Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

<p>Abstract</p> <p>Background</p> <p>Genome size and gene content in bacteria are associated with their lifestyles. Obligate intracellular bacteria (i.e., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle have not been studied comprehensively. The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles.</p> <p>Results</p> <p>Compared to free-living bacteria, host-dependent bacteria exhibit fewer rRNA genes, more split rRNA operons and fewer transcriptional regulators, linked to slower growth rates. We found a function-dependent and non-random loss of the same 100 orthologous genes in all obligate intracellular bacteria. Thus, we showed that obligate intracellular bacteria from different phyla are converging according to their lifestyle. Their specialization is an irreversible phenomenon characterized by translation modification and massive gene loss, including the loss of transcriptional regulators. Although both mutualists and parasites converge by genome reduction, these obligate intracellular bacteria have lost distinct sets of genes in the context of their specific host associations: mutualists have significantly more genes that enable nutrient provisioning whereas parasites have genes that encode Types II, IV, and VI secretion pathways.</p> <p>Conclusion</p> <p>Our findings suggest that gene loss, rather than acquisition of virulence factors, has been a driving force in the adaptation of parasites to eukaryotic cells. This comparative genomic analysis helps to explore the strategies by which obligate intracellular genomes specialize to particular host-associations and contributes to advance our knowledge about the mechanisms of bacterial evolution.</p> <p>Reviewers</p> <p>This article was reviewed by Eugene V. Koonin, Nicolas Galtier, and Jeremy Selengut.</p

The genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa.

International audienceFree-living protozoa allow horizontal gene transfer with and between the microorganisms that they host. They host mycobacteria for which the sources of transferred genes remain unknown. Using BLASTp, we searched within the genomes of 15 mycobacteria for homologous genes with 34 amoeba-resistant bacteria and the free-living protozoa Dictyostelium discoideum. Subsequent phylogenetic analysis of these sequences revealed that eight mycobacterial open-reading frames (ORFs) were probably acquired via horizontal transfer from beta- and gamma-Proteobacteria and from Firmicutes, but the transfer histories could not be reliably established in details. One further ORF encoding a pyridine nucleotide disulfide oxidoreductase (pyr-redox) placed non-tuberculous mycobacteria in a clade with Legionella spp., Francisella spp., Coxiella burnetii, the ciliate Tetrahymena thermophila and D. discoideum with a high reliability. Co-culturing Mycobacterium avium and Legionella pneumophila with the amoeba Acanthamoeba polyphaga demonstrated that these two bacteria could live together in amoebae for five days, indicating the biological relevance of intra-amoebal transfer of the pyr-redox gene. In conclusion, the results of this study support the hypothesis that protists can serve as a source and a place for gene transfer in mycobacteria

Evidence for an African Cluster of Human Head and Body Lice with Variable Colors and Interbreeding of Lice between Continents

BACKGROUND: Human head lice and body lice have been classified based on phenotypic characteristics, including geographical source, ecotype (preferred egg laying site hair or clothes), shape and color. More recently, genotypic studies have been based on mitochondrial genes, nuclear genes and intergenic spacers. Mitochondrial genetic analysis reclassified lice into three genotypes (A, B and C). However, no previous study has attempted to correlate both genotypic and phenotypic data. MATERIALS AND METHODS: Lice were collected in four African countries: Senegal, Burundi, Rwanda and Ethiopia and were photographed to compare their colors. The Multi-Spacer-Typing (MST) method was used to genotype lice belonging to the worldwide Clade A, allowing a comparison of phenotypic and genotypic data. RESULTS: No congruence between louse color and genotype has been identified. Phylogenetic analysis of the spacer PM2, performed including lice from other sources, showed the existence of an African cluster of human lice. However, the analysis of other spacers suggested that lice from different areas are interbreeding. CONCLUSIONS: We identified two geotypes of Clade A head and body lice including one that is specifically African, that can be either black or grey and can live on the head or in clothing. We also hypothesized that lice from different areas are interbreeding

Gene gain and loss events in Rickettsia and Orientia species

<p>Abstract</p> <p>Background</p> <p>Genome degradation is an ongoing process in all members of the <it>Rickettsiales </it>order, which makes these bacterial species an excellent model for studying reductive evolution through interspecies variation in genome size and gene content. In this study, we evaluated the degree to which gene loss shaped the content of some <it>Rickettsiales </it>genomes. We shed light on the role played by horizontal gene transfers in the genome evolution of <it>Rickettsiales</it>.</p> <p>Results</p> <p>Our phylogenomic tree, based on whole-genome content, presented a topology distinct from that of the whole core gene concatenated phylogenetic tree, suggesting that the gene repertoires involved have different evolutionary histories. Indeed, we present evidence for 3 possible horizontal gene transfer events from various organisms to <it>Orientia </it>and 6 to <it>Rickettsia </it>spp., while we also identified 3 possible horizontal gene transfer events from <it>Rickettsia </it>and <it>Orientia </it>to other bacteria. We found 17 putative genes in <it>Rickettsia </it>spp. that are probably the result of <it>de novo </it>gene creation; 2 of these genes appear to be functional. On the basis of these results, we were able to reconstruct the gene repertoires of "proto-<it>Rickettsiales</it>" and "proto-<it>Rickettsiaceae</it>", which correspond to the ancestors of <it>Rickettsiales </it>and <it>Rickettsiaceae</it>, respectively. Finally, we found that 2,135 genes were lost during the evolution of the <it>Rickettsiaceae </it>to an intracellular lifestyle.</p> <p>Conclusions</p> <p>Our phylogenetic analysis allowed us to track the gene gain and loss events occurring in bacterial genomes during their evolution from a free-living to an intracellular lifestyle. We have shown that the primary mechanism of evolution and specialization in strictly intracellular bacteria is gene loss. Despite the intracellular habitat, we found several horizontal gene transfers between <it>Rickettsiales </it>species and various prokaryotic, viral and eukaryotic species.</p> <p>Open peer review</p> <p>Reviewed by Arcady Mushegian, Eugene V. Koonin and Patrick Forterre. For the full reviews please go to the Reviewers' comments section.</p

Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm

International audienceBackground: Various methods are currently used to define species and are based on the phylogenetic marker 16S ribosomal RNA gene sequence, DNA-DNA hybridization and DNA GC content. However, these are restricted genetic tools and showed significant limitations. Results: In this work, we describe an alternative method to build taxonomy by analyzing the pan-genome composition of different species of the Klebsiella genus. Klebsiella species are Gram-negative bacilli belonging to the large Enterobacteriaceae family. Interestingly, when comparing the core/pan-genome ratio; we found a clear discontinuous variation that can define a new species. Conclusions: Using this pan-genomic approach, we showed that Klebsiella pneumoniae subsp. ozaenae and Klebsiella pneumoniae subsp. rhinoscleromatis are species of the Klebsiella genus, rather than subspecies of Klebsiella pneumoniae. This pan-genomic analysis, helped to develop a new tool for defining species introducing a quantic perspective for taxonomy

Metabolic role of lactobacilli in weight modification in humans and animals

International audienceObesity 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

In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens

International audienceAntibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new microorganisms that represent a potential source of interesting new antimicrobial substances to explore. The aim of this review is to present recently discovered nonribosomal peptide (NRP) and polyketide (PK) molecules with antimicrobial activity against human pathogens. We highlight the different in silico/in vitro strategies and approaches that led to their discovery. As a result of technological progress and a better understanding of the NRP and PK synthesis mechanisms, these new antibiotic compounds provide an additional option in human medical treatment and a potential way out of the impasse of antibiotic resistance

Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants

International audienceBackground: The emergence and diffusion of strains of pathogenic bacteria resistant to antibiotics constitutes a real public health challenge. Antibiotic resistance genes (ARGs) can be carried by both pathogenic and non-pathogenic bacteria, including commensal bacteria from the human microbiota, which require special monitoring in the fight against antimicrobial resistance. Methods: We analyzed the proteomes of 335 new bacterial species from human microbiota to estimate its whole range of ARGs using the BLAST program against ARGs reference databases. Results: We found 278 bacteria that harbor a total of 883 potential ARGs with the following distribution: 264 macrolides-lincosamides-streptogramin, 195 aminoglycosides, 156 tetracyclines, 58 β-lactamases, 58 fosfomycin, 51 glycopeptides, 36 nitroimidazoles, 33 phenicols and 32 rifamycin. Furthermore, evolutionary analyses revealed the potential horizontal transfer with pathogenic bacteria involving mobile genetic elements such as transposase and plasmid. We identified many ARGs that may represent new variants in fosfomycin and β-lactams resistance. Conclusion: These findings show that new bacterial species from human microbiota should be considered as an important reservoir of ARGs that can be transferred to pathogenic bacteria. In vitro analyses of their phenotypic potential are required to improve our understanding of the functional role of this bacterial community in the development of antibiotic resistance