Splits decomposition analysis of <i>L. garvieae</i> population and subgroups.

<p>Parallelograms identify interconnected network of phylogenetic relationships between strains.</p

<i>Lactococcus garvieae</i>: Where Is It From? A First Approach to Explore the Evolutionary History of This Emerging Pathogen

<div><p>The population structure and diversity of <i>Lactococcus garvieae</i>, an emerging pathogen of increasing clinical significance, was determined at both gene and genome level. Selected lactococcal isolates of various origins were analyzed by a multi locus sequence typing (MLST). This gene-based analysis was compared to genomic characteristics, estimated through the complete genome sequences available in database. The MLST identified two branches containing the majority of the strains and two branches bearing one strain each. One strain was particularly differentiated from the other <i>L. garvieae</i> strains, showing a significant genetic distance. The genomic characteristics, correlated to the MLST-based phylogeny, indicated that this “separated strain” appeared first and could be considered the evolutionary intermediate between <i>Lactococcus lactis</i> and <i>L. garvieae</i> main clusters. A preliminary genome analysis of <i>L. garvieae</i> indicated a pan-genome constituted of about 4100 genes, which included 1341 core genes and 2760 genes belonging to the dispensable genome. A total of 1491 Clusters of Orthologous Genes (COGs) were found to be specific to the 11 <i>L. garvieae</i> genomes, with the genome of the “separated strain” showing the highest presence of unique genes.</p></div

Polymorphism observed in seven housekeeping genes in <i>L. garvieae.</i>

<p>Conc: concatenated sequences of seven loci.</p><p>S_A = Subgroup A, S_B = Subgroup B.</p><p>^a Statistical significance: Not significant, p>0.10.</p><p>^b Statistical significance: Not significant, 0.10</p><p>^c linkage disequilibrium detected.</p><p>/: not determined.</p><p>π = defined as the average number of nucleotide differences per site for a group of DNA sequences sampled.</p><p>π _{MAX<b> = </b>}maximal nucleotide diversity, defined as the number of nucleotide differences per site between the two most divergent sequences within the population.</p

Major rule consensus tree based on Clonal Frame analysis of concatenated sequences of all loci, for the total population.

<p>The X-axis represents the estimated time to the most recent common ancestor of <i>L. garvieae</i>. Open and closed squares correspond to subgroups S_B and S_A, respectively.</p

<i>L. garvieae</i> strains analyzed and allelic profiles.

<p>ST: Sequence Type.</p><p>/: Unknown.</p

Pan-genome prediction.

<p>The distribution of the number of core COGs (A) and total pan-genome COGs (B) found upon sequential addition of <i>n</i> genomes. In panel A, an exponential regression to core genome data is shown as a solid curve. In panel B, power law fit to the pan-genome size is shown as solid curve.</p

General genome features of the <i>L. garvieae</i> strains, in comparison with genome features of <i>L. lactis</i> and <i>L. raffinolactis</i> strains.

<p>General genome features of the <i>L. garvieae</i> strains, in comparison with genome features of <i>L. lactis</i> and <i>L. raffinolactis</i> strains.</p

Phylogenetic relationships between <i>L. garvieae</i> strains.

<p>The unrooted neighbor-joining tree (bootstrap 1000, Kimura 2-parameter model) was constructed from the 5713 bp concatenated DNA sequences of the seven loci (<i>als</i>, <i>atp</i>A, <i>tuf</i>, <i>gap</i>C, <i>gyr</i>B, <i>rpo</i>C and <i>gal</i>P) of <i>L. garvieae</i>. Open and closed squares correspond to subgroups S_B and S_A, respectively. Strain origin is indicated by color code: green = vegetables, brown = cereals, red = meat, yellow = dairy, blue = fish, pink = human, black = animal intestine, white = mastitic cow. Grey shadows represent CCs.</p

Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests

<div><p>Anorexia nervosa (AN) is a psychiatric disease with devastating physical consequences, with a pathophysiological mechanism still to be elucidated. Metagenomic studies on anorexia nervosa have revealed profound gut microbiome perturbations as a possible environmental factor involved in the disease. In this study we performed a comprehensive analysis integrating data on gut microbiota with clinical, anthropometric and psychological traits to gain new insight in the pathophysiology of AN. Fifteen AN women were compared with fifteen age-, sex- and ethnicity-matched healthy controls. AN diet was characterized by a significant lower energy intake, but macronutrient analysis highlighted a restriction only in fats and carbohydrates consumption. Next generation sequencing showed that AN intestinal microbiota was significantly affected at every taxonomic level, showing a significant increase of <i>Enterobacteriaceae</i>, and of the archeon <i>Methanobrevibacter smithii</i> compared with healthy controls. On the contrary, the genera <i>Roseburia</i>, <i>Ruminococcus</i> and <i>Clostridium</i>, were depleted, in line with the observed reduction in AN of total short chain fatty acids, butyrate, and propionate. Butyrate concentrations inversely correlated with anxiety levels, whereas propionate directly correlated with insulin levels and with the relative abundance of <i>Roseburia inulinivorans</i>, a known propionate producer. BMI represented the best predictive value for gut dysbiosis and metabolic alterations, showing a negative correlation with <i>Bacteroides uniformis</i> (microbiota), with alanine aminotransferase (liver function), and with psychopathological scores (obsession-compulsion, anxiety, and depression), and a positive correlation with white blood cells count. In conclusion, our findings corroborate the hypothesis that the gut dysbiosis could take part in the AN neurobiology, in particular in sustaining the persistence of alterations that eventually result in relapses after renourishment and psychological therapy, but causality still needs to be proven.</p></div

Taxa significantly increased (+) or decreased (-) in abundance in anorexia nervosa subjects.

<p>Taxa significantly increased (+) or decreased (-) in abundance in anorexia nervosa subjects.</p