Abbreviations: AAI, pairwise amino acid identity; ANI, average nucleotide identity; cAAI, pairwise amino acid identity of conserved genes. †These authors also contributed equally to this work †These authors share senior authorship. Six supplementary tables and seven supplementary figures are available with the online version of this article.

Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species.

In this study, we succeeded in differentiating Lactobacillus plantarum, Lactobacillus pentosus, and Lactobacillus paraplantarum by means of recA gene sequence comparison. Short homologous regions of about 360 bp were amplified by PCR with degenerate consensus primers, sequenced, and analyzed, and 322 bp were considered for the inference of phylogenetic trees. Phylograms, obtained by parsimony, maximum likelihood, and analysis of data matrices with the neighbor-joining model, were coherent and clearly separated the three species. The validity of the recA gene and RecA protein as phylogenetic markers is discussed. Based on the same sequences, species-specific primers were designed, and a multiplex PCR protocol for the simultaneous distinction of these bacteria was optimized. The sizes of the amplicons were 318 bp for L. plantarum, 218 bp for L. pentosus, and 107 bp for L. paraplantarum. This strategy permitted the unambiguous identification of strains belonging to L. plantarum, L. pentosus, and L. paraplantarum in a single reaction, indicating its applicability to the speciation of isolates of the L. plantarum group.The species Lactobacillus plantarum, Lactobacillus pentosus, and Lactobacillus paraplantarum are genotypically closely related and show highly similar phenotypes. The genetic heterogeneity of the L. plantarum group has been demonstrated by Dellaglio et al. (8) on the basis of DNA-DNA hybridization data: three groups were identified which were later classified as L. plantarum sensu stricto (2), L. pentosus (28), and L. paraplantarum (7).Despite the importance of these species for fermented foods of plant, animal, and fish origin, their correct identification is complicated by the ambiguous response of traditional physiological tests and molecular methods: Fourier transform infrared spectroscopy of lactobacilli from breweries was not able to differentiate spectra from L. plantarum and L. pentosus (6). Randomly amplified polymorphic DNA-PCR and related numerical analysis gave satisfying results, but the methods were applied only to L. plantarum and L. pentosus (27). Finally, two papers reported the selection of species-specific PCR primers for the L. plantarum group; however, in one case specificity towards L. paraplantarum was not checked (21), and in the other the primers did not guarantee sufficient specificity (3). Satisfying results have been obtained by Southern-type hybridization with a pyrDFE probe (4), randomly amplified polymorphic DNA-PCR, and AFLP (Keygene NV, Wageningen, The Netherlands) (S. Torriani, F. Clementi, F. Dellaglio, B. Hoste, M. Vancanneyt, and J. J. Swings, Proc. Sixth Symp. Lactic Acid Bacteria, poster B2, 1999), but such methods are not suitable for routine identification requirements. The difficulty of correct identification of these species and the increasing interest in some of their properties, e.g., probiotic activities (13) and tannin degradation (19), indicates the need for a simple and reliable molecular method for the definite differentiation of L. plantarum, L. parap...

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Lactic Acid Bacteria (LAB) are a functional group of microorganisms comprising Gram-positive, catalase negative bacteria that produce lactic acid as the major metabolic end-product of carbohydrate fermentation. Among LAB, Lactobacillus is the genus including a high number of GRAS species (Generally Recognized As Safe) and many strains are among the most important bacteria in food microbiology and human nutrition, due to their contribution to fermented food production or their use as probiotics. From a taxonomic point of view, the genus Lactobacillus includes at present (October 2012), 152 validly described species, and it belongs to the family Lactobacillaceae together with genus Pediococcus, with whom it is phylogenetically intermixed. The updated phylogenetic analysis based on 16S rRNA gene sequence revealed that the family is divided into 15 groups of three or more species, 4 couples and 10 single lines of descents. In addition, other taxonomically relevant information for Lactobacillus species was collected. This study aims at updating the taxonomy of the genus Lactobacillus, presenting the phylogenetic structure of the Lactobacillaceae and discussing the clusters as possible nuclei of genera to be described in the future. It is expected that scientists and producers in the field of probiotics could benefit from information reported here about the correct identification procedures and nomenclature of beneficial strains of lactobacilli.

Recent demonstration that probiotics administration has positive effects on mood state in healthy populations suggests its possible role as an adjunctive therapy for depression in clinical populations and as a non-invasive strategy to prevent depressive mood state in healthy individuals. The present study extends current knowledge on the beneficial effects of probiotics on psychological well-being, as measured by changes in mood (e.g., cognitive reactivity to sad mood, depression, and anxiety), personality dimensions, and quality of sleep, which have been considered as related to mood. For this double-blind, placebo-controlled study 38 healthy volunteers assigned to an experimental or control group assumed a daily dose of a probiotic mixture (containing Lactobacillus fermentum LF16, L. rhamnosus LR06, L. plantarum LP01, and Bifidobacterium longum BL04) or placebo, respectively, for 6 weeks. Mood, personality dimensions, and sleep quality were assessed four times (before the beginning of the study, at 3 and 6 weeks, and at 3 weeks of washout). A significant improvement in mood was observed in the experimental group, with a reduction in depressive mood state, anger, and fatigue, and an improvement in sleep quality. No between-groups differences were found. These findings corroborate the positive effect of probiotics on mood state and suggest that probiotics administration may improve psychological well-being by ameliorating aspects of mood and sleep quality.

Pathogenesis of autoimmune disorders, including multiple sclerosis (MS), has been linked to an alteration of the resident microbial commensal community and of the interplay between the microbiota and the immune system. Dietary components such as fiber, acting on microbiota composition, could, in principle, result in immune modulation and, thus, could be used to obtain beneficial outcomes for patients. We verified this hypothesis in a pilot study involving two groups of clinically similar relapsing-remitting (RR) MS patients who had undergone either a high-vegetable/low-protein diet (HV/LP diet group; N = 10) or a "Western Diet" (WD group; N = 10) for at least 12 months. Gut microbiota composition, analyzed by 16 S V4 rRNA gene sequencing and immunological profiles, was examined after a minimum of 12 months of diet. Results showed that, in the HV/LP diet group compared to the WD group: (1) Lachnospiraceae family was significantly more abundant; (2) IL-17-producing T CD4+ lymphocytes (p = 0.04) and PD-1 expressing T CD4+ lymphocytes (p = 0.0004) were significantly decreased; and (3) PD-L1 expressing monocytes (p = 0.009) were significantly increased. In the HV/LP diet group, positive correlations between Lachnospiraceae and both CD14+/ IL-10+ and CD14+/TGFβ+monocytes (RSp = 0.707, p = 0.05, and RSp = 0.73, p = 0.04, respectively), as well as between Lachnospiraceae and CD4+/CD25+/ FoxP3+ T lymphocytes (RSp = 0.68, p = 0.02) were observed. Evaluation of clinical parameters showed that in the HV/LP diet group alone the relapse rate during the 12 months follow-up period and the Expanded Disability Status Scale score at the end of the study period were significantly reduced. Diet modulates dysbiosis and improves clinical parameters in MS patients by increasing anti-inflammatory circuits. Because Lachnospiraceae favor Treg differentiation as well as TGFβ and IL-10 production this effect could be associated with an increase of these bacteria in the microbiota.

In recent years, the concept of “microbial terroir” has been introduced in the frame of the more renowned notion of “vitivinicultural terroir,’ since several studies demonstrated that wine characteristics are related to regional microbial community compositions. Most of the existing research focused on grape berries microbiota, since it can directly impact wine quality. In this work we studied, for the first time through next-generation sequencing, the epiphytic bacterial community of vine bark and its relationships with grape microbiota. The study was carried out in two Italian wine appellations (situated in different regions) to explore the impact of biogeography, and the influence of two agronomical practices (biodynamic and conventional) was evaluated as well. Overall, our results show that grapevine bark harbors a rich epiphytic microbiota and displays a higher microbial biodiversity than grape berry. Moreover, this study suggests that geographic and anthropogenic factors impact both bark and grape bacteriomes, but to a different extent. The evidence of a “microbial terroir” seems to be even more marked in bark than in berries, possibly due to its permanence over time and to its physical proximity with soil. The importance of vine trunk bark, as potential source of inoculum for grapes and as interesting bacterial diversity habitat, is evidenced. This opens new fields of investigation, not only for researchers that aim at describing this little-known habitat within the vineyard, but also for stakeholders from the wine industry that want to understand the roles of microorganisms on the entire winemaking process, from vineyard to cellar.