On species descriptions based on a single strain: proposal to introduce the status species proponenda (sp. pr.).

A survey of the descriptions of novel bacterial species published in the period 1996–2006 revealed that a large number of taxonomic descriptions are still based on one or a few strains. This situation determines that not only species descriptions, but also proposals to create higher ranks, are actually based on very few strains, which could produce a highly biased scenario. The encouragement to include a reasonable number of strains in species descriptions has been largely disregarded after its proposal, since acceptance of such descriptions relies mainly on editors' and reviewers' opinions. This observation and other considerations lead us to propose the creation of the status species proponenda (sp. pr.), as a compromise between the need for scientific description of biodiversity and exchange of data and the good taxonomic practice of including a sufficient number of strains in descriptions of species and higher taxonomic ranks

Unravelling the Impact of Grape Washing, {SO}2, and Multi-Starter Inoculation in Lab-Scale Vinification Trials of Withered Black Grapes

Wine quality is strongly affected by chemical composition and microbial population of grape must, which, in turn, are influenced by several post-harvest treatments, including grape withering. Different strategies have been suggested to manage the fermenting must microbiota, as it plays a central role in the outcomes of both spontaneous and guided fermentations. This study aimed at evaluating the impact of grape washing, SO2 addition, and selected starter culture inoculation on population dynamics, fermentation kinetics, and main oenological parameters in lab-scale trials, focusing on withered grapes usually used for Amarone production. Although grape washing treatment was effective in removing heavy metals and undesirable microorganisms from grape berry surface, inoculation of multi-starter cultures impacted more fermentation rates. Further, both grape washing and starter inoculation procedures had a remarkable impact on wine chemical characteristics, while 30 mg/L SO2 addition did not significantly affect the fermentation process. In summary, the best strategy in terms of limiting off-flavors and potentially reducing the need for SO2 addition in wine from withered grapes was the use of yeast starters, particularly mixed cultures composed by selected strains of Metschnikowia spp. and Saccharomyces cerevisiae. Application of a washing step before winemaking showed a potential to improve organoleptic characteristics of win

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of the closed meeting by videoconference, 3 September 2020

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of the closed meeting by videoconference, 3 September 202

Molecular Identification and Quantification of Tetracycline and Erythromycin Resistance Genes in Spanish and Italian Retail Cheeses

Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is, tet(K), tet(L), tet(M), tet(O), tet(S), and tet(W), and two with respect to erythromycin, that is, erm(B) and erm(F). The most common resistance genes in the analysed cheeses were tet(S), tet(W), tet(M), and erm(B). The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to 10.18 log10/g). DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions for tet(W)-carrying cheeses, though the similarity of the sequences suggests this tet(W) to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants.The study was partially supported by a Spain-Italy bilateral collaboration program (Ref. IT2009-0080 and IT105MD12L). Financial support was further provided by projects from CICYT (Ref. AGL2011-24300-ALI) and INIA (Ref. RM2011-00005-00-00). A. B. Flórez and S. Delgado were supported by research contracts under Juan de la Cierva Program (Ref. JCI-2010-07457 and JCI-2008-02391, resp.). A. Alegría was awarded a scholarship of the Severo Ochoa program from FICYT (Ref. BP08-053).Peer Reviewe

Whole genome analysis as a tool for the safety assessment of antibiotic resistance in food-processing bacteria

Trabajo presentado en la 2nd EFSA Scientific Conference, celebrado en Milán, Italia, del 14 al 16 de octubre de 2015Acquisition of antibiotic resistances (AR) by pathogens leads ultimately to a failure of antibiotic therapy. The food chain is considered a key player in the transmission of AR determinants to pathogens from reservoirs in commensal and beneficial bacteria. Therefore, the absence of transmissible AR genes in bacteria used as starter and adjunct cultures for food and feed processing is considered to be critical (EFSA, 2012; EFSA Journal, 10:2740). Genome sequencing allows the inspection of the whole genetic makeup of bacteria in the search for the basis of desirable and undesirable traits, including that of AR. Thus, in silico sequence analysis and comparison against databases can be used as a tool for the safety assessment of microorganisms intended to be used in food systems. This communication reports on the genome analysis of three Leuconostoc mesenteroides strains of dairy origin showing atypical resistances to tetracycline (LbT16), erythromycin and clindamycin (LbE15), and kanamycin, streptomycin, tetracycline and virginiamycin (LbE16). Genes encoding for erythromycin [erm(B)] and tetracycline [tet(S)] resistance had already been detected by PCR. Genome analysis confirmed the presence of these genes and identified others which encode uncommon AR in lactic acid bacteria. Analysis of the genes and their flanking regions revealed a potential of some to be horizontally transferred to other bacteria. This study demonstrates the effectiveness of combining genome sequencing and bioinformatics analysis as an affordable tool for the safety assessment of food bacteria. This innovative approach could become a novel paradigm in the selection programs of starters for the food industry.Peer Reviewe

Culture-independent analysis of diversity in microbial communities: pros and cons of the partial sequence-based profiling

Among the culture-independent techniques developed so far, DGGE/TGGE analysis of amplified 16S rRNA fragments is currently used to a great extent for the characterization of microbial consortia, due to its fast response and highly descriptive power. This approach relies on the separations of partial 16S rRNA gene amplicons targeting two specific hypervariable regions, namely V3 and V6-V8. Separation is followed by sequencing and identification of different bands based on BLAST comparisons. Some case studies are presented here concerning the identification of bacterial species and genera - belonging to different phyla such as Actinobacteria (Bifidobacterium, Rhodococcus), Firmicutes (Bacillus, Enterococcus, and Lactobacillus), Alphaproteobacteria (Sinorhizobium), Betaproteobacteria (Burkholderia), and Gammaproteobacteria (Pseudomonas) \u2013 all relevant to environmental and industrial biotechnology

Metabarcoding analysis of gut microbiota of healthy individuals reveals impact of probiotic and maltodextrin consumption

In a previously published double-blind, placebo-controlled study, we showed that probiotics intake exerted a positive effect on sleep quality and a general improvement across time in different aspects of the profile of mood state, like sadness, anger, and fatigue in 33 healthy individuals. The present work investigates the impact of the probiotic product, constituted of Limosilactobacillus fermentum LF16, Lacticaseibacillus rhamnosus LR06, Lactiplantibacillus plantarum LP01 (all former members of Lactobacillus genus), and Bifidobacterium longum 04, on the gut microbiota composition of the same cohort through a metabarcoding analysis. Both the placebo and probiotic treatments had a significant impact on the microbiota composition. Statistical analysis showed that the microbiota of the individuals could be clustered into three groups, or bacteriotypes, at the baseline, and, inherently, bacterial compositions were linked to different responses to probiotic and placebo intakes. Interestingly, L. rhamnosus and L. fermentum were retrieved in the probiotic-treated cohort, while a bifidogenic effect of maltodextrin, used as placebo, was observed. The present study shed light on the importance of defining bacteriotypes to assess the impact of interventions on the gut microbiota and allowed to reveal microbial components which could be related to positive effects (i.e. sleep quality improvement) to be verified in further studies

Comparative genomics of the genus Lactobacillus reveals robust phylogroups that provide the basis for reclassification

The genus Lactobacillus includes over 200 species that are widely used in fermented food preservation and biotechnology or that are explored for beneficial effects on health. Naming, classifying, and comparing lactobacilli have been challenging due to the high level of phenotypic and genotypic diversity that they display and because of the uncertain degree of relatedness between them and associated genera. The aim of this study was to investigate the feasibility of dividing the genus Lactobacillus into more homogeneous genera/clusters, exploiting genome-based data. The relatedness of 269 species belonging primarily to the families Lactobacillaceae and Leuconostocaceae was investigated through phylogenetic analysis (by the use of ribosomal proteins and housekeeping genes) and the assessment of the average amino acid identity (AAI) and the percentage of conserved proteins (POCP). For each subgeneric group that emerged, conserved signature genes were identified. Both distance-based and sequence-based metrics showed that the Lactobacillus genus was paraphyletic and revealed the presence of 10 methodologically consistent subclades, which were also characterized by a distinct distribution of conserved signature orthologues. We present two ways to reclassify lactobacilli: a conservative division into two subgeneric groups based on the presence/absence of a key carbohydrate utilization gene or a more radical subdivision into 10 groups that satisfy more stringent criteria for genomic relatedness. Importance: Lactobacilli have significant scientific and economic value, but their extraordinary diversity means that they are not robustly classified. The 10 homogeneous genera/subgeneric entities that we identify here are characterized by uniform patterns of the presence/absence of specific sets of genes which offer potential as discovery tools for understanding differential biological features. Reclassification/subdivision of the genus Lactobacillus into more uniform taxonomic nuclei will also provide accurate molecular markers that will be enabling for regulatory approval applications. Reclassification will facilitate scientific communication related to lactobacilli and prevent misidentification issues, which are still the major cause of mislabeling of probiotic and food products reported worldwide

Carotenoid skin ornaments as flexible indicators of male foraging behavior in a marine predator: Variation among Mexican colonies of brown booby ( Sula leucogaster )

Carotenoid-dependent ornaments can reflect animals’ diet and foraging behaviors. However, this association should be spatially flexible and variable among populations to account for geographic variation in optimal foraging behaviors. We tested this hypothesis using populations of a marine predator (the brown booby, Sula leucogaster) that forage across a gradient in ocean depth in and near the Gulf of California. Specifically, we quantified green chroma for two skin traits (foot and gular color) and their relationship to foraging location and diet of males, as measured via global positioning system tracking and stable carbon isotope analysis of blood plasma. Our three focal colonies varied in which foraging attributes were linked to carotenoid-rich ornaments. For gular skin, our data showed a shift from a benthic prey-green skin association in the shallow waters in the north to a pelagic prey-green skin association in the deepest waters to the south. Mean foraging trip duration and distance of foraging site from coast also predicted skin coloration in some colonies. Finally, brown booby colonies varied in which trait (foot versus gular skin color) was associated with foraging metrics. Overall, our results indicate that male ornaments reflect quality of diet and foraging–information that may help females select mates who are adapted to local foraging conditions and therefore, are likely to provide better parental care. More broadly, our results stress that diet-dependent ornaments are closely linked to animals’ environments and that we cannot assume ornaments or ornament signal content are ubiquitous within species, even when ornaments appear similar among populations

The complex microbial community of withered berries of cv. Corvina as revealed by metagenomic analysis

Corvina is the most important of Verona\u2019s red grape varieties and forms the basis for the production of unique wines, such as Amarone and Recioto of the Valpolicella area (Italy). The distinctive features of such wines are linked to the peculiar winemaking techniques and especially to the post-harvest grape withering process, when the grapes are partially dried in attics for three/four months to concentrate sugars up to about 27% (w/v). Dehydratation increases the concentration of constituent substances in berries, determining also specific expression of grape genes. During this process, grapes are colonized with a complex microbiota to an extent which depends on environmental temperature and humidity. In this study, a whole metagenome sequencing (WMS) approach was used to analyse the microbial consortia present on Corvina berries at the end of the withering process performed in two different conditions (\u201ctraditional\u201d or \u201cfast\u201d). Representative berry samples were collected and washed to avoid grapevine DNA contamination. Bioinformatic analyses, performed on reads and scaffolds, revealed that traditionally withered berries were dominated by Clostridiales and Pseudomonadales, while the fast procedure determined the presence of Enterobacteriales and Lactobacillales. On the contrary, few consistent differences characterized the eukaryotic fraction, dominated by Aspergillus and Penicillium for both samples. Interestingly, the \u201cbinning\u201d procedure revealed 15 most abundant genomes characterizing the two conditions. These results provide insights into the microbial community of Corvina withered berries and reveal relevant variations attributable to environmental withering conditions. Further studies will be performed to determine whether the different microbial compositions could lead to significant chemical variations of the musts, with an impact on the organoleptic properties of wine. This study underlines how novel technologies, like WMS, could open novel perspectives in the knowledge and management of traditional processes as the withering process of Corvina, with an impact on the winemaking of important Italian wines