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International audience; Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.

International audience; ABSTRACT Fosfomycin is a decades-old antibiotic, currently reused because of its activity against multidrug-resistant bacteria. Here, we used a combined in vitro/in silico approach to search for fosfomycin resistance determinants in 25 new bacterial species isolated from the human microbiota. Putative resistance genes were cloned into a susceptible Escherichia coli strain. MIC values increased from 1 μg/ml to 1,024 μg/ml. Here, we report a new family of potential chromosomal fosfomycin resistance genes, named fosM .

The increasingly wide knowledge of the microbiota, as well as its continuous relation with several pathologies, favours the interest, discovery and classification of all the bacteria that are part of it. The isolation of strain P3519T is possible thanks to the application of new strategies such as culturomics and taxono-genomics. Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore-forming. The 16S rRNA gene sequence of Marseille-P3519 showed 98.57% of sequence similarity with Lactobacillus caviae MOZM2, the closest species, phylogenetically. Its genome had 2,237,367 bp with 45.42 mol% of G+C content. These findings support that strain Marseille-P3519 is a new member of the genus Lactobacillus for which the name Lactobacillus caccae sp. nov., is proposed.

We describe using a polyphasic approach that combines proteomic by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) analysis, genomic data and phenotypic characterization the features of Lactococcus garvieae strain M14 newly isolated from the fermented milk (known as raib) of an Algerian cow. The 2188835 bp containing genome sequence displays a metabolic capacity to form acid fermentation that is very useful for industrial applications and encodes for two bacteriocins responsible for its eventual bioprotective properties.

International audience; Background/objectives High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored. Methods/subjects We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by tax-onogenomics and their genome sequenced. Results Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut. Conclusions High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.

International audience; Genome remodeling and exchange of sequences are widespread in the prokaryotic world and mosaic genomes challenge the classification of prokaryotes, which cannot be properly achieved in terms of a single gene or group of genes. Here, we studied individually the gene collection of the archaic microorganism Lokiarchaeum sp., suggested as an archaeal host close to the emergence of the eukaryotes. The network or rhizome of all Lokiarchaeum sp. genes revealed that the genomic repertoire is mainly composed of genes from archaeal (similar to 36%) and bacterial origin (similar to 28%), distantly followed by components of eukaryotic origin (similar to 2%). Thirty-three percent of genes were unique to this species (ORFans). The mosaicity of archaea was also supported by studying Methanomassiliicoccus luminyensis, an archaea from the gut, in which 67% of the genomic repertoire arised from archaea and 22% from bacteria. Our results illustrate the intricate evolutionary relationships of the archaeal genome repertoire and highlight the rhizome-like processes of evolution in archaea, their mosaicity, and chimeric origin composed of different domains of life, questioning the reality of a tree of life.

International audience; Obesity represents a worldwide public health crisis. Trials suggested that intestinal microbiota may contribute to the development of obesity and highlighted the involvement of bacteria, including Lactobacillus spp., in changes to the host metabolism. Several experiments have shown significant effects of Lactobacillus probiotics on weight modification. Lactobacillus spp. are involved in the digestion of complex carbohydrates not digested by the host in the colon and also participate in the degradation of lipids and simple sugars in the duodenum and jejunum. Moreover, Lactobacillus species survive throughout the gastrointestinal tract, as they are able to survive in the presence of bile and low pH, and produce an antimicrobial agent, allowing them to reduce the number of bacteria in the gut. Hence, Lactobacillus spp. can have a significant impact on microbiota and, consequently, on weight change. Here, we review current studies of Lactobacillus spp. involved in weight change and discuss the different mechanisms of action by which Lactobacillus spp. acts on host digestion and appears to influence weight. Published by Elsevier Ltd.

Background Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan. Results Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome’s content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with Proteobacteria, and bacteria from vertebrates, which exchanged more with Firmicutes. The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats. Conclusions The presence of an intracytoplasmic membrane in PVC species seems to affect the genome’s evolution through the selection of transferred DNA, according to their encoded functions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0921-3) contains supplementary material, which is available to authorized users.

International audience; The history of infectious diseases raised the plague as one of the most devastating for human beings. Far too often considered an ancient disease, the frequent resurgence of the plague has led to consider it as a reemerging disease in Madagascar, Algeria, Libya, and Congo. The genetic factors associated with the pathogenicity of Yersinia pestis, the causative agent of the plague, involve the acquisition of the pPCP1 plasmid that promotes host invasion through the expression of the virulence factor Pla. The surveillance of plague foci after the 2003 outbreak in Algeria resulted in a positive detection of the specific pla gene of Y. pestis in rodents. However, the phenotypic characterization of the isolate identified a Citrobacter koseri. The comparative genomics of our sequenced C. koseri URMITE genome revealed a mosaic gene structure resulting from the lifestyle of our isolate and provided evidence for gene exchanges with different enteric bacteria. The most striking was the acquisition of a continuous 2 kb genomic fragment containing the virulence factor Pla of the Y. pestis pPCP1 plasmid; however, the subcutaneous injection of the CKU strain in mice did not produce any pathogenic effect. Our findings demonstrate that fast molecular detection of plague using solely the pla gene is unsuitable and should rather require Y. pestis gene marker combinations. We also suggest that the evolutionary force that might govern the expression of pathogenicity can occur through the acquisition of virulence genes but could also require the loss or the inactivation of resident genes such as antivirulence genes.

Clostridium ihumii strain AP5T sp. nov. is a new species within the genus Clostridium. This strain, whose genome is described here, was isolated from the stool sample of a 21-year-old French Caucasian female with anorexia nervosa. C. ihumii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,433,668 bp long genome contains 4,076 protein-coding and 85 RNA genes, including 9 rRNA genes. Electronic supplementary material The online version of this article (doi:10.1186/s40793-015-0025-x) contains supplementary material, which is available to authorized users.

We report the draft genome sequence of Lactobacillus agilis strain Marseille, isolated from stool samples of a child suffering from kwashiorkor. This strain can use two metabolic pathways allowing the assimilation of glucose and xylose. Here, we present the first draft genome of the Lactobacillus agilis species.

Lactobacillus mucosae strain Marseille, isolated from stool samples of a child suffering from a malnutrition disorder called Kwashiorkor, produces bacteriocin and seems to have specific carbohydrate and lipid metabolisms different from those of other Lactobacillus organisms. The draft genome sequence of this strain is presented here.