolutionary History of a Widespread Diatom Species Complex Open
In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse gro…
View article: Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism
Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism Open
Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus…
View article: A pseudomolecule‐scale genome assembly of the liverwort <i>Marchantia polymorpha</i>
A pseudomolecule‐scale genome assembly of the liverwort <i>Marchantia polymorpha</i> Open
Summary Marchantia polymorpha has recently become a prime model for cellular, evo‐devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule‐scale assembly of the M. polymorpha genome, making comparative genom…
View article: On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications
On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications Open
Advances in sequencing and computational biology have drastically increased our capability to explore the taxonomic and functional compositions of microbial communities that play crucial roles in industrial processes. Correspondingly, comm…
View article: Complete Genome Sequence of <i>Malassezia restricta</i> CBS 7877, an Opportunist Pathogen Involved in Dandruff and Seborrheic Dermatitis
Complete Genome Sequence of <i>Malassezia restricta</i> CBS 7877, an Opportunist Pathogen Involved in Dandruff and Seborrheic Dermatitis Open
Malassezia restricta , one of the predominant basidiomycetous yeasts present on human skin, is involved in scalp disorders. Here, we report the complete genome sequence of the lipophilic Malassezia restricta CBS 7877 strain, which will fac…
View article: A Short Indel-Lacking-Resistance Gene Triggers Silencing of the Photosynthetic Machinery Components Through TYLCSV-Associated Endogenous siRNAs in Tomato
A Short Indel-Lacking-Resistance Gene Triggers Silencing of the Photosynthetic Machinery Components Through TYLCSV-Associated Endogenous siRNAs in Tomato Open
Plant viruses modify gene expression in infected tissues by altering the micro (mi)RNA-mediated regulation of genes. Among conserved miRNA targets there are transcripts coding for transcription factors, RNA silencing core, and disease-resi…
View article: Spread of Carbapenem Resistance by Transposition and Conjugation Among Pseudomonas aeruginosa
Spread of Carbapenem Resistance by Transposition and Conjugation Among Pseudomonas aeruginosa Open
The emergence of carbapenem-resistant Pseudomonas aeruginosa represents a worldwide problem. To understand the carbapenem-resistance mechanisms and their spreading among P. aeruginosa strains, whole genome sequences were dete…
View article: Complete Genome Sequence of Escherichia coli AS19, an Antibiotic-Sensitive Variant of E. coli Strain B REL606
Complete Genome Sequence of Escherichia coli AS19, an Antibiotic-Sensitive Variant of E. coli Strain B REL606 Open
The chemically mutagenized Escherichia coli strain AS19 was isolated on the basis of its enhanced sensitivity to different antibiotics, in particular to actinomycin. The strain was later modified to study rRNA modifications that confer ant…
View article: Novel sequencing technologies to support industrial biotechnology
Novel sequencing technologies to support industrial biotechnology Open
Industrial biotechnology develops and applies microorganisms for the production of bioproducts and enzymes with applications ranging from food and feed ingredients and processing to bio-based chemicals, biofuels and pharmaceutical products…
View article: NCBI-compliant genome submissions: tips and tricks to save time and money: Table 1
NCBI-compliant genome submissions: tips and tricks to save time and money: Table 1 Open
Genome sequences nowadays play a central role in molecular biology and bioinformatics. These sequences are shared with the scientific community through sequence databases. The sequence repositories of the International Nucleotide Sequence …
View article: Homeologs of the <i>Nicotiana benthamiana</i> Antiviral ARGONAUTE1 Show Different Susceptibilities to microRNA168-Mediated Control
Homeologs of the <i>Nicotiana benthamiana</i> Antiviral ARGONAUTE1 Show Different Susceptibilities to microRNA168-Mediated Control Open
The plant ARGONAUTE1 protein (AGO1) is a central functional component of the posttranscriptional regulation of gene expression and the RNA silencing-based antiviral defense. By genomic and molecular approaches, we here reveal the presence …
View article: Genome Sequence of EU-Unauthorized Genetically Modified Bacillus subtilis Strain 2014-3557 Overproducing Riboflavin, Isolated from a Vitamin B2 80% Feed Additive
Genome Sequence of EU-Unauthorized Genetically Modified Bacillus subtilis Strain 2014-3557 Overproducing Riboflavin, Isolated from a Vitamin B2 80% Feed Additive Open
This paper announces the genome sequence and annotation of the genetically modified (GM) Bacillus subtilis strain 2014-3557 overproducing riboflavin (vitamin B2). This GM-strain is unauthorized in the European Union. Nevertheless, it has b…
View article: Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population
Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population Open
Over the past years deep sequencing experiments have opened novel doors to reconstruct viral populations in a high-throughput and cost-effective manner. Currently a substantial number of studies have been performed which employ next genera…