@article {pmid30992351, year = {2019}, author = {Knight, DR and Kullin, B and Androga, GO and Barbut, F and Eckert, C and Johnson, S and Spigaglia, P and Tateda, K and Tsai, PJ and Riley, TV}, title = {Evolutionary and Genomic Insights into Clostridioides difficile Sequence Type 11: a Diverse Zoonotic and Antimicrobial-Resistant Lineage of Global One Health Importance.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00446-19}, pmid = {30992351}, issn = {2150-7511}, abstract = {Clostridioides difficile (Clostridium difficile) sequence type 11 (ST11) is well established in production animal populations worldwide and contributes considerably to the global burden of C. difficile infection (CDI) in humans. Increasing evidence of shared ancestry and genetic overlap of PCR ribotype 078 (RT078), the most common ST11 sublineage, between human and animal populations suggests that CDI may be a zoonosis. We performed whole-genome sequencing (WGS) on a collection of 207 ST11 and closely related ST258 isolates of human and veterinary/environmental origin, comprising 16 RTs collected from Australia, Asia, Europe, and North America. Core genome single nucleotide variant (SNV) analysis identified multiple intraspecies and interspecies clonal groups (isolates separated by ≤2 core genome SNVs) in all the major RT sublineages: 078, 126, 127, 033, and 288. Clonal groups comprised isolates spread across different states, countries, and continents, indicative of reciprocal long-range dissemination and possible zoonotic/anthroponotic transmission. Antimicrobial resistance genotypes and phenotypes varied across host species, geographic regions, and RTs and included macrolide/lincosamide resistance (Tn6194 [ermB]), tetracycline resistance (Tn6190 [tetM] and Tn6164 [tet44]), and fluoroquinolone resistance (gyrA/B mutations), as well as numerous aminoglycoside resistance cassettes. The population was defined by a large "open" pan-genome (10,378 genes), a remarkably small core genome of 2,058 genes (only 19.8% of the gene pool), and an accessory genome containing a large and diverse collection of important prophages of the Siphoviridae and Myoviridae This study provides novel insights into strain relatedness and genetic variability of C. difficile ST11, a lineage of global One Health importance.IMPORTANCE Historically, Clostridioides difficile (Clostridium difficile) has been associated with life-threatening diarrhea in hospitalized patients. Increasing rates of C. difficile infection (CDI) in the community suggest exposure to C. difficile reservoirs outside the hospital, including animals, the environment, or food. C. difficile sequence type 11 (ST11) is known to infect/colonize livestock worldwide and comprises multiple ribotypes, many of which cause disease in humans, suggesting CDI may be a zoonosis. Using high-resolution genomics, we investigated the evolution and zoonotic potential of ST11 and a new closely related ST258 lineage sourced from diverse origins. We found multiple intra- and interspecies clonal transmission events in all ribotype sublineages. Clones were spread across multiple continents, often without any health care association, indicative of zoonotic/anthroponotic long-range dissemination in the community. ST11 possesses a massive pan-genome and numerous clinically important antimicrobial resistance elements and prophages, which likely contribute to the success of this globally disseminated lineage of One Health importance.}, }
@article {pmid30986243, year = {2019}, author = {Wyres, KL and Wick, RR and Judd, LM and Froumine, R and Tokolyi, A and Gorrie, CL and Lam, MMC and Duchêne, S and Jenney, A and Holt, KE}, title = {Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae.}, journal = {PLoS genetics}, volume = {15}, number = {4}, pages = {e1008114}, doi = {10.1371/journal.pgen.1008114}, pmid = {30986243}, issn = {1553-7404}, abstract = {Klebsiella pneumoniae has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) healthcare-associated infections and drug susceptible community-acquired invasive infections. These pathotypes are generally associated with two distinct subsets of K. pneumoniae lineages or 'clones' that are distinguished by the presence of acquired resistance genes and several key virulence loci. Genomic evolutionary analyses of the most notorious MDR and invasive community-associated ('hypervirulent') clones indicate differences in terms of chromosomal recombination dynamics and capsule polysaccharide diversity, but it remains unclear if these differences represent generalised trends. Here we leverage a collection of >2200 K. pneumoniae genomes to identify 28 common clones (n ≥ 10 genomes each), and perform the first genomic evolutionary comparison. Eight MDR and 6 hypervirulent clones were identified on the basis of acquired resistance and virulence gene prevalence. Chromosomal recombination, surface polysaccharide locus diversity, pan-genome, plasmid and phage dynamics were characterised and compared. The data showed that MDR clones were highly diverse, with frequent chromosomal recombination generating extensive surface polysaccharide locus diversity. Additional pan-genome diversity was driven by frequent acquisition/loss of both plasmids and phage. In contrast, chromosomal recombination was rare in the hypervirulent clones, which also showed a significant reduction in pan-genome diversity, largely driven by a reduction in plasmid diversity. Hence the data indicate that hypervirulent clones may be subject to some sort of constraint for horizontal gene transfer that does not apply to the MDR clones. Our findings are relevant for understanding the risk of emergence of individual K. pneumoniae strains carrying both virulence and acquired resistance genes, which have been increasingly reported and cause highly virulent infections that are extremely difficult to treat. Specifically, our data indicate that MDR clones pose the greatest risk, because they are more likely to acquire virulence genes than hypervirulent clones are to acquire resistance genes.}, }
@article {pmid30975079, year = {2019}, author = {Du, Y and Ma, J and Yin, Z and Liu, K and Yao, G and Xu, W and Fan, L and Du, B and Ding, Y and Wang, C}, title = {Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {283}, doi = {10.1186/s12864-019-5646-9}, pmid = {30975079}, issn = {1471-2164}, support = {2017YFD0200804//the National Key Research and Development Program of China/ ; 31700094//National Natural Science Foundation of China/ ; 31770115//National Natural Science Foundation of China/ ; 31600090//National Natural Science Foundation of China/ ; 2014BAD16B02//the National Science and Technology Pillar Program of China/ ; SYL2017XTTD03//the funds of Shandong &quot;Double Tops&quot; Program/ ; }, abstract = {BACKGROUND: Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis.<br><br>RESULTS: A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis.<br><br>CONCLUSIONS: This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis. Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation.}, }
@article {pmid30963617, year = {2019}, author = {Vakirlis, N and Monerawela, C and McManus, G and Ribeiro, O and McLysaght, A and James, T and Bond, U}, title = {Evolutionary Journey and Characterisation of a Novel Pan-Gene Associated with Beer Strains of S. cerevisiae.}, journal = {Yeast (Chichester, England)}, volume = {}, number = {}, pages = {}, doi = {10.1002/yea.3391}, pmid = {30963617}, issn = {1097-0061}, abstract = {The sequencing of over a thousand Saccharomyces cerevisiae genomes revealed a complex pangenome. Over one-third of the discovered genes are not present in the S. cerevisiae core genome but instead are often restricted to a sub-set of yeast isolates and thus may be important for adaptation to specific environmental niches. We refer to these genes as &quot;pan-genes&quot;, being part of the pangenome but not the core genome. Here we describe the evolutionary journey and characterisation of a novel pan-gene, originally named HYPO (Hypothetical Open Reading Frame). Phylogenetic analysis reveals that HYPO has been predominantly retained in S. cerevisiae strains associated with brewing but has been repeatedly lost in most other fungal species during evolution. There is also evidence that HYPO was horizontally transferred at least once, from S. cerevisiae to S. paradoxus. The phylogenetic analysis of HYPO exemplifies the complexity and intricacy of evolutionary trajectories of genes within the S. cerevisiae pangenome. To examine possible functions for Hypo, we overexpressed a HYPO-GFP fusion protein in both S. cerevisiae and S. pastorianus. The protein localised to the plasma membrane where it accumulated initially in distinct foci. Time-lapse fluorescent imaging revealed that when cells are grown in wort, Hypo-gfp fluorescence spreads throughout the membrane during cell growth. The over-expression of Hypo-gfp in S. cerevisiae or S. pastorianus strains did not significantly alter cell growth in medium containing glucose, maltose, maltotriose or wort at different concentrations.}, }
@article {pmid30957837, year = {2019}, author = {Quijada, NM and Rodríguez-Lázaro, D and Hernández, M}, title = {TORMES: an automated pipeline for whole bacterial genome analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz220}, pmid = {30957837}, issn = {1367-4811}, abstract = {MOTIVATION: The progress of High Throughput Sequencing (HTS) technologies and the reduction in the sequencing costs are such that Whole Genome Sequencing (WGS) could replace many traditional laboratory assays and procedures. Exploiting the volume of data produced by HTS platforms requires substantial computing skills and this is the main bottleneck in the implementation of WGS as a routine laboratory technique. The way in which the vast amount of results are presented to researchers and clinicians with no specialist knowledge of genome sequencing is also a significant issue.<br><br>RESULTS: Here we present TORMES, a user-friendly pipeline for WGS analysis of bacteria from any origin generated by HTS on Illumina platforms. TORMES is designed for non-bioinformatician users, and automates the steps required for WGS analysis directly from the raw sequence data: sequence quality filtering, de novo assembly, draft genome ordering against a reference, genome annotation, multi-locus sequence typing (MLST), searching for antibiotic resistance and virulence genes, and pangenome comparisons. Once the analysis is finished, TORMES generates and interactive web-like report that can be opened in any web browser and shared and revised by researchers in a simple manner. TORMES can be run by using very simple commands and represent a quick an easy way to perform WGS analysis.<br><br>AVAILABILITY: TORMES is free available at https://github.com/nmquijada/tormes.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data, manual and examples are available at Bioinformatics online and at the TORMES main page.}, }
@article {pmid30953542, year = {2019}, author = {Raymond, F and Boissinot, M and Ouameur, AA and Déraspe, M and Plante, PL and Kpanou, SR and Bérubé, È and Huletsky, A and Roy, PH and Ouellette, M and Bergeron, MG and Corbeil, J}, title = {Culture-enriched human gut microbiomes reveal core and accessory resistance genes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {56}, doi = {10.1186/s40168-019-0669-7}, pmid = {30953542}, issn = {2049-2618}, support = {Selectomics to monitor and predict the emergence of resistance to antibiotics//Québec Consortium for Drug Discovery/ ; Medical Genomics//Canada Research Chairs/ ; Antimicrobial Resistance//Canada Research Chairs/ ; RAC//Compute Canada/ ; }, abstract = {BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.<br><br>RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.<br><br>CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.}, }
@article {pmid30949149, year = {2019}, author = {Park, CJ and Andam, CP}, title = {Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {552}, doi = {10.3389/fmicb.2019.00552}, pmid = {30949149}, issn = {1664-302X}, abstract = {Streptomyces rimosus is best known as the primary source of the tetracycline class of antibiotics, most notably oxytetracycline, which have been widely used against many gram-positive and gram-negative pathogens and protozoan parasites. However, despite the medical and agricultural importance of S. rimosus, little is known of its evolutionary history and genome dynamics. In this study, we aim to elucidate the pan-genome characteristics and phylogenetic relationships of 32 S. rimosus genomes. The S. rimosus pan-genome contains more than 22,000 orthologous gene clusters, and approximately 8.8% of these genes constitutes the core genome. A large part of the accessory genome is composed of 9,646 strain-specific genes. S. rimosus exhibits an open pan-genome (decay parameter α = 0.83) and high gene diversity between strains (genomic fluidity φ = 0.12). We also observed strain-level variation in the distribution and abundance of biosynthetic gene clusters (BGCs) and that each individual S. rimosus genome has a unique repertoire of BGCs. Lastly, we observed variation in recombination, with some strains donating or receiving DNA more often than others, strains that tend to frequently recombine with specific partners, genes that often experience recombination more than others, and variable sizes of recombined DNA sequences. We conclude that the high levels of inter-strain genomic variation in S. rimosus is partly explained by differences in recombination among strains. These results have important implications on current efforts for natural drug discovery, the ecological role of strain-level variation in microbial populations, and addressing the fundamental question of why microbes have pan-genomes.}, }
@article {pmid30930881, year = {2019}, author = {Cho, H and Song, ES and Heu, S and Baek, J and Lee, YK and Lee, S and Lee, SW and Park, DS and Lee, TH and Kim, JG and Hwang, I}, title = {Prediction of Host-Specific Genes by Pan-Genome Analyses of the Korean Ralstonia solanacearum Species Complex.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {506}, doi = {10.3389/fmicb.2019.00506}, pmid = {30930881}, issn = {1664-302X}, abstract = {The soil-borne pathogenic Ralstonia solanacearum species complex (RSSC) is a group of plant pathogens that is economically destructive worldwide and has a broad host range, including various solanaceae plants, banana, ginger, sesame, and clove. Previously, Korean RSSC strains isolated from samples of potato bacterial wilt were grouped into four pathotypes based on virulence tests against potato, tomato, eggplant, and pepper. In this study, we sequenced the genomes of 25 Korean RSSC strains selected based on these pathotypes. The newly sequenced genomes were analyzed to determine the phylogenetic relationships between the strains with average nucleotide identity values, and structurally compared via multiple genome alignment using Mauve software. To identify candidate genes responsible for the host specificity of the pathotypes, functional genome comparisons were conducted by analyzing pan-genome orthologous group (POG) and type III secretion system effectors (T3es). POG analyses revealed that a total of 128 genes were shared only in tomato-non-pathogenic strains, 8 genes in tomato-pathogenic strains, 5 genes in eggplant-non-pathogenic strains, 7 genes in eggplant-pathogenic strains, 1 gene in pepper-non-pathogenic strains, and 34 genes in pepper-pathogenic strains. When we analyzed T3es, three host-specific effectors were predicted: RipS3 (SKWP3) and RipH3 (HLK3) were found only in tomato-pathogenic strains, and RipAC (PopC) were found only in eggplant-pathogenic strains. Overall, we identified host-specific genes and effectors that may be responsible for virulence functions in RSSC in silico. The expected characters of those genes suggest that the host range of RSSC is determined by the comprehensive actions of various virulence factors, including effectors, secretion systems, and metabolic enzymes.}, }
@article {pmid30929798, year = {2019}, author = {Bedoya-Correa, CM and Rincón Rodríguez, RJ and Parada-Sanchez, MT}, title = {Genomic and phenotypic diversity of Streptococcus mutans.}, journal = {Journal of oral biosciences}, volume = {61}, number = {1}, pages = {22-31}, doi = {10.1016/j.job.2018.11.001}, pmid = {30929798}, issn = {1880-3865}, abstract = {BACKGROUND: Streptococcus mutans (S. mutans) is a commensal microorganism found in the human oral cavity. However, due to environmental changes, selective pressures, and the presence of a variable genome, it adapts and may acquire new physiological and metabolic properties that alter dental biofilm homeostasis, promoting the development of dental caries. Although the plasticity and heterogeneity of S. mutans is widely recognized, very little is known about the mechanisms for the expression of pathogenic properties in specific genotypes.<br><br>HIGHLIGHT: The implementation of molecular biology techniques in the study of S. mutans has provided information on the genomic diversity of this species. This variability is generated by genome rearrangements, natural genetic transformation, and horizontal gene transfer, and continues to grow due to an open pan-genome. The main virulence factors associated with the cariogenic potential of S. mutans include adhesion, acid production (acidogenicity), and acid tolerance (aciduricity), and also show variability. These factors coordinate the modification of the physicochemical properties of the biofilm, which results in the accumulation of S. mutans and other acidogenic and aciduric species in the oral cavity.<br><br>CONCLUSION: We review the current literature on the main processes that generate S. mutans genomic diversity, as well as the phenotypic variability of its main virulence factors. S. mutans achieves its pathogenesis by sensing the intra- and extracellular environments and regulating gene transcription according to perceived environmental modifications. Consequently, this regulation gives rise to differential synthesis of proteins, allowing this species to potentially express virulence factors.}, }
@article {pmid30929020, year = {2019}, author = {Pinholt, M and Bayliss, SC and Gumpert, H and Worning, P and Jensen, VVS and Pedersen, M and Feil, EJ and Westh, H}, title = {WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dkz118}, pmid = {30929020}, issn = {1460-2091}, abstract = {OBJECTIVES: From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium (VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized.<br><br>METHODS: WGS of 1058 E. faecium isolates was carried out on the Illumina platform to perform SNP analysis and to identify the pan-genome. One isolate was also sequenced on the PacBio platform to close the genome. Epidemiological data were collected from laboratory information systems.<br><br>RESULTS: Phylogeny of 892 VREfm and 166 VSEfm revealed a polyclonal structure, with a single clonal group (ST80) accounting for 40% of the VREfm isolates. VREfm and VSEfm co-occurred within many clonal groups; however, no VSEfm were related to the dominant VREfm group. A similar vanA plasmid was identified in ≥99% of isolates belonging to the dominant group and 69% of the remaining VREfm. Ten plasmids were identified in the completed genome, and ∼29% of this genome consisted of dispensable accessory genes. The size of the pan-genome among isolates in the dominant group was 5905 genes.<br><br>CONCLUSIONS: Most probably, VREfm emerged owing to importation of a successful VREfm clone which rapidly transmitted to the majority of hospitals in the region whilst simultaneously disseminating a vanA plasmid to pre-existing VSEfm. Acquisition of a heterogeneous accessory genome may account for the success of this clone by facilitating adaptation to new environmental challenges.}, }
@article {pmid30918968, year = {2019}, author = {Smith, BA and Leligdon, C and Baltrus, DA}, title = {Just the Two of Us? A Family of Pseudomonas Megaplasmids Offers a Rare Glimpse Into the Evolution of Large Mobile Elements.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz066}, pmid = {30918968}, issn = {1759-6653}, abstract = {Pseudomonads are ubiquitous group of environmental proteobacteria, well known for their roles in biogeochemical cycling, in the breakdown of xenobiotic materials, as plant growth promoters, and as pathogens of a variety of host organisms. We have previously identified a large megaplasmid present within one isolate of the plant pathogen Pseudomonas syringae, and here we report that a second member of this megaplasmid family is found within an environmental Pseudomonad isolate most closely related to P. putida. Many of the shared genes are involved in critical cellular processes like replication, transcription, translation, and DNA repair. We argue that presence of these shared pathways sheds new light on discussions about the types of genes that undergo horizontal gene transfer (i.e. the complexity hypothesis) as well as the evolution of pangenomes. Furthermore, although both megaplasmids display a high level of synteny, genes that are shared differ by over 50% on average at the amino acid level. This combination of conservation in gene order despite divergence in gene sequence suggests that this Pseudomonad megaplasmid family is relatively old, that gene order is under strong selection within this family, and that there are likely many more members of this megaplasmid family waiting to be found in nature.}, }
@article {pmid30917781, year = {2019}, author = {Shelyakin, PV and Bochkareva, OO and Karan, AA and Gelfand, MS}, title = {Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {83}, doi = {10.1186/s12862-019-1403-6}, pmid = {30917781}, issn = {1471-2148}, support = {16-54-21004//Russian Foundation of Basic Research/ ; &quot;Molecular and Cellular Biology&quot;//Russian Academy of Sciences/ ; }, abstract = {BACKGROUND: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.<br><br>RESULTS: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity. Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.<br><br>CONCLUSIONS: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.}, }
@article {pmid30906288, year = {2019}, author = {Legendre, M and Alempic, JM and Philippe, N and Lartigue, A and Jeudy, S and Poirot, O and Ta, NT and Nin, S and Couté, Y and Abergel, C and Claverie, JM}, title = {Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Pandoraviridae Genomes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {430}, doi = {10.3389/fmicb.2019.00430}, pmid = {30906288}, issn = {1664-302X}, abstract = {With genomes of up to 2.7 Mb propagated in μm-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including three others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, pandoravirus celtis, closely related (96% identical genome) to the previously described p. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs, with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in p. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.}, }
@article {pmid30902757, year = {2019}, author = {Banerjee, R and Shine, O and Rajachandran, V and Govind, K and Minnick, MF and Paul, S and Chattopadhyay, S}, title = {Gene duplication and deletion, not horizontal transfer, drove intra-species mosaicism of Bartonella henselae.}, journal = {Genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ygeno.2019.03.009}, pmid = {30902757}, issn = {1089-8646}, abstract = {Bartonella henselae is a facultative intracellular pathogen that occurs worldwide and is responsible primarily for cat-scratch disease in young people and bacillary angiomatosis in immunocompromised patients. The principal source of genome-level diversity that contributes to B. henselae's host-adaptive features is thought to be horizontal gene transfer events. However, our analyses did not reveal the acquisition of horizontally-transferred islands in B. henselae after its divergence from other Bartonella. Rather, diversity in gene content and genome size was apparently acquired through two alternative mechanisms, including deletion and, more predominantly, duplication of genes. Interestingly, a majority of these events occurred in regions that were horizontally transferred long before B. henselae's divergence from other Bartonella species. Our study indicates the possibility that gene duplication, in response to positive selection pressures in specific clones of B. henselae, might be linked to the pathogen's adaptation to arthropod vectors, the cat reservoir, or humans as incidental host-species.}, }
@article {pmid30900970, year = {2019}, author = {de Carvalho, SP and de Almeida, JB and de Freitas, LM and Guimarães, AMS and do Nascimento, NC and Dos Santos, AP and Campos, GB and Messick, JB and Timenetsky, J and Marques, LM}, title = {Genomic profile of Brazilian methicillin-resistant Staphylococcus aureus resembles clones dispersed worldwide.}, journal = {Journal of medical microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/jmm.0.000956}, pmid = {30900970}, issn = {1473-5644}, abstract = {PURPOSE: Comparative genomic analysis of strains may help us to better understand the wide diversity of their genetic profiles. The aim of this study was to analyse the genomic features of the resistome and virulome of Brazilian first methicillin-resistant Staphylococcus aureus (MRSA) isolates and their relationship to other Brazilian and international MRSA strains.<br><br>METHODOLOGY: The whole genomes of three MRSA strains previously isolated in Vitória da Conquista were sequenced, assembled, annotated and compared with other MRSA genomes. A phylogenetic tree was constructed and the pan-genome and accessory and core genomes were constructed. The resistomes and virulomes of all strains were identified.Results/Key findings. Phylogenetic analysis of all 49 strains indicated different clones showing high similarity. The pan-genome of the analysed strains consisted of 4484 genes, with 31 % comprising the gene portion of the core genome, 47 % comprising the accessory genome and 22 % being singletons. Most strains showed at least one gene related to virulence factors associated with immune system evasion, followed by enterotoxins. The strains showed multiresistance, with the most recurrent genes conferring resistance to beta-lactams, fluoroquinolones, aminoglycosides and macrolides.<br><br>CONCLUSIONS: Our comparative genomic analysis showed that there is no pattern of virulence gene distribution among the clones analysed in the different regions. The Brazilian strains showed similarity with clones from several continents.}, }
@article {pmid30893420, year = {2019}, author = {Correia, K and Yu, SM and Mahadevan, R}, title = {AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, doi = {10.1093/database/baz022}, pmid = {30893420}, issn = {1758-0463}, abstract = {Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. Insight into the evolution of orthologs, paralogs and xenologs in the yeast pan-genome can help bridge these genotypes; however, existing phylogenomic databases do not span diverse yeasts, and sometimes cannot distinguish between these homologs. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML reconstructed the phylogeny of all homolog groups. Ortholog assignments for enzymes and small metabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://lmse.github.io/aybrah/), including functional annotations, predictions for mitochondrial localization and transmembrane domains, literature references and phylogenetic reconstructions. Ortholog assignments in AYbRAH were compared to HOGENOM, KEGG Orthology, OMA, eggNOG and PANTHER. PANTHER and OMA had the most congruent ortholog groups with AYbRAH, while the other phylogenomic databases had greater amounts of under-clustering, over-clustering or no ortholog annotations for proteins. Future plans are discussed for AYbRAH, and recommendations are made for other research communities seeking to create curated ortholog databases.}, }
@article {pmid30871454, year = {2019}, author = {Naz, K and Naz, A and Ashraf, ST and Rizwan, M and Ahmad, J and Baumbach, J and Ali, A}, title = {PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {123}, doi = {10.1186/s12859-019-2713-9}, pmid = {30871454}, issn = {1471-2105}, abstract = {BACKGROUND: A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine designing and development process. Reverse vaccinology is considered as a cost-effective and proficient approach to screen the entire pathogen genome. To look for broad-spectrum immunogenic targets and analysis of closely-related bacterial species, the assimilation of pangenome concept into reverse vaccinology approach is essential. The categories of species pangenome such as core, accessory, and unique genes sets can be analyzed for the identification of vaccine candidates through reverse vaccinology.<br><br>RESULTS: We have designed an integrative computational pipeline term as &quot;PanRV&quot; that employs both the pangenome and reverse vaccinology approaches. PanRV comprises of four functional modules including i) Pangenome Estimation Module (PGM) ii) Reverse Vaccinology Module (RVM) iii) Functional Annotation Module (FAM) and iv) Antibiotic Resistance Association Module (ARM). The pipeline is tested by using genomic data from 301 genomes of Staphylococcus aureus and the results are verified by experimentally known antigenic data.<br><br>CONCLUSION: The proposed pipeline has proved to be the first comprehensive automated pipeline that can precisely identify putative vaccine candidates exploiting the microbial pangenome. PanRV is a Linux based package developed in JAVA language. An executable installer is provided for ease of installation along with a user manual at https://sourceforge.net/projects/panrv2/ .}, }
@article {pmid30863859, year = {2019}, author = {Li, H and Ding, X and Chen, C and Zheng, X and Han, H and Li, C and Gong, J and Xu, T and Li, QX and Ding, GC and Li, J}, title = {Enrichment of phosphate solubilizing bacteria during late developmental stages of eggplant (Solanum melongena L.).}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiz023}, pmid = {30863859}, issn = {1574-6941}, abstract = {Understanding the ecology of phosphate solubilizing bacteria (PSBs) is critical for developing better strategies to increase crop productivity. In this study, the diversity of PSBs and of the total bacteria in the rhizosphere of eggplant (Solanum melongena L.) cultivated in organic, integrated and conventional farming systems was compared at four developmental stages of its lifecycle. Both selective culture and high-throughput sequencing analysis of 16S rRNA amplicons indicated that Enterobacter with strong or very strong in vivo phosphate solubilization activities was enriched in the rhizosphere during the fruiting stage. The high-throughput sequencing analysis results demonstrated that farming systems explained 23% of total bacterial community variation. Plant development and farming systems synergistically shaped the rhizospheric bacterial community, in which the degree of variation influenced by farming systems decreased over the plant development phase from 56% to 26.3% to 16.3%, and finally to no significant effect as the plant reached at fruiting stage. Pangenome analysis indicated that two-component and transporter systems varied between the rhizosphere and soil PSBs. This study elucidated the complex interactions among farming systems, plant development and rhizosphere microbiomes.}, }
@article {pmid30859492, year = {2019}, author = {Burgueño-Roman, A and Castañeda-Ruelas, GM and Pacheco-Arjona, R and Jimenez-Edeza, M}, title = {Pathogenic potential of non-typhoidal Salmonella serovars isolated from aquatic environments in Mexico.}, journal = {Genes &amp; genomics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s13258-019-00798-7}, pmid = {30859492}, issn = {2092-9293}, support = {CB-2014-01-235989//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {BACKGROUND: River water has been implicated as a source of non-typhoidal Salmonella (NTS) serovars in Mexico.<br><br>OBJECTIVE: To dissect the molecular pathogenesis and defense strategies of seven NTS strains isolated from river water in Mexico.<br><br>METHODS: The genome of Salmonella serovars Give, Pomona, Kedougou, Stanley, Oranienburg, Sandiego, and Muenchen were sequenced using the whole-genome shotgun methodology in the Illumina Miseq platform. The genoma annotation and evolutionary analyses were conducted in the RAST and FigTree servers, respectively. The MLST was performed using the SRST2 tool and the comparisons between strains were clustered and visualized using the Gview server. Experimental virulence assay was included to evaluate the pathogenic potential of strains.<br><br>RESULTS: We report seven high-quality draft genomes, ranging from ~ 4.61 to ~ 5.12 Mb, with a median G + C value, coding DNA sequence, and protein values of 52.1%, 4697 bp, and 4,589 bp, respectively. The NTS serovars presented with an open pan-genome, offering novel genetic content. Each NTS serovar had an indistinguishable virulotype with a core genome (352 virulence genes) closely associated with Salmonella pathogenicity; 13 genes were characterized as serotype specific, which could explain differences in pathogenicity. All strains maintained highly conserved genetic content regarding the Salmonella pathogenicity islands (1-5) (86.9-100%), fimbriae (84.6%), and hypermutation (100%) genes. Adherence and invasion capacity were confirmed among NTS strains in Caco-2 cells.<br><br>CONCLUSION: Our results demonstrated the arsenal of virulence and defense molecular factors harbored on NTS serovars and highlight that environmental NTS strains are waterborne pathogens worthy of attention.}, }
@article {pmid30858837, year = {2019}, author = {van Tonder, AJ and Bray, JE and Jolley, KA and Jansen van Rensburg, M and Quirk, SJ and Haraldsson, G and Maiden, MCJ and Bentley, SD and Haraldsson, Á and Erlendsdóttir, H and Kristinsson, KG and Brueggemann, AB}, title = {Genomic Analyses of &gt;3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {317}, doi = {10.3389/fmicb.2019.00317}, pmid = {30858837}, issn = {1664-302X}, abstract = {Understanding the structure of a bacterial population is essential in order to understand bacterial evolution. Estimating the core genome (those genes common to all, or nearly all, strains of a species) is a key component of such analyses. The size and composition of the core genome varies by dataset, but we hypothesized that the variation between different collections of the same bacterial species would be minimal. To investigate this, we analyzed the genome sequences of 3,118 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (United States), and Maela (Thailand). The analyses revealed a &quot;supercore&quot; genome (genes shared by all 3,118 pneumococci) of 558 genes, although an additional 354 core genes were shared by pneumococci from Reykjavik, Southampton, and Boston. Overall, the size and composition of the core and pan-genomes among pneumococci recovered in Reykjavik, Southampton, and Boston were similar. Maela pneumococci were distinctly different in that they had a smaller core genome and larger pan-genome. The pan-genome of Maela pneumococci contained several >25 Kb sequence regions (flanked by pneumococcal genes) that were homologous to genomic regions found in other bacterial species. Overall, our work revealed that some subsets of the global pneumococcal population are highly heterogeneous, and our hypothesis was rejected. This is an important finding in terms of understanding genetic variation among pneumococci and is also an essential point of consideration before generalizing the findings from a single dataset to the wider pneumococcal population.}, }
@article {pmid30858412, year = {2019}, author = {Obolski, U and Gori, A and Lourenço, J and Thompson, C and Thompson, R and French, N and Heyderman, RS and Gupta, S}, title = {Identifying genes associated with invasive disease in S. pneumoniae by applying a machine learning approach to whole genome sequence typing data.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4049}, doi = {10.1038/s41598-019-40346-7}, pmid = {30858412}, issn = {2045-2322}, abstract = {Streptococcus pneumoniae, a normal commensal of the upper respiratory tract, is a major public health concern, responsible for substantial global morbidity and mortality due to pneumonia, meningitis and sepsis. Why some pneumococci invade the bloodstream or CSF (so-called invasive pneumococcal disease; IPD) is uncertain. In this study we identify genes associated with IPD. We transform whole genome sequence (WGS) data into a sequence typing scheme, while avoiding the caveat of using an arbitrary genome as a reference by substituting it with a constructed pangenome. We then employ a random forest machine-learning algorithm on the transformed data, and find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of the genes we identified as associated with IPD, we find 23 genes previously shown to be directly relevant to IPD, as well as 18 uncharacterized genes. We suggest that these uncharacterized genes identified by us are also likely to be relevant for IPD.}, }
@article {pmid30853944, year = {2019}, author = {Khaleque, HN and González, C and Shafique, R and Kaksonen, AH and Holmes, DS and Watkin, ELJ}, title = {Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {155}, doi = {10.3389/fmicb.2019.00155}, pmid = {30853944}, issn = {1664-302X}, abstract = {There are few naturally occurring environments where both acid and salinity stress exist together, consequently, there has been little evolutionary pressure for microorganisms to develop systems that enable them to deal with both stresses simultaneously. Members of the genus Acidihalobacter are iron- and sulfur-oxidizing, halotolerant acidophiles that have developed the ability to tolerate acid and saline stress and, therefore, have the potential to bioleach ores with brackish or saline process waters under acidic conditions. The genus consists of four members, A. prosperus DSM 5130T, A. prosperus DSM 14174, A. prosperus F5 and &quot;A. ferrooxidans&quot; DSM 14175. An in depth genome comparison was undertaken in order to provide a more comprehensive description of the mechanisms of halotolerance used by the different members of this genus. Pangenome analysis identified 29, 3 and 9 protein families related to halotolerance in the core, dispensable and unique genomes, respectively. The genes for halotolerance showed Ka/Ks ratios between 0 and 0.2, confirming that they are conserved and stabilized. All the Acidihalobacter genomes contained similar genes for the synthesis and transport of ectoine, which was recently found to be the dominant osmoprotectant in A. prosperus DSM 14174 and A. prosperus DSM 5130T. Similarities also existed in genes encoding low affinity potassium pumps, however, A. prosperus DSM 14174 was also found to contain genes encoding high affinity potassium pumps. Furthermore, only A. prosperus DSM 5130T and &quot;A. ferrooxidans&quot; DSM 14175 contained genes allowing the uptake of taurine as an osmoprotectant. Variations were also seen in genes encoding proteins involved in the synthesis and/or transport of periplasmic glucans, sucrose, proline, and glycine betaine. This suggests that versatility exists in the Acidihalobacter genus in terms of the mechanisms they can use for halotolerance. This information is useful for developing hypotheses for the search for life on exoplanets and moons.}, }
@article {pmid30851098, year = {2019}, author = {Tahir Ul Qamar, M and Zhu, X and Xing, F and Chen, LL}, title = {ppsPCP: A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz168}, pmid = {30851098}, issn = {1367-4811}, abstract = {SUMMARY: Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics. To aid the eukaryotic pan-genomic studies, here we present ppsPCP pipeline which is designed for eukaryotes especially for plants. It is capable of scanning presence/absence variants (PAVs) and constructing a fully annotated pan-genome. We believe with these unique features of PAV scanning and building a pan-genome together with its annotation, ppsPCP will be useful for plant pan-genomic studies and aid researchers to study genetic/phenotypic variations and genomic diversity.<br><br>The ppsPCP is freely available at github DOI: https://doi.org/10.5281/zenodo.2567390 and webpage http://cbi.hzau.edu.cn/ppsPCP/.}, }
@article {pmid30851095, year = {2019}, author = {Rautiainen, M and Mäkinen, V and Marschall, T}, title = {Bit-parallel sequence-to-graph alignment.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz162}, pmid = {30851095}, issn = {1367-4811}, abstract = {MOTIVATION: Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction, and variant calling with respect to a variation graph.<br><br>RESULTS: We generalize two linear sequence-to-sequence algorithms to graphs: the Shift-And algorithm for exact matching and Myers' bitvector algorithm for semi-global alignment. These linear algorithms are both based on processing w sequence characters with a constant number of operations, where w is the word size of the machine (commonly 64), and achieve a speedup of up to w over naive algorithms. For a graph with nodes and edges and a sequence of length m, our bitvector-based graph alignment algorithm reaches a worst case runtime of for acyclic graphs and for arbitrary cyclic graphs. We apply it to five different types of graphs and observe a speedup between 3-fold and 20-fold compared to a previous (asymptotically optimal) alignment algorithm by Navarro (2000).<br><br>AVAILABILITY: https://github.com/maickrau/GraphAligner.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30847473, year = {2019}, author = {Velsko, IM and Perez, MS and Richards, VP}, title = {Resolving phylogenetic relationships for Streptococcus mitis and Streptococcus oralis through core and pan genome analyses.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz049}, pmid = {30847473}, issn = {1759-6653}, abstract = {Taxonomic and phylogenetic relationships of Streptococcus mitis and Streptococcus oralis have been difficult to establish biochemically and genetically. We used core genome analyses of S. mitis and S. oralis, as well as the closely-related species S. pneumoniae and S. parasanguinis, to clarify the phylogenetic relationships between S. mitis and S. oralis, as well as within subclades of S. oralis. All S. mitis (n = 67), S. oralis (n = 89), S. parasanguinis (n = 27), and 27 S. pneumoniae genome assemblies were downloaded from NCBI and re-annotated. All genes were delineated into homologous clusters and maximum-likelihood phylogenies built from putatively non-recombinant core gene sets. Population structure was determined using Bayesian genome clustering, and patristic distance calculated between populations. Population-specific gene content was assessed using a phylogenetic-based genome-wide association approach. Streptococcus mitis and S. oralis formed distinct clades, but species mixing suggests taxonomic mis-assignment. Patristic distance between populations suggest S. oralis subsp. dentisani is a distinct species, while S. oralis subsp. tigurinus and subsp. oralis are supported as subspecies, and that S. mitis comprises two subspecies. None of the genes within the pan-genomes of S. mitis and S. oralis could be statistically correlated with either, and the dispensable genomes showed extensive variation among isolates. These are likely important factors contributing to established overlap in biochemical characteristics for these taxa. Based on core genome analysis, the substructure of S. oralis and S. mitis should be re-defined, and species assignments within S. oralis and S. mitis should be made based on whole genome analysis to be robust to mis-assignment.}, }
@article {pmid30825936, year = {2019}, author = {Eisenbach, L and Geissler, AJ and Ehrmann, MA and Vogel, RF}, title = {Comparative genomics of Lactobacillus sakei supports the development of starter strain combinations.}, journal = {Microbiological research}, volume = {221}, number = {}, pages = {1-9}, doi = {10.1016/j.micres.2019.01.001}, pmid = {30825936}, issn = {1618-0623}, abstract = {Strains of Lactobacillus sakei can be isolated from a variety of sources including meat, fermented sausages, sake, sourdough, sauerkraut or kimchi. Selected strains are widely used as starter cultures for sausage fermentation. Recently we have demonstrated that control about the lactic microbiota in fermenting sausages is achieved rather by pairs or strain sets than by single strains. In this work we characterized the pan genome of L. sakei to enable exploitation of the genomic diversity of L. sakei for the establishment of assertive starter strain sets. We have established the full genome sequences of nine L. sakei strains from different sources of isolation and included in the analysis the genome of L. sakei 23K. Comparative genomics revealed an accessory genome comprising about 50% of the pan genome and different lineages of strains with no relation to their source of isolation. Group and strain specific differences could be found, which namely referred to agmatine and citrate metabolism. The presence of genes encoding metabolic pathways for fructose, sucrose and trehalose as well as gluconate in all strains suggests a general adaptation to plant/sugary environments and a life in communities with other genera. Analysis of the plasmidome did not reveal any specific mechanisms of adaptation to a habitat. The predicted differences of metabolic settings enable prediction of partner strains, which can occupy the meat environment to a large extent and establish competitive exclusion of autochthonous microbiota. This may assist the development of a new generation of meat starter cultures containing L. sakei strains.}, }
@article {pmid30814318, year = {2019}, author = {Raphael, BH and Huynh, T and Brown, E and Smith, JC and Ruberto, I and Getsinger, L and White, S and Winchell, JM}, title = {Culture of Clinical Specimens Reveals Extensive Diversity of Legionella pneumophila Strains in Arizona.}, journal = {mSphere}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSphere.00649-18}, pmid = {30814318}, issn = {2379-5042}, abstract = {Between 2000 and 2017, a total of 236 Legionella species isolates from Arizona were submitted to the CDC for reference testing. Most of these isolates were recovered from bronchoalveolar lavage specimens. Although the incidence of legionellosis in Arizona is less than the overall U.S. incidence, Arizona submits the largest number of isolates to the CDC for testing compared to those from other states. In addition to a higher proportion of culture confirmation of legionellosis cases in Arizona than in other states, all Legionellapneumophila isolates are forwarded to the CDC for confirmatory testing. Compared to that from other states, a higher proportion of isolates from Arizona were identified as belonging to L. pneumophila serogroups 6 (28.2%) and 8 (8.9%). Genome sequencing was conducted on 113 L. pneumophila clinical isolates not known to be associated with outbreaks in order to understand the genomic diversity of strains causing legionellosis in Arizona. Whole-genome multilocus sequence typing (wgMLST) revealed 17 clusters of isolates sharing at least 99% identical allele content. Only two of these clusters contained isolates from more than one individual with exposure at the same facility. Additionally, wgMLST analysis revealed a group of 31 isolates predominantly belonging to serogroup 6 and containing isolates from three separate clusters. Single nucleotide polymorphism (SNP) and pangenome analysis were used to further resolve genome sequences belonging to a subset of isolates. This study demonstrates that culture of clinical specimens for Legionella spp. reveals a highly diverse population of strains causing legionellosis in Arizona which could be underappreciated using other diagnostic approaches.IMPORTANCE Culture of clinical specimens from patients with Legionnaires' disease is rarely performed, restricting our understanding of the diversity and ecology of Legionella Culture of Legionella from patient specimens in Arizona revealed a greater proportion of non-serogroup 1 Legionellapneumophila isolates than in other U.S. isolates examined. Disease caused by such isolates may go undetected using other diagnostic methods. Moreover, genome sequence analysis revealed that these isolates were genetically diverse, and understanding these populations may help in future environmental source attribution studies.}, }
@article {pmid30811910, year = {2019}, author = {Gabbett, MT and Laporte, J and Sekar, R and Nandini, A and McGrath, P and Sapkota, Y and Jiang, P and Zhang, H and Burgess, T and Montgomery, GW and Chiu, R and Fisk, NM}, title = {Molecular Support for Heterogonesis Resulting in Sesquizygotic Twinning.}, journal = {The New England journal of medicine}, volume = {380}, number = {9}, pages = {842-849}, doi = {10.1056/NEJMoa1701313}, pmid = {30811910}, issn = {1533-4406}, support = {T12-403/15-N/// ; }, abstract = {Sesquizygotic multiple pregnancy is an exceptional intermediate between monozygotic and dizygotic twinning. We report a monochorionic twin pregnancy with fetal sex discordance. Genotyping of amniotic fluid from each sac showed that the twins were maternally identical but chimerically shared 78% of their paternal genome, which makes them genetically in between monozygotic and dizygotic; they are sesquizygotic. We observed no evidence of sesquizygosis in 968 dizygotic twin pairs whom we screened by means of pangenome single-nucleotide polymorphism genotyping. Data from published repositories also show that sesquizygosis is a rare event. Detailed genotyping implicates chimerism arising at the juncture of zygotic division, termed heterogonesis, as the likely initial step in the causation of sesquizygosis.}, }
@article {pmid30808378, year = {2019}, author = {Caputo, A and Fournier, PE and Raoult, D}, title = {Genome and pan-genome analysis to classify emerging bacteria.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {5}, doi = {10.1186/s13062-019-0234-0}, pmid = {30808378}, issn = {1745-6150}, abstract = {BACKGROUND: In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of rapid identification by MALDI-TOF, or 16S rRNA. Bacterial taxonomy is undergoing many changes as a consequence. With the help of pan-genomic analyses, species can be redefined, and new species definitions generated.<br><br>RESULTS: Genomics, coupled with culturomics, has led to the discovery of many novel bacterial species or genera, including Akkermansia muciniphila and Microvirga massiliensis. Using the genome to define species has been applied within the genus Klebsiella. A discontinuity or an abrupt break in the core/pan-genome ratio can uncover novel species.<br><br>CONCLUSIONS: Applying genomic and pan-genomic analyses to the reclassification of other bacterial species or genera will be important in the future of medical microbiology. The pan-genome is one of many new innovative tools in bacterial taxonomy.<br><br>REVIEWERS: This article was reviewed by William Martin, Eric Bapteste and James Mcinerney.<br><br>OPEN PEER REVIEW: Reviewed by William Martin, Eric Bapteste and James Mcinerney.}, }
@article {pmid30801025, year = {2019}, author = {Entwistle, S and Li, X and Yin, Y}, title = {Orphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial Pathogenicity.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00290-18}, pmid = {30801025}, issn = {2379-5077}, abstract = {Orphan genes (also known as ORFans [i.e., orphan open reading frames]) are new genes that enable an organism to adapt to its specific living environment. Our focus in this study is to compare ORFans between pathogens (P) and nonpathogens (NP) of the same genus. Using the pangenome idea, we have identified 130,169 ORFans in nine bacterial genera (505 genomes) and classified these ORFans into four groups: (i) SS-ORFans (P), which are only found in a single pathogenic genome; (ii) SS-ORFans (NP), which are only found in a single nonpathogenic genome; (iii) PS-ORFans (P), which are found in multiple pathogenic genomes; and (iv) NS-ORFans (NP), which are found in multiple nonpathogenic genomes. Within the same genus, pathogens do not always have more genes, more ORFans, or more pathogenicity-related genes (PRGs)-including prophages, pathogenicity islands (PAIs), virulence factors (VFs), and horizontal gene transfers (HGTs)-than nonpathogens. Interestingly, in pathogens of the nine genera, the percentages of PS-ORFans are consistently higher than those of SS-ORFans, which is not true in nonpathogens. Similarly, in pathogens of the nine genera, the percentages of PS-ORFans matching the four types of PRGs are also always higher than those of SS-ORFans, but this is not true in nonpathogens. All of these findings suggest the greater importance of PS-ORFans for bacterial pathogenicity. IMPORTANCE Recent pangenome analyses of numerous bacterial species have suggested that each genome of a single species may have a significant fraction of its gene content unique or shared by a very few genomes (i.e., ORFans). We selected nine bacterial genera, each containing at least five pathogenic and five nonpathogenic genomes, to compare their ORFans in relation to pathogenicity-related genes. Pathogens in these genera are known to cause a number of common and devastating human diseases such as pneumonia, diphtheria, melioidosis, and tuberculosis. Thus, they are worthy of in-depth systems microbiology investigations, including the comparative study of ORFans between pathogens and nonpathogens. We provide direct evidence to suggest that ORFans shared by more pathogens are more associated with pathogenicity-related genes and thus are more important targets for development of new diagnostic markers or therapeutic drugs for bacterial infectious diseases.}, }
@article {pmid30783197, year = {2019}, author = {Lin, JN and Lai, CH and Yang, CH and Huang, YH and Lin, HH}, title = {Genomic Features, Comparative Genomics, and Antimicrobial Susceptibility Patterns of Elizabethkingia bruuniana.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2267}, doi = {10.1038/s41598-019-38998-6}, pmid = {30783197}, issn = {2045-2322}, support = {EDPJ106075//E-Da Hospital/ ; MOST 106-2314-B-214-009-MY2//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; }, abstract = {Elizabethkingia bruuniana is a novel species of the Elizabethkingia genus. There is scant information on this microorganism. Here, we report the whole-genome features and antimicrobial susceptibility patterns of E. bruuniana strain EM798-26. Elizabethkingia strain EM798-26 was initially identified as E. miricola. This isolate contained a circular genome of 4,393,011 bp. The whole-genome sequence-based phylogeny revealed that Elizabethkingia strain EM798-26 was in the same group of the type strain E. bruuniana G0146T. Both in silico DNA-DNA hybridization and average nucleotide identity analysis clearly demonstrated that Elizabethkingia strain EM798-26 was a species of E. bruuniana. The pan-genome analysis identified 2,875 gene families in the core genome and 5,199 gene families in the pan genome of eight publicly available E. bruuniana genome sequences. The unique genes accounted for 0.2-12.1% of the pan genome in each E. bruuniana. A total of 59 potential virulence factor homologs were predicted in the whole-genome of E. bruuniana strain EM798-26. This isolate was nonsusceptible to multiple antibiotics, but susceptible to aminoglycosides, minocycline, and levofloxacin. The whole-genome sequence analysis of E. bruuniana EM798-26 revealed 29 homologs of antibiotic resistance-related genes. This study presents the genomic features of E. bruuniana. Knowledge of the genomic characteristics provides valuable insights into a novel species.}, }
@article {pmid30782660, year = {2019}, author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S}, title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02852-18}, pmid = {30782660}, issn = {2150-7511}, abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel &quot;chromids,&quot; or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.}, }
@article {pmid30781742, year = {2019}, author = {Issa, E and Salloum, T and Panossian, B and Ayoub, D and Abboud, E and Tokajian, S}, title = {Genome Mining and Comparative Analysis of Streptococcus intermedius Causing Brain Abscess in a Child.}, journal = {Pathogens (Basel, Switzerland)}, volume = {8}, number = {1}, pages = {}, doi = {10.3390/pathogens8010022}, pmid = {30781742}, issn = {2076-0817}, abstract = {Streptococcus intermedius (SI) is associated with prolonged hospitalization and low survival rates. The genetic mechanisms involved in brain abscess development and genome evolution in comparison to other members of the Streptococcus anginosus group are understudied. We performed a whole-genome comparative analysis of an SI isolate, LAU_SINT, associated with brain abscess following sinusitis with all SI genomes in addition to S. constellatus and S. anginosus. Selective pressure on virulence factors, phages, pan-genome evolution and single-nucleotide polymorphism analysis were assessed. The structural details of the type seven secretion system (T7SS) was elucidated and compared with different organisms. ily and nanA were both abundant and conserved. Nisin resistance determinants were found in 47% of the isolates. Pan-genome and SNPs-based analysis didn't reveal significant geo-patterns. Our results showed that two SC isolates were misidentified as SI. We propose the presence of four T7SS modules (I⁻IV) located on various genomic islands. We detected a variety of factors linked to metal ions binding on the GIs carrying T7SS. This is the first detailed report characterizing the T7SS and its link to nisin resistance and metal ions binding in SI. These and yet uncharacterized T7SS transmembrane proteins merit further studies and could represent potential therapeutic targets.}, }
@article {pmid30779737, year = {2019}, author = {Grytten, I and Rand, KD and Nederbragt, AJ and Storvik, GO and Glad, IK and Sandve, GK}, title = {Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.}, journal = {PLoS computational biology}, volume = {15}, number = {2}, pages = {e1006731}, doi = {10.1371/journal.pcbi.1006731}, pmid = {30779737}, issn = {1553-7358}, abstract = {Graph-based representations are considered to be the future for reference genomes, as they allow integrated representation of the steadily increasing data on individual variation. Currently available tools allow de novo assembly of graph-based reference genomes, alignment of new read sets to the graph representation as well as certain analyses like variant calling and haplotyping. We here present a first method for calling ChIP-Seq peaks on read data aligned to a graph-based reference genome. The method is a graph generalization of the peak caller MACS2, and is implemented in an open source tool, Graph Peak Caller. By using the existing tool vg to build a pan-genome of Arabidopsis thaliana, we validate our approach by showing that Graph Peak Caller with a pan-genome reference graph can trace variants within peaks that are not part of the linear reference genome, and find peaks that in general are more motif-enriched than those found by MACS2.}, }
@article {pmid30775379, year = {2019}, author = {Lu, QF and Cao, DM and Su, LL and Li, SB and Ye, GB and Zhu, XY and Wang, JP}, title = {Genus-Wide Comparative Genomics Analysis of Neisseria to Identify New Genes Associated with Pathogenicity and Niche Adaptation of Neisseria Pathogens.}, journal = {International journal of genomics}, volume = {2019}, number = {}, pages = {6015730}, doi = {10.1155/2019/6015730}, pmid = {30775379}, issn = {2314-436X}, abstract = {N. gonorrhoeae and N. meningitidis, the only two human pathogens of Neisseria, are closely related species. But the niches they survived in and their pathogenic characteristics are distinctly different. However, the genetic basis of these differences has not yet been fully elucidated. In this study, comparative genomics analysis was performed based on 15 N. gonorrhoeae, 75 N. meningitidis, and 7 nonpathogenic Neisseria genomes. Core-pangenome analysis found 1111 conserved gene families among them, and each of these species groups had opening pangenome. We found that 452, 78, and 319 gene families were unique in N. gonorrhoeae, N. meningitidis, and both of them, respectively. Those unique gene families were regarded as candidates that related to their pathogenicity and niche adaptation. The relationships among them have been partly verified by functional annotation analysis. But at least one-third genes for each gene set have not found the certain functional information. Simple sequence repeat (SSR), the basis of gene phase variation, was found abundant in the membrane or related genes of each unique gene set, which may facilitate their adaptation to variable host environments. Protein-protein interaction (PPI) analysis found at least five distinct PPI clusters in N. gonorrhoeae and four in N. meningitides, and 167 and 52 proteins with unknown function were contained within them, respectively.}, }
@article {pmid30760727, year = {2019}, author = {Stevens, MJA and Tasara, T and Klumpp, J and Stephan, R and Ehling-Schulz, M and Johler, S}, title = {Whole-genome-based phylogeny of Bacillus cytotoxicus reveals different clades within the species and provides clues on ecology and evolution.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1984}, doi = {10.1038/s41598-018-36254-x}, pmid = {30760727}, issn = {2045-2322}, abstract = {Bacillus cytotoxicus is a member of the Bacillus cereus group linked to fatal cases of diarrheal disease. Information on B. cytotoxicus is very limited; in particular comprehensive genomic data is lacking. Thus, we applied a genomic approach to characterize B. cytotoxicus and decipher its population structure. To this end, complete genomes of ten B. cytotoxicus were sequenced and compared to the four publicly available full B. cytotoxicus genomes and genomes of other B. cereus group members. Average nucleotide identity, core genome, and pan genome clustering resulted in clear distinction of B. cytotoxicus strains from other strains of the B. cereus group. Genomic content analyses showed that a hydroxyphenylalanine operon is present in B. cytotoxicus, but absent in all other members of the B. cereus group. It enables degradation of aromatic compounds to succinate and pyruvate and was likely acquired from another Bacillus species. It allows for utilization of tyrosine and might have given a B. cytotoxicus ancestor an evolutionary advantage resulting in species differentiation. Plasmid content showed that B. cytotoxicus is flexible in exchanging genes, allowing for quick adaptation to the environment. Genome-based phylogenetic analyses divided the B. cytotoxicus strains into four clades that also differed in virulence gene content.}, }
@article {pmid30745056, year = {2019}, author = {Lye, ZN and Purugganan, MD}, title = {Copy Number Variation in Domestication.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2019.01.003}, pmid = {30745056}, issn = {1878-4372}, abstract = {Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of domestication. Ongoing work demonstrates the importance of CNVs as a source of genetic variation during domestication, and during the diversification of domesticated taxa. Here, we review how CNVs contribute to evolutionary processes underlying domestication, and review examples of domestication traits caused by CNVs. We draw from examples in plant species, but also highlight cases in animal systems that could illuminate the roles of CNVs in the domestication process.}, }
@article {pmid30657445, year = {2019}, author = {Wilson, K and Ely, B}, title = {Analyses of four new Caulobacter Phicbkviruses indicate independent lineages.}, journal = {The Journal of general virology}, volume = {100}, number = {2}, pages = {321-331}, doi = {10.1099/jgv.0.001218}, pmid = {30657445}, issn = {1465-2099}, abstract = {Bacteriophages with genomes larger than 200 kbp are considered giant phages, and the giant Phicbkviruses are the most frequently isolated Caulobacter crescentus phages. In this study, we compare six bacteriophage genomes that differ from the genomes of the majority of Phicbkviruses. Four of these genomes are much larger than those of the rest of the Phicbkviruses, with genome sizes that are more than 250 kbp. A comparison of 16 Phicbkvirus genomes identified a 'core genome' of 69 genes that is present in all of these Phicbkvirus genomes, as well as shared accessory genes and genes that are unique for each phage. Most of the core genes are clustered into the regions coding for structural proteins or those involved in DNA replication. A phylogenetic analysis indicated that these 16 CaulobacterPhicbkvirus genomes are related, but they represent four distinct branches of the Phicbkvirus genomic tree with distantly related branches sharing little nucleotide homology. In contrast, pairwise comparisons within each branch of the phylogenetic tree showed that more than 80 % of the entire genome is shared among phages within a group. This conservation of the genomes within each branch indicates that horizontal gene transfer events between the groups are rare. Therefore, the Phicbkvirus genus consists of at least four different phylogenetic branches that are evolving independently from one another. One of these branches contains a 27-gene inversion relative to the other three branches. Also, an analysis of the tRNA genes showed that they are relatively mobile within the Phicbkvirus genus.}, }
@article {pmid30718880, year = {2019}, author = {Arora, S and Steuernagel, B and Gaurav, K and Chandramohan, S and Long, Y and Matny, O and Johnson, R and Enk, J and Periyannan, S and Singh, N and Asyraf Md Hatta, M and Athiyannan, N and Cheema, J and Yu, G and Kangara, N and Ghosh, S and Szabo, LJ and Poland, J and Bariana, H and Jones, JDG and Bentley, AR and Ayliffe, M and Olson, E and Xu, SS and Steffenson, BJ and Lagudah, E and Wulff, BBH}, title = {Resistance gene cloning from a wild crop relative by sequence capture and association genetics.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {139-143}, doi = {10.1038/s41587-018-0007-9}, pmid = {30718880}, issn = {1546-1696}, abstract = {Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel.}, }
@article {pmid30718868, year = {2019}, author = {Zou, Y and Xue, W and Luo, G and Deng, Z and Qin, P and Guo, R and Sun, H and Xia, Y and Liang, S and Dai, Y and Wan, D and Jiang, R and Su, L and Feng, Q and Jie, Z and Guo, T and Xia, Z and Liu, C and Yu, J and Lin, Y and Tang, S and Huo, G and Xu, X and Hou, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Li, J and Jia, H and Xiao, L}, title = {1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {179-185}, doi = {10.1038/s41587-018-0008-8}, pmid = {30718868}, issn = {1546-1696}, abstract = {Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.}, }
@article {pmid30714895, year = {2019}, author = {McCarthy, CGP and Fitzpatrick, DA}, title = {Pan-genome analyses of model fungal species.}, journal = {Microbial genomics}, volume = {}, number = {}, pages = {}, doi = {10.1099/mgen.0.000243}, pmid = {30714895}, issn = {2057-5858}, abstract = {The concept of the species 'pan-genome', the union of 'core' conserved genes and all 'accessory' non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining 'accessory' gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.}, }
@article {pmid30709821, year = {2019}, author = {Lugli, GA and Mancino, W and Milani, C and Duranti, S and Mancabelli, L and Napoli, S and Mangifesta, M and Viappiani, A and Anzalone, R and Longhi, G and van Sinderen, D and Ventura, M and Turroni, F}, title = {Dissecting the evolutionary development of the Bifidobacterium animalis species through comparative genomics analyses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02806-18}, pmid = {30709821}, issn = {1098-5336}, abstract = {Bifidobacteria are members of the gut microbiota of animals, including mammals, birds and social insects. In this study, we analyzed and determined the pan-genome of Bifidobacterium animalis species, encompassing Bifidobacterium animalis subsp. animalis and the Bifidobacterium animalis subsp. lactis taxon, which is one of the most intensely exploited probiotic bifidobacterial species. In order to reveal differences within the B. animalis species, detailed comparative genomics and phylogenomics analyses were performed, indicating that these two subspecies recently arose through divergent evolutionary events. A subspecies-specific core genome was identified for both B. animalis subspecies, revealing the existence of subspecies-defining genes involved in carbohydrate metabolism. Notably, these in silico analyses coupled with carbohydrate profiling assays suggest genetic adaptations toward a distinct glycan milieu for each member of the B. animalis subspecies, resulting in a divergent evolutionary development of the two subspecies.IMPORTANCEThe majority of characterized B. animalis strains have been isolated from human fecal samples. In order to explore genome variability within this species, we isolated 15 novel strains from the GIT of different animals, including mammals and birds. The current study allowed us to reconstruct the pan-genome of this taxon, including the genome contents of 56 B. animalis strains. Through careful assessment of subspecies-specific core-genes of the B. animalis subsp. animalis/lactis taxon, we identified genes encoding enzymes involved in carbohydrate transport and metabolism, while unveiling specific gene-acquisition and -loss events that caused the evolutionary emergence of these two subspecies.}, }
@article {pmid30704472, year = {2019}, author = {Nono, AD and Chen, K and Liu, X}, title = {Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes.}, journal = {BMC medical genomics}, volume = {12}, number = {Suppl 1}, pages = {22}, doi = {10.1186/s12920-018-0452-9}, pmid = {30704472}, issn = {1755-8794}, abstract = {BACKGROUND: Identifying cancer driver genes (CDG) is a crucial step in cancer genomic toward the advancement of precision medicine. However, driver gene discovery is a very challenging task because we are not only dealing with huge amount of data; but we are also faced with the complexity of the disease including the heterogeneity of background somatic mutation rate in each cancer patient. It is generally accepted that CDG harbor variants conferring growth advantage in the malignant cell and they are positively selected, which are critical to cancer development; whereas, non-driver genes harbor random mutations with no functional consequence on cancer. Based on this fact, function prediction based approaches for identifying CDG have been proposed to interrogate the distribution of functional predictions among mutations in cancer genomes (eLS 1-16, 2016). Assuming most of the observed mutations are passenger mutations and given the quantitative predictions for the functional impact of the mutations, genes enriched of functional or deleterious mutations are more likely to be drivers. The promises of these methods have been continually refined and can therefore be applied to increase accuracy in detecting new candidate CDGs. However, current function prediction based approaches only focus on coding mutations and lack a systematic way to pick the best mutation deleteriousness prediction algorithms for usage.<br><br>RESULTS: In this study, we propose a new function prediction based approach to discover CDGs through a gene-based permutation approach. Our method not only covers both coding and non-coding regions of the genes; but it also accounts for the heterogeneous mutational context in cohort of cancer patients. The permutation model was implemented independently using seven popular deleteriousness prediction scores covering splicing regions (SPIDEX), coding regions (MetaLR, and VEST3) and pan-genome (CADD, DANN, Fathmm-MKL coding and Fathmm-MKL noncoding). We applied this new approach to somatic single nucleotide variants (SNVs) from whole-genome sequences of 119 breast and 24 lung cancer patients and compared the seven deleteriousness prediction scores for their performance in this study.<br><br>CONCLUSION: The new function prediction based approach not only predicted known cancer genes listed in the Cancer Gene Census (CGC), but also new candidate CDGs that are worth further investigation. The results showed the advantage of utilizing pan-genome deleteriousness prediction scores in function prediction based methods. Although VEST3 score, a deleteriousness prediction score for missense mutations, has the best performance in breast cancer, it was topped by CADD and Fathmm-MKL coding, two pan-genome deleteriousness prediction scores, in lung cancer.}, }
@article {pmid30701191, year = {2019}, author = {Leviatan, S and Segal, E}, title = {A Significant Expansion of Our Understanding of the Composition of the Human Microbiome.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00010-19}, pmid = {30701191}, issn = {2379-5077}, abstract = {Shotgun sequencing of samples taken from the human microbiome often reveals only partial mapping of the sequenced metagenomic reads to existing reference genomes. Such partial mappability indicates that many genomes are missing in our reference genome set. This is particularly true for non-Western populations and for samples that do not originate from the gut. Pasolli et al. (E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, et al., Cell, 2019, https://doi.org/10.1016/j.cell.2019.01.001) perform a grand effort to expand the reference set, and to better classify its members, revealing a wider pangenome of existing species as well as identifying new species of previously unknown taxonomic branches.}, }
@article {pmid30687297, year = {2018}, author = {Sánchez-Osuna, M and Cortés, P and Barbé, J and Erill, I}, title = {Origin of the Mobile Di-Hydro-Pteroate Synthase Gene Determining Sulfonamide Resistance in Clinical Isolates.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3332}, doi = {10.3389/fmicb.2018.03332}, pmid = {30687297}, issn = {1664-302X}, abstract = {Sulfonamides are synthetic chemotherapeutic agents that work as competitive inhibitors of the di-hydro-pteroate synthase (DHPS) enzyme, encoded by the folP gene. Resistance to sulfonamides is widespread in the clinical setting and predominantly mediated by plasmid- and integron-borne sul1-3 genes encoding mutant DHPS enzymes that do not bind sulfonamides. In spite of their clinical importance, the genetic origin of sul1-3 genes remains unknown. Here we analyze sul genes and their genetic neighborhoods to uncover sul signature elements that enable the elucidation of their genetic origin. We identify a protein sequence Sul motif associated with sul-encoded proteins, as well as consistent association of a phosphoglucosamine mutase gene (glmM) with the sul2 gene. We identify chromosomal folP genes bearing these genetic markers in two bacterial families: the Rhodobiaceae and the Leptospiraceae. Bayesian phylogenetic inference of FolP/Sul and GlmM protein sequences clearly establishes that sul1-2 and sul3 genes originated as a mobilization of folP genes present in, respectively, the Rhodobiaceae and the Leptospiraceae, and indicate that the Rhodobiaceae folP gene was transferred from the Leptospiraceae. Analysis of %GC content in folP/sul gene sequences supports the phylogenetic inference results and indicates that the emergence of the Sul motif in chromosomally encoded FolP proteins is ancient and considerably predates the clinical introduction of sulfonamides. In vitro assays reveal that both the Rhodobiaceae and the Leptospiraceae, but not other related chromosomally encoded FolP proteins confer resistance in a sulfonamide-sensitive Escherichia coli background, indicating that the Sul motif is associated with sulfonamide resistance. Given the absence of any known natural sulfonamides targeting DHPS, these results provide a novel perspective on the emergence of resistance to synthetic chemotherapeutic agents, whereby preexisting resistant variants in the vast bacterial pangenome may be rapidly selected for and disseminated upon the clinical introduction of novel chemotherapeuticals.}, }
@article {pmid30687252, year = {2018}, author = {Slama, HB and Cherif-Silini, H and Chenari Bouket, A and Qader, M and Silini, A and Yahiaoui, B and Alenezi, FN and Luptakova, L and Triki, MA and Vallat, A and Oszako, T and Rateb, ME and Belbahri, L}, title = {Screening for Fusarium Antagonistic Bacteria From Contrasting Niches Designated the Endophyte Bacillus halotolerans as Plant Warden Against Fusarium.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3236}, doi = {10.3389/fmicb.2018.03236}, pmid = {30687252}, issn = {1664-302X}, abstract = {Date palm (Phoenix dactylifera L.) plantations in North Africa are nowadays threatened with the spread of the Bayoud disease caused by Fusarium oxysporum f. sp. albedinis, already responsible for destroying date production in other infected areas, mainly in Morocco. Biological control holds great promise for sustainable and environmental-friendly management of the disease. In this study, the additional benefits to agricultural ecosystems of using plant growth promoting rhizobacteria (PGPR) or endophytes are addressed. First, PGPR or endophytes can offer an interesting bio-fertilization, meaning that it can add another layer to the sustainability of the approach. Additionally, screening of contrasting niches can yield bacterial actors that could represent wardens against whole genera or groups of plant pathogenic agents thriving in semi-arid to arid ecosystems. Using this strategy, we recovered four bacterial isolates, designated BFOA1, BFOA2, BFOA3 and BFOA4, that proved very active against F. oxysporum f. sp. albedinis. BFOA1-BFOA4 proved also active against 16 Fusarium isolates belonging to four species: F. oxysporum (with strains phytopathogenic of Olea europaea and tomato), F. solani (with different strains attacking O. europaea and potato), F. acuminatum (pathogenic on O. europaea) and F. chlamydosporum (phytopathogenic of O. europaea). BFOA1-BFOA4 bacterial isolates exhibited strong activities against another four major phytopathogens: Botrytis cinerea, Alternaria alternata, Phytophthora infestans, and Rhizoctonia bataticola. Isolates BFOA1-BFOA4 had the ability to grow at temperatures up to 35°C, pH range of 5-10, and tolerate high concentrations of NaCl and up to 30% PEG. The isolates also showed relevant direct and indirect PGP features, including growth on nitrogen-free medium, phosphate solubilization and auxin biosynthesis, as well as resistance to metal and xenobiotic stress. Phylogenomic analysis of BFOA1-BFOA4 isolates indicated that they all belong to Bacillus halotolerans, which could therefore considered as a warden against Fusarium infection in plants. Comparative genomics allowed us to functionally describe the open pan genome of B. halotolerans and LC-HRMS and GCMS analyses, enabling the description of diverse secondary metabolites including pulegone, 2-undecanone, and germacrene D, with important antimicrobial and insecticidal properties. In conclusion, B. halotolerans could be used as an efficient bio-fertilizer and bio-control agent in semi-arid and arid ecosystems.}, }
@article {pmid30679463, year = {2019}, author = {Arabaghian, H and Salloum, T and Alousi, S and Panossian, B and Araj, GF and Tokajian, S}, title = {Molecular Characterization of Carbapenem Resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae Isolated from Lebanon.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {531}, doi = {10.1038/s41598-018-36554-2}, pmid = {30679463}, issn = {2045-2322}, abstract = {Klebsiella pneumoniae is a Gram-negative organism and a major public health threat. In this study, we used whole-genome sequences to characterize 32 carbapenem-resistant K. pneumoniae (CRKP) and two carbapenem-resistant K. quasipneumoniae (CRKQ). Antimicrobial resistance was assessed using disk diffusion and E-test, while virulence was assessed in silico. The capsule type was determined by sequencing the wzi gene. The plasmid diversity was assessed by PCR-based replicon typing to detect the plasmid incompatibility (Inc) groups. The genetic relatedness was determined by multilocus sequence typing, pan-genome, and recombination analysis. All of the isolates were resistant to ertapenem together with imipenem and/or meropenem. Phenotypic resistance was due to blaOXA-48, blaNDM-1, blaNDM-7, or the coupling of ESBLs and outer membrane porin modifications. This is the first comprehensive study reporting on the WGS of CRKP and the first detection of CRKQ in the region. The presence and dissemination of CRKP and CRKQ, with some additionally having characteristics of hypervirulent clones such as the hypermucoviscous phenotype and the capsular type K2, are particularly concerning. Additionally, mining the completely sequenced K. pneumoniae genomes revealed the key roles of mobile genetic elements in the spread of antibiotic resistance and in understanding the epidemiology of these clinically significant pathogens.}, }
@article {pmid30658579, year = {2019}, author = {Zhu, D and He, J and Yang, Z and Wang, M and Jia, R and Chen, S and Liu, M and Zhao, X and Yang, Q and Wu, Y and Zhang, S and Liu, Y and Zhang, L and Yu, Y and You, Y and Chen, X and Cheng, A}, title = {Comparative analysis reveals the Genomic Islands in Pasteurella multocida population genetics: on Symbiosis and adaptability.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {63}, doi = {10.1186/s12864-018-5366-6}, pmid = {30658579}, issn = {1471-2164}, support = {No. 2017YFD050080//the National Key Research and Development Program of China/ ; No. CARS-42-17//China Agricultural Research System/ ; No. 2016JPT0004//Special Fund for Key Laboratory of Animal Disease and Human Health of Sichuan Province/ ; CARS-SVDIP//Sichuan Veterinary Medicine and Drug Innovation Group of China Agricultural Research System/ ; }, abstract = {BACKGROUND: Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria acquire large fragments of foreign genes. However, the effects of GIs on P. multocida are unknown in the evolution of bacterial populations.<br><br>RESULTS: Ten avian-sourced P. multocida obtained through high-throughput sequencing together with 104 publicly available P. multocida genomes were used to analyse their population genetics, thus constructed a pan-genome containing 3948 protein-coding genes. Through the pan-genome, the open evolutionary pattern of P. multocida was revealed, and the functional components of 944 core genes, 2439 accessory genes and 565 unique genes were analysed. In addition, a total of 280 GIs were predicted in all strains. Combined with the pan-genome of P. multocida, the GIs accounted for 5.8% of the core genes in the pan-genome, mainly related to functional metabolic activities; the accessory genes accounted for 42.3%, mainly for the enrichment of adaptive genes; and the unique genes accounted for 35.4%, containing some defence mechanism-related genes.<br><br>CONCLUSIONS: The effects of GIs on the population genetics of P. multocida evolution and adaptation to the environment are reflected by the proportion and function of the pan-genome acquired from GIs, and the large quantities of GI data will aid in additional population genetics studies.}, }
@article {pmid30647471, year = {2019}, author = {Sherman, RM and Forman, J and Antonescu, V and Puiu, D and Daya, M and Rafaels, N and Boorgula, MP and Chavan, S and Vergara, C and Ortega, VE and Levin, AM and Eng, C and Yazdanbakhsh, M and Wilson, JG and Marrugo, J and Lange, LA and Williams, LK and Watson, H and Ware, LB and Olopade, CO and Olopade, O and Oliveira, RR and Ober, C and Nicolae, DL and Meyers, DA and Mayorga, A and Knight-Madden, J and Hartert, T and Hansel, NN and Foreman, MG and Ford, JG and Faruque, MU and Dunston, GM and Caraballo, L and Burchard, EG and Bleecker, ER and Araujo, MI and Herrera-Paz, EF and Campbell, M and Foster, C and Taub, MA and Beaty, TH and Ruczinski, I and Mathias, RA and Barnes, KC and Salzberg, SL}, title = {Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41588-018-0335-1}, pmid = {30647471}, issn = {1546-1718}, abstract = {In the version of this article initially published, the statement &quot;there are no pan-genomes for any other animal or plant species&quot; was incorrect. The statement has been corrected to &quot;there are no reported pan-genomes for any other animal species, to our knowledge.&quot; We thank David Edwards for bringing this error to our attention. The error has been corrected in the HTML and PDF versions of the article.}, }
@article {pmid30637341, year = {2019}, author = {Blaustein, RA and McFarland, AG and Ben Maamar, S and Lopez, A and Castro-Wallace, S and Hartmann, EM}, title = {Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, doi = {10.1128/mSystems.00281-18}, pmid = {30637341}, issn = {2379-5077}, abstract = {Understanding underlying mechanisms involved in microbial persistence in the built environment (BE) is essential for strategically mitigating potential health risks. To test the hypothesis that BEs impose selective pressures resulting in characteristic adaptive responses, we performed a pangenomics meta-analysis leveraging 189 genomes (accessed from GenBank) of two epidemiologically important taxa, Bacillus cereus and Staphylococcus aureus, isolated from various origins: the International Space Station (ISS; a model BE), Earth-based BEs, soil, and humans. Our objectives were to (i) identify differences in the pangenomic composition of generalist and host-associated organisms, (ii) characterize genes and functions involved in BE-associated selection, and (iii) identify genomic signatures of ISS-derived strains of potential relevance for astronaut health. The pangenome of B. cereus was more expansive than that of S. aureus, which had a dominant core component. Genomic contents of both taxa significantly correlated with isolate origin, demonstrating an importance for biogeography and potential niche adaptations. ISS/BE-enriched functions were often involved in biosynthesis, catabolism, materials transport, metabolism, and stress response. Multiple origin-enriched functions also overlapped across taxa, suggesting conserved adaptive processes. We further characterized two mobile genetic elements with local neighborhood genes encoding biosynthesis and stress response functions that distinctively associated with B. cereus from the ISS. Although antibiotic resistance genes were present in ISS/BE isolates, they were also common in counterparts elsewhere. Overall, despite differences in microbial lifestyle, some functions appear common to remaining viable in the BE, and those functions are not typically associated with direct impacts on human health. IMPORTANCE The built environment contains a variety of microorganisms, some of which pose critical human health risks (e.g., hospital-acquired infection, antibiotic resistance dissemination). We uncovered a combination of complex biological functions that may play a role in bacterial survival under the presumed selective pressures in a model built environment-the International Space Station-by using an approach to compare pangenomes of bacterial strains from two clinically relevant species (B. cereus and S. aureus) isolated from both built environments and humans. Our findings suggest that the most crucial bacterial functions involved in this potential adaptive response are specific to bacterial lifestyle and do not appear to have direct impacts on human health.}, }
@article {pmid30631083, year = {2019}, author = {Abreo, E and Altier, N}, title = {Pangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {46}, doi = {10.1038/s41598-018-37118-0}, pmid = {30631083}, issn = {2045-2322}, abstract = {Serratia marcescens is a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-based approach, based on publicly available genomes, to apply whole genome multilocus sequence type schemes to assess whether there is an association between source and genotype, aiming at differentiating between isolates from nosocomial sources and the environment, and between strains reported as PGPR from other environmental strains. Most genomes from a nosocomial setting and environmental origin could be assigned to the proposed nosocomial or environmental MLSTs, which is indicative of an association between source and genotype. The fact that a few genomes from a nosocomial source showed an environmental MLST suggests that a minority of nosocomial strains have recently derived from the environment. PGPR strains were assigned to different environmental types and clades but only one clade comprised strains accumulating a low number of known virulence and antibiotic resistance determinants and was exclusively from environmental sources. This clade is envisaged as a group of promissory MLSTs for selecting prospective PGPR strains.}, }
@article {pmid30622973, year = {2018}, author = {Hisham, Y and Ashhab, Y}, title = {Identification of Cross-Protective Potential Antigens against Pathogenic Brucella spp. through Combining Pan-Genome Analysis with Reverse Vaccinology.}, journal = {Journal of immunology research}, volume = {2018}, number = {}, pages = {1474517}, doi = {10.1155/2018/1474517}, pmid = {30622973}, issn = {2314-7156}, abstract = {Brucellosis is a zoonotic infectious disease caused by bacteria of the genus Brucella. Brucella melitensis, Brucella abortus, and Brucella suis are the most pathogenic species of this genus causing the majority of human and domestic animal brucellosis. There is a need to develop a safe and potent subunit vaccine to overcome the serious drawbacks of the live attenuated Brucella vaccines. The aim of this work was to discover antigen candidates conserved among the three pathogenic species. In this study, we employed a reverse vaccinology strategy to compute the core proteome of 90 completed genomes: 55 B. melitensis, 17 B. abortus, and 18 B. suis. The core proteome was analyzed by a metasubcellular localization prediction pipeline to identify surface-associated proteins. The identified proteins were thoroughly analyzed using various in silico tools to obtain the most potential protective antigens. The number of core proteins obtained from analyzing the 90 proteomes was 1939 proteins. The surface-associated proteins were 177. The number of potential antigens was 87; those with adhesion score ≥ 0.5 were considered antigen with &quot;high potential,&quot; while those with a score of 0.4-0.5 were considered antigens with &quot;intermediate potential.&quot; According to a cumulative score derived from protein antigenicity, density of MHC-I and MHC-II epitopes, MHC allele coverage, and B-cell epitope density scores, a final list of 34 potential antigens was obtained. Remarkably, most of the 34 proteins are associated with bacterial adhesion, invasion, evasion, and adaptation to the hostile intracellular environment of macrophages which is adjusted to deprive Brucella of required nutrients. Our results provide a manageable list of potential protective antigens for developing a potent vaccine against brucellosis. Moreover, our elaborated analysis can provide further insights into novel Brucella virulence factors. Our next step is to test some of these antigens using an appropriate antigen delivery system.}, }
@article {pmid30619233, year = {2018}, author = {Livingstone, PG and Morphew, RM and Whitworth, DE}, title = {Genome Sequencing and Pan-Genome Analysis of 23 Corallococcus spp. Strains Reveal Unexpected Diversity, With Particular Plasticity of Predatory Gene Sets.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3187}, doi = {10.3389/fmicb.2018.03187}, pmid = {30619233}, issn = {1664-302X}, abstract = {Corallococcus is an abundant genus of predatory soil myxobacteria, containing two species, C. coralloides (for which a genome sequence is available) and C. exiguus. To investigate the genomic basis of predation, we genome-sequenced 23 Corallococcus strains. Genomic similarity metrics grouped the sequenced strains into at least nine distinct genomospecies, divided between two major sub-divisions of the genus, encompassing previously described diversity. The Corallococcus pan-genome was found to be open, with strains exhibiting highly individual gene sets. On average, only 30.5% of each strain's gene set belonged to the core pan-genome, while more than 75% of the accessory pan-genome genes were present in less than four of the 24 genomes. The Corallococcus accessory pan-proteome was enriched for the COG functional category &quot;Secondary metabolism,&quot; with each genome containing on average 55 biosynthetic gene clusters (BGCs), of which only 20 belonged to the core pan-genome. Predatory activity was assayed against ten prey microbes and found to be mostly incongruent with phylogeny or BGC complement. Thus, predation seems multifactorial, depending partially on BGC complement, but also on the accessory pan-genome - genes most likely acquired horizontally. These observations encourage further exploration of Corallococcus as a source for novel bioactive secondary metabolites and predatory proteins.}, }
@article {pmid30619175, year = {2018}, author = {Wu, Y and Zaiden, N and Cao, B}, title = {The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3096}, doi = {10.3389/fmicb.2018.03096}, pmid = {30619175}, issn = {1664-302X}, abstract = {Comamonas is often reported to be one of the major members of microbial communities in various natural and engineered environments. Versatile catabolic capabilities of Comamonas have been studied extensively in the last decade. In contrast, little is known about the ecological roles and adaptation of Comamonas to different environments as well as the virulence of potentially pathogenic Comamonas strains. In this study, we provide genomic insights into the potential ecological roles and virulence of Comamonas by analysing the entire gene set (pangenome) and the genes present in all genomes (core genome) using 34 genomes of 11 different Comamonas species. The analyses revealed that the metabolic pathways enabling Comamonas to acquire energy from various nutrient sources are well conserved. Genes for denitrification and ammonification are abundant in Comamonas, suggesting that Comamonas plays an important role in the nitrogen biogeochemical cycle. They also encode sophisticated redox sensory systems and diverse c-di-GMP controlling systems, allowing them to be able to effectively adjust their biofilm lifestyle to changing environments. The virulence factors in Comamonas were found to be highly species-specific. The conserved strategies used by potentially pathogenic Comamonas for surface adherence, motility control, nutrient acquisition and stress tolerance were also revealed.}, }
@article {pmid30618776, year = {2018}, author = {Kayani, MR and Zheng, YC and Xie, FC and Kang, K and Li, HY and Zhao, HT}, title = {Genome Sequences and Comparative Analysis of Two Extended-Spectrum Extensively-Drug Resistant Mycobacterium tuberculosis Strains.}, journal = {Frontiers in pharmacology}, volume = {9}, number = {}, pages = {1492}, doi = {10.3389/fphar.2018.01492}, pmid = {30618776}, issn = {1663-9812}, }
@article {pmid30608550, year = {2019}, author = {diCenzo, GC and Mengoni, A and Perrin, E}, title = {Chromids aid genome expansion and functional diversification in the family Burkholderiaceae.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msy248}, pmid = {30608550}, issn = {1537-1719}, abstract = {Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipartite genomes. Nearly all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that inter-replicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon's pangenome indicates a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also over-represented on the chromosomes of the environmental genera (Paraburkholderia, Cupriavidus) compared to the pathogenic genera (Burkholderia, Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in a replicon enriched in genes associated with adaptation to novel environments.}, }
@article {pmid30606234, year = {2019}, author = {Dillon, MM and Thakur, S and Almeida, RND and Wang, PW and Weir, BS and Guttman, DS}, title = {Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {3}, doi = {10.1186/s13059-018-1606-y}, pmid = {30606234}, issn = {1474-760X}, abstract = {BACKGROUND: Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crops. We examine the evolutionary relationships of 391 agricultural and environmental strains using whole-genome sequencing and evolutionary genomic analyses.<br><br>RESULTS: We describe the phylogenetic distribution of all 77,728 orthologous gene families in the pan-genome, reconstruct the core genome phylogeny using the 2410 core genes, hierarchically cluster the accessory genome, identify the diversity and distribution of type III secretion systems and their effectors, predict ecologically and evolutionary relevant loci, and establish the molecular evolutionary processes operating on gene families. Phylogenetic and recombination analyses reveals that the species complex is subdivided into primary and secondary phylogroups, with the former primarily comprised of agricultural isolates, including all of the well-studied P. syringae strains. In contrast, the secondary phylogroups include numerous environmental isolates. These phylogroups also have levels of genetic diversity typically found among distinct species. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also find that &quot;ecologically significant&quot; virulence-associated loci and &quot;evolutionarily significant&quot; loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange.<br><br>CONCLUSIONS: While inter-phylogroup recombination occurs relatively rarely, it is an important force maintaining the genetic cohesion of the species complex, particularly among primary phylogroup strains. This level of genetic cohesion, and the shared plant-associated niche, argues for considering the primary phylogroups as a single biological species.}, }
@article {pmid30598532, year = {2018}, author = {Hübner, S and Bercovich, N and Todesco, M and Mandel, JR and Odenheimer, J and Ziegler, E and Lee, JS and Baute, GJ and Owens, GL and Grassa, CJ and Ebert, DP and Ostevik, KL and Moyers, BT and Yakimowski, S and Masalia, RR and Gao, L and Ćalić, I and Bowers, JE and Kane, NC and Swanevelder, DZH and Kubach, T and Muños, S and Langlade, NB and Burke, JM and Rieseberg, LH}, title = {Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance.}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41477-018-0329-0}, pmid = {30598532}, issn = {2055-0278}, abstract = {Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.}, }
@article {pmid30594655, year = {2018}, author = {Tao, Y and Zhao, X and Mace, E and Henry, R and Jordan, D}, title = {Exploring and exploiting pan-genomics for crop improvement.}, journal = {Molecular plant}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molp.2018.12.016}, pmid = {30594655}, issn = {1752-9867}, abstract = {Genetic variation ranging from single nucleotide polymorphisms (SNPs) to large structural variants (SVs) can cause variation of gene content among individuals within the same species. There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic diversity of a species. Pan-genome analysis offers a platform to evaluate genetic diversity of a species via investigation of its entire genome repertoire. Although a recent wave of pan-genomic studies has shed new light on crop diversity and improvement using advanced sequencing technology, the potential applications of crop pan-genomics in crop improvement are yet to be fully exploited. In this review, we highlight the progress achieved in understanding crop pan-genomics, discuss biological activities that cause SVs, review important agronomical traits affected by SVs and present our perspective on the application of pan-genomics in crop improvement.}, }
@article {pmid30588394, year = {2018}, author = {Brankovics, B and Kulik, T and Sawicki, J and Bilska, K and Zhang, H and de Hoog, GS and van der Lee, TA and Waalwijk, C and van Diepeningen, AD}, title = {First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5963}, doi = {10.7717/peerj.5963}, pmid = {30588394}, issn = {2167-8359}, abstract = {There is a gradual shift from representing a species' genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The &quot;intronless&quot; mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the &quot;host&quot; gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.}, }
@article {pmid30587126, year = {2018}, author = {Bochkareva, OO and Moroz, EV and Davydov, II and Gelfand, MS}, title = {Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {965}, doi = {10.1186/s12864-018-5245-1}, pmid = {30587126}, issn = {1471-2164}, support = {18-14-00358//Russian Science Foundation/ ; 16-54-21004//Russian Foundation of Basic Research/ ; IZLRZ3\163872//Swiss National Science Foundation/ ; }, abstract = {BACKGROUND: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.<br><br>RESULTS: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.<br><br>CONCLUSIONS: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.}, }
@article {pmid30587114, year = {2018}, author = {Tyakht, AV and Manolov, AI and Kanygina, AV and Ischenko, DS and Kovarsky, BA and Popenko, AS and Pavlenko, AV and Elizarova, AV and Rakitina, DV and Baikova, JP and Ladygina, VG and Kostryukova, ES and Karpova, IY and Semashko, TA and Larin, AK and Grigoryeva, TV and Sinyagina, MN and Malanin, SY and Shcherbakov, PL and Kharitonova, AY and Khalif, IL and Shapina, MV and Maev, IV and Andreev, DN and Belousova, EA and Buzunova, YM and Alexeev, DG and Govorun, VM}, title = {Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {968}, doi = {10.1186/s12864-018-5306-5}, pmid = {30587114}, issn = {1471-2164}, support = {16-15-00258//Russian Science Foundation/ ; }, abstract = {BACKGROUND: Crohn's disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.<br><br>METHODS: We performed a metagenomic study investigating the gut microbiota of patients with Crohn's disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.<br><br>RESULTS: The abnormal shifts in the microbial community structures in Crohn's disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.<br><br>CONCLUSIONS: The genomic diversity of Crohn's disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn's disease and the development of new strategies for the prevention and treatment of this disease.}, }
@article {pmid30586440, year = {2018}, author = {Cheleuitte-Nieves, C and Gulvik, CA and McQuiston, JR and Humrighouse, BW and Bell, ME and Villarma, A and Fischetti, VA and Westblade, LF and Lipman, NS}, title = {Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209231}, doi = {10.1371/journal.pone.0209231}, pmid = {30586440}, issn = {1932-6203}, abstract = {Corynebacterium bovis is an opportunistic bacterial pathogen shown to cause eye and prosthetic joint infections as well as abscesses in humans, mastitis in dairy cattle, and skin disease in laboratory mice and rats. Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species. The overall aim of this study was to sequence and compare the genome of C. bovis isolates obtained from different species, locations, and time points. Whole-genome sequencing was conducted on 20 C. bovis isolates (six human, four bovine, nine mouse and one rat) using the Illumina MiSeq platform and submitted to various comparative analysis tools. Sequencing generated high-quality contigs (over 2.53 Mbp) that were comparable to the only reported assembly using C. bovis DSM 20582T (97.8 ± 0.36% completeness). The number of protein-coding DNA sequences (2,174 ± 12.4) was similar among all isolates. A Corynebacterium genus neighbor-joining tree was created, which revealed Corynebacterium falsenii as the nearest neighbor to C. bovis (95.87% similarity), although the reciprocal comparison shows Corynebacterium jeikeium as closest neighbor to C. falsenii. Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate group. The average number of genomic islands and putative virulence factors were significantly higher (p<0.001) in the mouse and rat isolates as compared to human/bovine isolates. Corynebacterium bovis' pan-genome contained a total of 3,067 genes of which 1,354 represented core genes. The known core genes of all isolates were primarily related to ''metabolism&quot; and ''information storage/processing.&quot; However, most genes were classified as ''function unknown&quot; or &quot;unclassified&quot;. Surprisingly, no intact prophages were found in any isolate; however, almost all isolates had at least one complete CRISPR-Cas system.}, }
@article {pmid30574560, year = {2018}, author = {Velsko, IM and Chakraborty, B and Nascimento, MM and Burne, RA and Richards, VP}, title = {Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00158-18}, pmid = {30574560}, issn = {2379-5077}, abstract = {Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral probiotic strains. ADS and antagonistic activities can vary dramatically among individuals, but the genetic basis for these differences is unknown. We sequenced whole genomes of a diverse set of clinical oral Streptococcus isolates and examined the genetic basis of variability in ADS and antagonistic activities. A total of 113 isolates were included and represented 10 species: Streptococcus australis, A12-like, S. cristatus, S. gordonii, S. intermedius, S. mitis, S. oralis including S. oralis subsp. dentisani, S. parasanguinis, S. salivarius, and S. sanguinis. Mean ADS activity and antagonism on Streptococcus mutans UA159 were measured for each isolate, and each isolate was whole genome shotgun sequenced on an Illumina MiSeq. Phylogenies were built of genes known to be involved in ADS activity and antagonism. Several approaches to correlate the pan-genome with phenotypes were performed. Phylogenies of genes previously identified in ADS activity and antagonism grouped isolates by species, but not by phenotype. A genome-wide association study (GWAS) identified additional genes potentially involved in ADS activity or antagonism across all the isolates we sequenced as well as within several species. Phenotypic heterogeneity in oral streptococci is not necessarily reflected by genotype and is not species specific. Probiotic strains must be carefully selected based on characterization of each strain and not based on inclusion within a certain species. IMPORTANCE Representative type strains are commonly used to characterize bacterial species, yet species are phenotypically and genotypically heterogeneous. Conclusions about strain physiology and activity based on a single strain therefore may be inappropriate and misleading. When selecting strains for probiotic use, the assumption that all strains within a species share the same desired probiotic characteristics may result in selection of a strain that lacks the desired traits, and therefore makes a minimally effective or ineffective probiotic. Health-associated oral streptococci are promising candidates for anticaries probiotics, but strains need to be carefully selected based on observed phenotypes. We characterized the genotypes and anticaries phenotypes of strains from 10 species of oral streptococci and demonstrate poor correlation between genotype and phenotype across all species.}, }
@article {pmid30563902, year = {2018}, author = {Potter, RF and Lainhart, W and Twentyman, J and Wallace, MA and Wang, B and Burnham, CA and Rosen, DA and Dantas, G}, title = {Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella variicola.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.02481-18}, pmid = {30563902}, issn = {2150-7511}, abstract = {Klebsiella variicola is a member of the Klebsiella genus and often misidentified as Klebsiella pneumoniae or Klebsiella quasipneumoniae The importance of K. pneumoniae human infections has been known; however, a dearth of relative knowledge exists for K. variicola Despite its growing clinical importance, comprehensive analyses of K. variicola population structure and mechanistic investigations of virulence factors and antibiotic resistance genes have not yet been performed. To address this, we utilized in silico, in vitro, and in vivo methods to study a cohort of K. variicola isolates and genomes. We found that the K. variicola population structure has two distant lineages composed of two and 143 genomes, respectively. Ten of 145 K. variicola genomes harbored carbapenem resistance genes, and 6/145 contained complete virulence operons. While the β-lactam blaLEN and quinolone oqxAB antibiotic resistance genes were generally conserved within our institutional cohort, unexpectedly 11 isolates were nonresistant to the β-lactam ampicillin and only one isolate was nonsusceptible to the quinolone ciprofloxacin. K. variicola isolates have variation in ability to cause urinary tract infections in a newly developed murine model, but importantly a strain had statistically significant higher bladder CFU than the model uropathogenic K. pneumoniae strain TOP52. Type 1 pilus and genomic identification of altered fim operon structure were associated with differences in bladder CFU for the tested strains. Nine newly reported types of pilus genes were discovered in the K. variicola pan-genome, including the first identified P-pilus in Klebsiella spp.IMPORTANCE Infections caused by antibiotic-resistant bacterial pathogens are a growing public health threat. Understanding of pathogen relatedness and biology is imperative for tracking outbreaks and developing therapeutics. Here, we detail the phylogenetic structure of 145 K. variicola genomes from different continents. Our results have important clinical ramifications as high-risk antibiotic resistance genes are present in K. variicola genomes from a variety of geographic locations and as we demonstrate that K. variicola clinical isolates can establish higher bladder titers than K. pneumoniae Differential presence of these pilus genes inK. variicola isolates may indicate adaption for specific environmental niches. Therefore, due to the potential of multidrug resistance and pathogenic efficacy, identification of K. variicola and K. pneumoniae to a species level should be performed to optimally improve patient outcomes during infection. This work provides a foundation for our improved understanding of K. variicola biology and pathogenesis.}, }
@article {pmid30563853, year = {2018}, author = {Pang, TY and Lercher, MJ}, title = {Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1718997115}, pmid = {30563853}, issn = {1091-6490}, abstract = {Even closely related prokaryotes often show an astounding diversity in their ability to grow in different nutritional environments. It has been hypothesized that complex metabolic adaptations-those requiring the independent acquisition of multiple new genes-can evolve via selectively neutral intermediates. However, it is unclear whether this neutral exploration of phenotype space occurs in nature, or what fraction of metabolic adaptations is indeed complex. Here, we reconstruct metabolic models for the ancestors of a phylogeny of 53 Escherichia coli strains, linking genotypes to phenotypes on a genome-wide, macroevolutionary scale. Based on the ancestral and extant metabolic models, we identify 3,323 phenotypic innovations in the history of the E. coli clade that arose through changes in accessory genome content. Of these innovations, 1,998 allow growth in previously inaccessible environments, while 1,325 increase biomass yield. Strikingly, every observed innovation arose through the horizontal acquisition of a single DNA segment less than 30 kb long. Although we found no evidence for the contribution of selectively neutral processes, 10.6% of metabolic innovations were facilitated by horizontal gene transfers on earlier phylogenetic branches, consistent with a stepwise adaptation to successive environments. Ninety-eight percent of metabolic phenotypes accessible to the combined E. coli pangenome can be bestowed on any individual strain by transferring a single DNA segment from one of the extant strains. These results demonstrate an amazing ability of the E. coli lineage to adapt to novel environments through single horizontal gene transfers (followed by regulatory adaptations), an ability likely mirrored in other clades of generalist bacteria.}, }
@article {pmid30550841, year = {2018}, author = {Jatuponwiphat, T and Chumnanpuen, P and Othman, S and E-Kobon, T and Vongsangnak, W}, title = {Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.micpath.2018.12.013}, pmid = {30550841}, issn = {1096-1208}, abstract = {Pasteurella multocida causes respiratory infectious diseases in a multitude of birds and mammals. A number of virulence-associated genes were reported across different strains of P. multocida, including those involved in the iron transport and metabolism. Comparative iron-associated genes of P. multocida among different animal hosts towards their interaction networks have not been fully revealed. Therefore, this study aimed to identify the iron-associated genes from core- and pan-genomes of fourteen P. multocida strains and to construct iron-associated protein interaction networks using genome-scale network analysis which might be associated with the virulence. Results showed that these fourteen strains had 1587 genes in the core-genome and 3400 genes constituting their pan-genome. Out of these, 2651 genes associated with iron transport and metabolism were selected to construct the protein interaction networks and 361 genes were incorporated into the iron-associated protein interaction network (iPIN) consisting of nine different iron-associated functional modules. After comparing with the virulence factor database (VFDB), 21 virulence-associated proteins were determined and 11 of these belonged to the heme biosynthesis module. From this study, the core heme biosynthesis module and the core outer membrane hemoglobin receptor HgbA were proposed as candidate targets to design novel antibiotics and vaccines for preventing pasteurellosis across the serotypes or animal hosts for enhanced precision agriculture to ensure sustainability in food security.}, }
@article {pmid30550564, year = {2018}, author = {Moradigaravand, D and Palm, M and Farewell, A and Mustonen, V and Warringer, J and Parts, L}, title = {Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.}, journal = {PLoS computational biology}, volume = {14}, number = {12}, pages = {e1006258}, doi = {10.1371/journal.pcbi.1006258}, pmid = {30550564}, issn = {1553-7358}, abstract = {The emergence of microbial antibiotic resistance is a global health threat. In clinical settings, the key to controlling spread of resistant strains is accurate and rapid detection. As traditional culture-based methods are time consuming, genetic approaches have recently been developed for this task. The detection of antibiotic resistance is typically made by measuring a few known determinants previously identified from genome sequencing, and thus requires the prior knowledge of its biological mechanisms. To overcome this limitation, we employed machine learning models to predict resistance to 11 compounds across four classes of antibiotics from existing and novel whole genome sequences of 1936 E. coli strains. We considered a range of methods, and examined population structure, isolation year, gene content, and polymorphism information as predictors. Gradient boosted decision trees consistently outperformed alternative models with an average accuracy of 0.91 on held-out data (range 0.81-0.97). While the best models most frequently employed gene content, an average accuracy score of 0.90 could be obtained using population structure information alone. Single nucleotide variation data were less useful, and significantly improved prediction only for two antibiotics, including ciprofloxacin. These results demonstrate that antibiotic resistance in E. coli can be accurately predicted from whole genome sequences without a priori knowledge of mechanisms, and that both genomic and epidemiological data can be informative. This paves way to integrating machine learning approaches into diagnostic tools in the clinic.}, }
@article {pmid30538677, year = {2018}, author = {Colson, P and Levasseur, A and La Scola, B and Sharma, V and Nasir, A and Pontarotti, P and Caetano-Anollés, G and Raoult, D}, title = {Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2668}, doi = {10.3389/fmicb.2018.02668}, pmid = {30538677}, issn = {1664-302X}, abstract = {Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named 'TRUC' (for &quot;Things Resisting Uncompleted Classifications&quot;) alongside Bacteria, Archaea, and Eukarya. Their origin and ancestrality remain controversial. Here, we specify the evolution and definition of giant viruses. Phylogenetic and phenetic analyses of informational gene repertoires of giant viruses and selected bacteria, archaea and eukaryota were performed, including structural phylogenomics based on protein structural domains grouped into 289 universal fold superfamilies (FSFs). Hierarchical clustering analysis was performed based on a binary presence/absence matrix constructed using 727 informational COGs from cellular organisms. The presence/absence of 'universal' FSF domains was used to generate an unrooted maximum parsimony phylogenomic tree. Comparison of the gene content of a giant virus with those of a bacterium, an archaeon, and a eukaryote with small genomes was also performed. Overall, both cladistic analyses based on gene sequences of very central and ancient proteins and on highly conserved protein fold structures as well as phenetic analyses were congruent regarding the delineation of a fourth branch of microbes comprised by giant viruses. Giant viruses appeared as a basal group in the tree of all proteomes. A pangenome and core genome determined for Rickettsia bellii (bacteria), Methanomassiliicoccus luminyensis (archaeon), Encephalitozoon intestinalis (eukaryote), and Tupanvirus (giant virus) showed a substantial proportion of Tupanvirus genes that overlap with those of the cellular microbes. In addition, a substantial genome mosaicism was observed, with 51, 11, 8, and 0.2% of Tupanvirus genes best matching with viruses, eukaryota, bacteria, and archaea, respectively. Finally, we found that genes themselves may be subject to lateral sequence transfers. In summary, our data highlight the quantum leap between classical and giant viruses. Phylogenetic and phyletic analyses and the study of protein fold superfamilies confirm previous evidence of the existence of a fourth TRUC of life that includes giant viruses, and highlight its ancestrality and mosaicism. They also point out that best evolutionary representations for giant viruses and cellular microorganisms are rhizomes, and that sequence transfers rather than gene transfers have to be considered.}, }
@article {pmid30535304, year = {2018}, author = {Lees, JA and Galardini, M and Bentley, SD and Weiser, JN and Corander, J}, title = {pyseer: a comprehensive tool for microbial pangenome-wide association studies.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {24}, pages = {4310-4312}, doi = {10.1093/bioinformatics/bty539}, pmid = {30535304}, issn = {1367-4811}, abstract = {Summary: Genome-wide association studies (GWAS) in microbes have different challenges to GWAS in eukaryotes. These have been addressed by a number of different methods. pyseer brings these techniques together in one package tailored to microbial GWAS, allows greater flexibility of the input data used, and adds new methods to interpret the association results.<br><br>pyseer is written in python and is freely available at https://github.com/mgalardini/pyseer, or can be installed through pip. Documentation and a tutorial are available at http://pyseer.readthedocs.io.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30530095, year = {2018}, author = {Fritsch, L and Felten, A and Palma, F and Mariet, JF and Radomski, N and Mistou, MY and Augustin, JC and Guillier, L}, title = {Insights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L. monocytogenes' ability to grow in cold conditions.}, journal = {International journal of food microbiology}, volume = {291}, number = {}, pages = {181-188}, doi = {10.1016/j.ijfoodmicro.2018.11.028}, pmid = {30530095}, issn = {1879-3460}, abstract = {Intraspecific variability of the behavior of most foodborne pathogens is well described and taken into account in Quantitative Microbial Risk Assessment (QMRA), but factors (strain origin, serotype, …) explaining these differences are scarce or contradictory between studies. Nowadays, Whole Genome Sequencing (WGS) offers new opportunities to explain intraspecific variability of food pathogens, based on various recently published bioinformatics tools. The objective of this study is to get a better insight into different existing bioinformatics approaches to associate bacterial phenotype(s) and genotype(s). Therefore, a dataset of 51 L. monocytogenes strains, isolated from multiple sources (i.e. different food matrices and environments) and belonging to 17 clonal complexes (CC), were selected to represent large population diversity. Furthermore, the phenotypic variability of growth at low temperature was determined (i.e. qualitative phenotype), and the whole genomes of selected strains were sequenced. The almost exhaustive gene content, as well as the core genome SNPs based phylogenetic reconstruction, were derived from the whole sequenced genomes. A Bayesian inference method was applied to identify the branches on which the phenotype distribution evolves within sub-lineages. Two different Genome Wide Association Studies (i.e. gene- and SNP-based GWAS) were independently performed in order to link genetic mutations to the phenotype of interest. The genomic analyses presented in this study were successfully applied on the selected dataset. The Bayesian phylogenetic approach emphasized an association with &quot;slow&quot; growth ability at 2 °C of the lineage I, as well as CC9 of the lineage II. Moreover, both gene- and SNP-GWAS approaches displayed significant statistical associations with the tested phenotype. A list of 114 significantly associated genes, including genes already known to be involved in the cold adaption mechanism of L. monocytogenes and genes associated to mobile genetic elements (MGE), resulted from the gene-GWAS. On the other hand, a group of 184 highly associated SNPs were highlighted by SNP-GWAS, including SNPs detected in genes which were already likely involved in cold adaption; hypothetical proteins; and intergenic regions where for example promotors and regulators can be located. The successful application of combined bioinformatics approaches associating WGS-genotypes and specific phenotypes, could contribute to improve prediction of microbial behaviors in food. The implementation of this information in hazard identification and exposure assessment processes will open new possibilities to feed QMRA-models.}, }
@article {pmid30509172, year = {2018}, author = {Timms, VJ and Nguyen, T and Crighton, T and Yuen, M and Sintchenko, V}, title = {Genome-wide comparison of Corynebacterium diphtheriae isolates from Australia identifies differences in the Pan-genomes between respiratory and cutaneous strains.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {869}, doi = {10.1186/s12864-018-5147-2}, pmid = {30509172}, issn = {1471-2164}, support = {Program Round 4//NSW Ministry of Health/ ; }, abstract = {BACKGROUND: Corynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects against infection with potent toxin producing strains. However a growing number of apparently non-toxigenic but potentially invasive C. diphtheriae strains are identified in countries with low prevalence of diphtheria, raising key questions about genomic structures and population dynamics of the species. This study examined genomic diversity among 48 C. diphtheriae isolates collected in Australia over a 12-year period using whole genome sequencing. Phylogeny was determined using SNP-based mapping and genome wide analysis.<br><br>RESULTS: C. diphtheriae sequence type (ST) 32, a non-toxigenic clone with evidence of enhanced virulence that has been also circulating in Europe, appears to be endemic in Australia. Isolates from temporospatially related patients displayed the same ST and similarity in their core genomes. The genome-wide analysis highlighted a role of pilins, adhesion factors and iron utilization in infections caused by non-toxigenic strains.<br><br>CONCLUSIONS: The genomic diversity of toxigenic and non-toxigenic strains of C. diphtheriae in Australia suggests multiple sources of infection and colonisation. Genomic surveillance of co-circulating toxigenic and non-toxigenic C. diphtheriae offer new insights into the evolution and virulence of pathogenic clones and can inform targeted public health actions and policy. The genomes presented in this investigation will contribute to the global surveillance of C. diphtheriae both for the monitoring of antibiotic resistance genes and virulent strains such as those belonging to ST32.}, }
@article {pmid30497358, year = {2018}, author = {Bonnici, V and Giugno, R and Manca, V}, title = {PanDelos: a dictionary-based method for pan-genome content discovery.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 15}, pages = {437}, doi = {10.1186/s12859-018-2417-6}, pmid = {30497358}, issn = {1471-2105}, abstract = {BACKGROUND: Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. The retrieval of a complete gene distribution among a class of genomes is an NP-hard problem because computational costs increase with the number of analyzed genomes, in fact, all-against-all gene comparisons are required to completely solve the problem. In presence of phylogenetically distant genomes, due to the variability introduced in gene duplication and transmission, the task of recognizing homologous genes becomes even more difficult. A challenge on this field is that of designing fast and adaptive similarity measures in order to find a suitable pan-genome structure of homology relations.<br><br>RESULTS: We present PanDelos, a stand alone tool for the discovery of pan-genome contents among phylogenetic distant genomes. The methodology is based on information theory and network analysis. It is parameter-free because thresholds are automatically deduced from the context. PanDelos avoids sequence alignment by introducing a measure based on k-mer multiplicity. The k-mer length is defined according to general arguments rather than empirical considerations. Homology candidate relations are integrated into a global network and groups of homologous genes are extracted by applying a community detection algorithm.<br><br>CONCLUSIONS: PanDelos outperforms existing approaches, Roary and EDGAR, in terms of running times and quality content discovery. Tests were run on collections of real genomes, previously used in analogous studies, and in synthetic benchmarks that represent fully trusted golden truth. The software is available at https://github.com/GiugnoLab/PanDelos .}, }
@article {pmid30496396, year = {2018}, author = {Freschi, L and Vincent, AT and Jeukens, J and Emond-Rheault, JG and Kukavica-Ibrulj, I and Dupont, MJ and Charette, SJ and Boyle, B and Levesque, RC}, title = {The Pseudomonas aeruginosa pan-genome provides new insights on its population structure, horizontal gene transfer and pathogenicity.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evy259}, pmid = {30496396}, issn = {1759-6653}, abstract = {The huge increase in the availability of bacterial genomes led us to a point in which we can investigate and query pan-genomes, i.e. the full set of genes of a given bacterial species or clade. Here, we used a dataset of 1,311 high-quality genomes from the human pathogen Pseudomonas aeruginosa, 619 of which were newly sequenced, to show that a pan-genomic approach can greatly refine the population structure of bacterial species, provide new insights to define species boundaries, and generate hypotheses on the evolution of pathogenicity. The 665-gene P. aeruginosa core genome presented here, which constitutes only 1% of the entire pan-genome, is the first to be in the same order of magnitude as the minimal bacterial genome and represents a conservative estimate of the actual core genome. Moreover, the phylogeny based on this core genome provides strong evidence for a five-group population structure that includes two previously undescribed groups of isolates. Comparative genomics focusing on antimicrobial resistance and virulence genes showed that variation among isolates was partly linked to this population structure. Finally, we hypothesized that horizontal gene transfer had an important role in this respect, and found a total of 3,010 putative complete and fragmented plasmids, 5 and 12% of which contained resistance or virulence genes, respectively. This work provides data and strategies to study the evolutionary trajectories of resistance and virulence in Pseudomonas aeruginosa.}, }
@article {pmid30487573, year = {2018}, author = {Méric, G and Mageiros, L and Pensar, J and Laabei, M and Yahara, K and Pascoe, B and Kittiwan, N and Tadee, P and Post, V and Lamble, S and Bowden, R and Bray, JE and Morgenstern, M and Jolley, KA and Maiden, MCJ and Feil, EJ and Didelot, X and Miragaia, M and de Lencastre, H and Moriarty, TF and Rohde, H and Massey, R and Mack, D and Corander, J and Sheppard, SK}, title = {Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5034}, doi = {10.1038/s41467-018-07368-7}, pmid = {30487573}, issn = {2041-1723}, abstract = {Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.}, }
@article {pmid30483518, year = {2018}, author = {Wang, R and Li, L and Huang, T and Huang, W and Lei, A and Chen, M}, title = {Capsular Switching and ICE Transformation Occurred in Human Streptococcus agalactiae ST19 With High Pathogenicity to Fish.}, journal = {Frontiers in veterinary science}, volume = {5}, number = {}, pages = {281}, doi = {10.3389/fvets.2018.00281}, pmid = {30483518}, issn = {2297-1769}, abstract = {Although Streptococcus agalactiae (GBS) cross-infection between human and fish has been confirmed in experimental and clinical studies, the mechanisms underlying GBS cross-species infection remain largely unclear. We have found different human GBS ST19 strains exhibiting strong or weak pathogenic to fish (sGBS and wGBS). In this study, our objective was to identify the genetic elements responsible for GBS cross species infection based on genome sequence data and comparative genomics. The genomes of 11 sGBS strains and 11 wGBS strains were sequenced, and the genomic analysis was performed base on pan-genome, CRISPRs, phylogenetic reconstruction and genome comparison. The results from the pan-genome, CRISPRs analysis and phylogenetic reconstruction indicated that genomes between sGBS were more conservative than that of wGBS. The genomic differences between sGBS and wGBS were primarily in the Cps region (about 111 kb) and its adjacent ICE region (about 106 kb). The Cps region included the entire cps operon, and all sGBS were capsular polysaccharide (CPS) type V, while all wGBS were CPS type III. The ICE region of sGBS contained integrative and conjugative elements (ICE) with IQ element and erm(TR), and was very conserved, whereas the ICE region of wGBS contained ICE with mega elements and the variation was large. The capsular switching (III-V) and transformation of ICE adjacent to the Cps region occurred in human GBS ST19 with different pathogenicity to fish, which may be related to the capability of GBS cross-infection.}, }
@article {pmid30482178, year = {2018}, author = {Gallo, G and Presta, L and Perrin, E and Gallo, M and Marchetto, D and Puglia, AM and Fani, R and Baldi, F}, title = {Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {198}, doi = {10.1186/s12866-018-1330-5}, pmid = {30482178}, issn = {1471-2180}, support = {FFR 2012-2013//Università degli Studi di Palermo/ ; FFR 2018//Università degli Studi di Palermo/ ; PRIN-2010AXENJ8//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; FFABR 2017//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; Assegno premiale//Università degli Studi di Firenze/ ; ADiR//Università Ca' Foscari di Venezia/ ; }, abstract = {BACKGROUND: Klebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM 29614 strain is multi metal resistant and produces metal nanoparticles that are embedded in its very peculiar capsular exopolysaccharide. These metal nanoparticles were effective as antimicrobial and anticancer compounds, chemical catalysts and nano-fertilizers.<br><br>RESULTS: The DSM 29614 strain genome was sequenced and analysed by a combination of in silico procedures. Comparative genomics, performed between 85 K. oxytoca representatives and K. oxytoca DSM 29614, revealed that this bacterial group has an open pangenome, characterized by a very small core genome (1009 genes, about 2%), a high fraction of unique (43,808 genes, about 87%) and accessory genes (5559 genes, about 11%). Proteins belonging to COG categories &quot;Carbohydrate transport and metabolism&quot; (G), &quot;Amino acid transport and metabolism&quot; (E), &quot;Coenzyme transport and metabolism&quot; (H), &quot;Inorganic ion transport and metabolism&quot; (P), and &quot;membrane biogenesis-related proteins&quot; (M) are particularly abundant in the predicted proteome of DSM 29614 strain. The results of a protein functional enrichment analysis - based on a previous proteomic analysis - revealed metabolic optimization during Fe(III)-citrate anaerobic utilization. In this growth condition, the observed high levels of Fe(II) may be due to different flavin metal reductases and siderophores as inferred form genome analysis. The presence of genes responsible for the synthesis of exopolysaccharide and for the tolerance to heavy metals was highlighted too. The inferred genomic insights were confirmed by a set of phenotypic tests showing specific metabolic capability in terms of i) Fe2+ and exopolysaccharide production and ii) phosphatase activity involved in precipitation of metal ion-phosphate salts.<br><br>CONCLUSION: The K. oxytoca DSM 29614 unique capabilities of using Fe(III)-citrate as sole carbon and energy source in anaerobiosis and tolerating diverse metals coincides with the presence at the genomic level of specific genes that can support i) energy metabolism optimization, ii) cell protection by the biosynthesis of a peculiar exopolysaccharide armour entrapping metal ions and iii) general and metal-specific detoxifying activities by different proteins and metabolites.}, }
@article {pmid30465642, year = {2018}, author = {Abudahab, K and Prada, JM and Yang, Z and Bentley, SD and Croucher, NJ and Corander, J and Aanensen, DM}, title = {PANINI: Pangenome Neighbour Identification for Bacterial Populations.}, journal = {Microbial genomics}, volume = {}, number = {}, pages = {}, doi = {10.1099/mgen.0.000220}, pmid = {30465642}, issn = {2057-5858}, abstract = {The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce panini (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm. panini is browser-based and integrates with the Microreact platform for rapid online visualization and exploration of both core and accessory genome evolutionary signals, together with relevant epidemiological, geographical, temporal and other metadata. Several case studies with single- and multi-clone pneumococcal populations are presented to demonstrate the ability to identify biologically important signals from gene content data. panini is available at http://panini.pathogen.watch and code at http://gitlab.com/cgps/panini.}, }
@article {pmid30458797, year = {2018}, author = {Wang, D and Li, J and Wang, L}, title = {Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis.}, journal = {Biomedical engineering online}, volume = {17}, number = {Suppl 1}, pages = {133}, doi = {10.1186/s12938-018-0563-8}, pmid = {30458797}, issn = {1475-925X}, abstract = {BACKGROUND: Pseudomonas aeruginosa is a common bacterium which is recognized for its association with hospital-acquired infections and its advanced antibiotic resistance mechanisms. Tuberculosis, one of the major causes of mortality, is initiated by the deposition of Mycobacterium tuberculosis. Accessory sequences shared by a subset of strains of a species play an important role in a species' evolution, antibiotic resistance and infectious potential.<br><br>RESULTS: Here, with a multiple sequence aligner, we segmented 25 P. aeruginosa genomes and 28 M. tuberculosis genomes into core blocks (include sequences shared by all the input genomes) and dispensable blocks (include sequences shared by a subset of the input genomes), respectively. For each input genome, we then constructed a scaffold consisting of its core and dispensable blocks sorted by blocks' locations on the chromosomes. Consecutive dispensable blocks on these scaffold formed instable regions. After a comprehensive study of these instable regions, three characteristics of instable regions are summarized: instable regions were short, site specific and varied in different strains. Three DNA elements (directed repeats (DRs), transposons and integrons) were then studied to see whether these DNA elements are associated with the variation of instable regions. A pipeline was developed to search for DR pairs on the flank of every instable sequence. 27 DR pairs in P. aeruginosa strains and 6 pairs in M. tuberculosis strains were found to exist in the instable regions. On the average, 14% and 12% of instable regions in P. aeruginosa strains covered transposase genes and integrase genes, respectively. In M. tuberculosis strains, an average of 43% and 8% of instable regions contain transposase genes and integrase genes, respectively.<br><br>CONCLUSIONS: Instable regions were short, site specific and varied in different strains for both P. aeruginosa and M. tuberculosis. Our experimental results showed that DRs, transposons and integrons may be associated with variation of instable regions.}, }
@article {pmid30455414, year = {2018}, author = {Sherman, RM and Forman, J and Antonescu, V and Puiu, D and Daya, M and Rafaels, N and Boorgula, MP and Chavan, S and Vergara, C and Ortega, VE and Levin, AM and Eng, C and Yazdanbakhsh, M and Wilson, JG and Marrugo, J and Lange, LA and Williams, LK and Watson, H and Ware, LB and Olopade, CO and Olopade, O and Oliveira, RR and Ober, C and Nicolae, DL and Meyers, DA and Mayorga, A and Knight-Madden, J and Hartert, T and Hansel, NN and Foreman, MG and Ford, JG and Faruque, MU and Dunston, GM and Caraballo, L and Burchard, EG and Bleecker, ER and Araujo, MI and Herrera-Paz, EF and Campbell, M and Foster, C and Taub, MA and Beaty, TH and Ruczinski, I and Mathias, RA and Barnes, KC and Salzberg, SL}, title = {Assembly of a pan-genome from deep sequencing of 910 humans of African descent.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41588-018-0273-y}, pmid = {30455414}, issn = {1546-1718}, abstract = {We used a deeply sequenced dataset of 910 individuals, all of African descent, to construct a set of DNA sequences that is present in these individuals but missing from the reference human genome. We aligned 1.19 trillion reads from the 910 individuals to the reference genome (GRCh38), collected all reads that failed to align, and assembled these reads into contiguous sequences (contigs). We then compared all contigs to one another to identify a set of unique sequences representing regions of the African pan-genome missing from the reference genome. Our analysis revealed 296,485,284 bp in 125,715 distinct contigs present in the populations of African descent, demonstrating that the African pan-genome contains ~10% more DNA than the current human reference genome. Although the functional significance of nearly all of this sequence is unknown, 387 of the novel contigs fall within 315 distinct protein-coding genes, and the rest appear to be intergenic.}, }
@article {pmid30453061, year = {2018}, author = {Kayansamruaj, P and Soontara, C and Unajak, S and Dong, HT and Rodkhum, C and Kondo, H and Hirono, I and Areechon, N}, title = {Comparative genomics inferred two distinct populations of piscine pathogenic Streptococcus agalactiae, serotype Ia ST7 and serotype III ST283, in Thailand and Vietnam.}, journal = {Genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ygeno.2018.11.016}, pmid = {30453061}, issn = {1089-8646}, abstract = {The genomes of Streptococcus agalactiae (group B streptococcus; GBS) collected from diseased fish in Thailand and Vietnam over a nine-year period (2008-2016) were sequenced and compared (n = 21). Based on capsular serotype and multilocus sequence typing (MLST), GBS isolates are divided into 2 groups comprised of i) serotype Ia; sequence type (ST)7 and ii) serotype III; ST283. Population structure inferred by core genome (cg)MLST and Bayesian clustering analysis also strongly indicated distribution of two GBS populations in both Thailand and Vietnam. Deep phylogenetic analysis implied by CRISPR array's spacer diversity was able to cluster GBS isolates according to their temporal and geographic origins, though ST7 has varying CRISPR1-spacer profiles when compared to ST283 strains. Based on overall genotypic features, Thai ST283 strains were closely related to the Singaporean ST283 strain causing foodborne illness in humans in 2015, thus, signifying zoonotic potential of this GBS population in the country.}, }
@article {pmid30446793, year = {2018}, author = {Monat, C and Schreiber, M and Stein, N and Mascher, M}, title = {Prospects of pan-genomics in barley.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00122-018-3234-z}, pmid = {30446793}, issn = {1432-2242}, support = {031B0190A//Bundesministerium für Bildung und Forschung/ ; SAW-2015-IPK-1//Leibniz-Gemeinschaft/ ; }, abstract = {The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants. The large size and complex structure of Triticeae genomes were for a long time an obstacle for genomic research in barley and its relatives. Now that a reference genome is available, computational pipelines for high-quality sequence assembly are in place, and sequence costs continue to drop, investigations into the structural diversity of the barley genome seem within reach. Here, we review the recent progress on pan-genomics in the model grass Brachypodium distachyon, and the cereal crops rice and maize, and devise a multi-tiered strategy for a pan-genome project in barley. Our design involves: (1) the construction of high-quality de novo sequence assemblies for a small core set of representative genotypes, (2) short-read sequencing of a large diversity panel of genebank accessions to medium coverage and (3) the use of complementary methods such as chromosome-conformation capture sequencing and k-mer-based association genetics. The in silico representation of the barley pan-genome may inform about the mechanisms of structural genome evolution in the Triticeae and supplement quantitative genetics models of crop performance for better accuracy and predictive ability.}, }
@article {pmid30445215, year = {2018}, author = {Mohapatra, B and Kazy, SK and Sar, P}, title = {Comparative genome analysis of arsenic reducing, hydrocarbon metabolizing groundwater bacterium Achromobacter sp. KAs 3-5T explains its competitive edge for survival in aquifer environment.}, journal = {Genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ygeno.2018.11.004}, pmid = {30445215}, issn = {1089-8646}, abstract = {Whole genome sequence of arsenic reducing, hydrocarbon metabolizing groundwater bacterium Achromobacter sp. KAs 3-5T was explored to understand the genomic basis of its As-ecophysiology and niche adaptation in aquifer environment. The genome (5.6 Mbp, 65.5 G + C %) encodes 4840 proteins, 1138 enzymes, 53 tRNAs, 11 rRNAs, 608 signal peptides, and 1.13% horizontally transferred genes. Presence of genes encoding cytosolic As5+-reduction (arsCBH, ACR3), aromatics utilization (bph/naph, catABC, boxABCD, genACB), Fe-transformation (tonB, achromobactin, FUR, FeR), and denitrification (nar, nap) processes were observed and validated through proteomics. Phylogenomic analysis (< 90% ANI, < 50% DDH) confirmed strain KAs 3-5T to be novel representative of the genus Achromobacter. An asymptotic open pan-genome (20,855 genes) and high correlation between genomic and ecological diversity suggested niche preference ability of this genus. Assemblage of species specific genes affiliated to transcription-regulation, membrane transport, and redox-transformation explained the strain's competitive survival strategies in As-rich oligotrophic groundwater.}, }
@article {pmid30425707, year = {2018}, author = {Fontana, A and Zacconi, C and Morelli, L}, title = {Genetic Signatures of Dairy Lactobacillus casei Group.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2611}, doi = {10.3389/fmicb.2018.02611}, pmid = {30425707}, issn = {1664-302X}, abstract = {Lactobacillus casei/Lactobacillus paracasei group of species contains strains adapted to a wide range of environments, from dairy products to intestinal tract of animals and fermented vegetables. Understanding the gene acquisitions and losses that induced such different adaptations, implies a comparison between complete genomes, since evolutionary differences spread on the whole sequence. This study compared 12 complete genomes of L. casei/paracasei dairy-niche isolates and 7 genomes of L. casei/paracasei isolated from other habitats (i.e., corn silage, human intestine, sauerkraut, beef, congee). Phylogenetic tree construction and average nucleotide identity (ANI) metric showed a clustering of the two dairy L. casei strains ATCC393 and LC5, indicating a lower genetic relatedness in comparison to the other strains. Genomic analysis revealed a core of 313 genes shared by dairy and non-dairy Lactic Acid bacteria (LAB), within a pan-genome of 9,462 genes. Functional category analyses highlighted the evolutionary genes decay of dairy isolates, particularly considering carbohydrates and amino acids metabolisms. Specifically, dairy L. casei/paracasei strains lost the ability to metabolize myo-inositol and taurine (i.e., iol and tau gene clusters). However, gene acquisitions by dairy strains were also highlighted, mostly related to defense mechanisms and host-pathogen interactions (i.e., yueB, esaA, and sle1). This study aimed to be a preliminary investigation on dairy and non-dairy marker genes that could be further characterized for probiotics or food applications.}, }
@article {pmid30425695, year = {2018}, author = {Hiller, NL and Sá-Leão, R}, title = {Puzzling Over the Pneumococcal Pangenome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2580}, doi = {10.3389/fmicb.2018.02580}, pmid = {30425695}, issn = {1664-302X}, abstract = {The Gram positive bacterium Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human host, and in the nasopharynx, sinus, and middle ear it survives as a biofilm. This mode of growth is optimal for multi-strain colonization and genetic exchange. Over the last decades, the far-reaching use of antibiotics and the widespread implementation of pneumococcal multivalent conjugate vaccines have posed considerable selective pressure on pneumococci. This scenario provides an exceptional opportunity to study the evolution of the pangenome of a clinically important bacterium, and has the potential to serve as a case study for other species. The goal of this review is to highlight key findings in the studies of pneumococcal genomic diversity and plasticity.}, }
@article {pmid30421490, year = {2018}, author = {Biessy, A and Novinscak, A and Blom, J and Léger, G and Thomashow, LS and Cazorla, FM and Josic, D and Filion, M}, title = {Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14476}, pmid = {30421490}, issn = {1462-2920}, abstract = {Plant-beneficial Pseudomonas spp. competitively colonize the rhizosphere and display plant-growth promotion and/or disease-suppression activities. Some strains within the P. fluorescens species complex produce phenazine derivatives, such as phenazine-1-carboxylic acid. These antimicrobial compounds are broadly inhibitory to numerous soil-dwelling plant pathogens and play a role in the ecological competence of phenazine-producing Pseudomonas spp. We assembled a collection encompassing 63 strains representative of the worldwide diversity of plant-beneficial phenazine-producing Pseudomonas spp. In this study, we report the sequencing of 58 complete genomes using PacBio RS II sequencing technology. Distributed among four subgroups within the P. fluorescens species complex, the diversity of our collection is reflected by the large pangenome which accounts for 25,413 protein-coding genes. We identified genes and clusters encoding for numerous phytobeneficial traits, including antibiotics, siderophores and cyclic lipopeptides biosynthesis, some of which were previously unknown in these microorganisms. Finally, we gained insight into the evolutionary history of the phenazine biosynthetic operon. Given its diverse genomic context, it is likely that this operon was relocated several times during Pseudomonas evolution. Our findings acknowledge the tremendous diversity of plant-beneficial phenazine-producing Pseudomonas spp., paving the way for comparative analyses to identify new genetic determinants involved in biocontrol, plant-growth promotion and rhizosphere competence. This article is protected by copyright. All rights reserved.}, }
@article {pmid30411512, year = {2018}, author = {Nanayakkara, BS and O'Brien, CL and Gordon, DM}, title = {Diversity and distribution of Klebsiella capsules in E. coli.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12710}, pmid = {30411512}, issn = {1758-2229}, abstract = {E. coli strains responsible for elevated counts in freshwater reservoirs in Australia carry a capsule originating from Klebsiella. The occurrence of Klebsiella capsules in E. coli was about 7% overall and 23 different capsule types were detected. Capsules were observed in strains from phylogroups A, B1, and C, but were absent from phylogroup B2, D, E, and F strains. In general, few A, B1, or C lineages were capsule-positive, but when a lineage was encapsulated multiple different capsule types were present. All Klebsiella capsule-positive strains were of serogroups O8, O9, and O89. Regardless of the phylogroup, O9 strains were more likely to be capsule-positive than O8 strains. Given the sequence similarity, it appears that both the capsule region and the O-antigen gene region are transferred to E. coli from Klebsiella as a single block via horizontal gene transfer events. Pan genome analysis indicated that there were only modest differences between encapsulated and non-encapsulated strains belonging to phylogroup A. The possession of a Klebsiella capsule, but not the type of capsule, is likely a key determinant of the bloom status. This article is protected by copyright. All rights reserved.}, }
@article {pmid30405580, year = {2018}, author = {Al-Bassam, MM and Haist, J and Neumann, SA and Lindenberg, S and Tschowri, N}, title = {Expression Patterns, Genomic Conservation and Input Into Developmental Regulation of the GGDEF/EAL/HD-GYP Domain Proteins in Streptomyces.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2524}, doi = {10.3389/fmicb.2018.02524}, pmid = {30405580}, issn = {1664-302X}, abstract = {To proliferate, antibiotic-producing Streptomyces undergo a complex developmental transition from vegetative growth to the production of aerial hyphae and spores. This morphological switch is controlled by the signaling molecule cyclic bis-(3',5') di-guanosine-mono-phosphate (c-di-GMP) that binds to the master developmental regulator, BldD, leading to repression of key sporulation genes during vegetative growth. However, a systematical analysis of all the GGDEF/EAL/HD-GYP proteins that control c-di-GMP levels in Streptomyces is still lacking. Here, we have FLAG-tagged all 10 c-di-GMP turnover proteins in Streptomyces venezuelae and characterized their expression patterns throughout the life cycle, revealing that the diguanylate cyclase (DGC) CdgB and the phosphodiesterase (PDE) RmdB are the most abundant GGDEF/EAL proteins. Moreover, we have deleted all the genes coding for c-di-GMP turnover enzymes individually and analyzed morphogenesis of the mutants in macrocolonies. We show that the composite GGDEF-EAL protein CdgC is an active DGC and that deletion of the DGCs cdgB and cdgC enhance sporulation whereas deletion of the PDEs rmdA and rmdB delay development in S. venezuelae. By comparing the pan genome of 93 fully sequenced Streptomyces species we show that the DGCs CdgA, CdgB, and CdgC, and the PDE RmdB represent the most conserved c-di-GMP-signaling proteins in the genus Streptomyces.}, }
@article {pmid30391557, year = {2018}, author = {Pinto, M and González-Díaz, A and Machado, MP and Duarte, S and Vieira, L and Carriço, JA and Marti, S and Bajanca-Lavado, MP and Gomes, JP}, title = {Insights into the population structure and pan-genome of Haemophilus influenzae.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.meegid.2018.10.025}, pmid = {30391557}, issn = {1567-7257}, abstract = {The human-restricted bacterium Haemophilus influenzae is responsible for respiratory infections in both children and adults. While colonization begins in the upper airways, it can spread throughout the respiratory tract potentially leading to invasive infections. Although the spread of H. influenzae serotype b (Hib) has been prevented by vaccination, the emergence of infections by other serotypes as well as by non-typeable isolates (NTHi) have been observed, prompting the need for novel prevention strategies. Here, we aimed to study the population structure of H. influenzae and to get some insights into its pan-genome. We studied 305H. influenzae strains, enrolling 217 publicly available genomes, as well as 88 newly sequenced H. influenzae invasive strains isolated in Portugal, spanning a 24-year period. NTHi isolates presented a core-SNP-based genetic diversity about 10-fold higher than the one observed for Hib. The analysis of key factors involved in pathogenesis, such as lipooligosaccharides, hemagglutinating pili and High Molecular Weight-adhesins, suggests that NTHi shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion and persistence. Discreet NTHi subpopulations structures are proposed based on core-genome supported with 17 candidate genetic markers identified in the accessory genome. Additionally, this study provides two bioinformatics tools for in silico rapid identification of H. influenzae serotypes and NTHi clades previously proposed, obviating laboratory-based demanding procedures. The present study constitutes an important genomic framework that could lay way for future studies on the genetic determinants underlying invasiveness and disease and population structure of H. influenzae.}, }
@article {pmid30386310, year = {2018}, author = {Wüthrich, D and Irmler, S and Berthoud, H and Guggenbühl, B and Eugster, E and Bruggmann, R}, title = {Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2415}, doi = {10.3389/fmicb.2018.02415}, pmid = {30386310}, issn = {1664-302X}, abstract = {Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei - a flavor-enhancing adjunct culture species - can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L. paracasei strains. From 24 selected L. paracasei strains, 16 strains can grow in medium with methionine as sole sulfur source. We sequenced these strains to perform gene-trait matching. We found that one gene cluster - consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase - is present in all strains that grow in medium with methionine as sole sulfur source. In contrast, strains that depend on other sulfur sources do not have this gene cluster. We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species.}, }
@article {pmid30383521, year = {2018}, author = {Fleshman, A and Mullins, K and Sahl, J and Hepp, C and Nieto, N and Wiggins, K and Hornstra, H and Kelly, D and Chan, TC and Phetsouvanh, R and Dittrich, S and Panyanivong, P and Paris, D and Newton, P and Richards, A and Pearson, T}, title = {Corrigendum: Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity.}, journal = {Microbial genomics}, volume = {4}, number = {10}, pages = {}, doi = {10.1099/mgen.0.000230}, pmid = {30383521}, issn = {2057-5858}, }
@article {pmid30371758, year = {2018}, author = {Franz, E and Rotariu, O and Lopes, BS and MacRae, M and Bono, JL and Laing, C and Gannon, V and Söderlund, R and van Hoek, AHAM and Friesema, I and French, NP and George, T and Biggs, PJ and Jaros, P and Rivas, M and Chinen, I and Campos, J and Jernberg, C and Gobius, K and Mellor, GE and Chandry, PS and Perez-Reche, F and Forbes, KJ and Strachan, NJC}, title = {Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciy919}, pmid = {30371758}, issn = {1537-6591}, abstract = {Background: Shiga toxin-producing Escherchia coli O157:H7 is a zoonotic pathogen which causes numerous food and waterborne disease outbreaks. It is globally distributed but its origin and temporal sequence of geographical spread is unknown.<br><br>Methods: We analysed Whole Genome Sequencing data of 757 isolates from 4 continents and performed a pan genome analysis to identify the core genome and from this extracted single nucleotide polymorphisms. Timed phylogeographic analysis was performed on a subset of the isolates to investigate it's worldwide spread.<br><br>Results: The common ancestor of this set of isolates occurred around 1890 (1845-1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental from Europe to Australia around 1937 (1909-1958), to USA in 1941 (1921-1962), to Canada in 1960 (1943-1979), and from Australia to New Zealand in 1966 (1943-1982). This pre-dates the first reported human case of E. coli O157:H7 in 1975 from the USA.<br><br>Conclusions: Inter- and intra- continental transmission events have resulted in the current international distribution of E. coli O157:H7 and it is likely that these events were facilitated by animal movements (e.g. Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce further spread of E. coli O157:H7 and other (emerging) STEC strains globally.}, }
@article {pmid30366996, year = {2018}, author = {De Filippis, F and La Storia, A and Villani, F and Ercolini, D}, title = {Strain-level diversity analysis of Pseudomonas fragi after in situ pangenome reconstruction shows distinctive spoilage-associated metabolic traits clearly selected by different storage conditions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02212-18}, pmid = {30366996}, issn = {1098-5336}, abstract = {Microbial spoilage of raw meat causes huge economic losses every year. Understanding the microbial ecology associated to the spoilage and its dynamics during refrigerated storage of meat can help in preventing and delaying the spoilage-related activities. Raw meat microbiota is usually complex but only few members will develop during storage and cause spoilage, upon the pressure of several external factors, such as temperature and oxygen availability. We characterized the metagenome of beef packed aerobically or under-vacuum during refrigerated storage to explore how different packaging conditions may influence microbial composition and potential spoilage-associated activities. Different population dynamics and spoilage-associated genomic repertoires occurred in beef stored in air or vacuum-packaging. Moreover, pangenomics of Pseudomonas fragi strains extracted from metagenomes was carried out. We demonstrated the presence of specific, storage-driven strain-level profiles of Pseudomonas fragi, characterized by a different gene repertoire, thus potentially able to act differently during meat spoilage. The results provide new knowledge on strain-level microbial ecology associated to meat spoilage and can be of value for future strategies of spoilage prevention and food waste reduction.IMPORTANCE This work provides insights on the mechanisms involved in raw beef spoilage during refrigerated storage and on the selective pressure exerted by the packaging conditions. We highlighted the presence of different microbial metagenomes during spoilage of beef packaged aerobically or under-vacuum. The packaging condition was able to select specific Pseudomonas fragi strains, with a distinctive genomic repertoire. This study may help in deciphering the behaviour of different biomes directly in-situ in food and in understanding the specific contribution of different strains to food spoilage.}, }
@article {pmid30359301, year = {2018}, author = {Hii, SYF and Ahmad, N and Hashim, R and Liow, YL and Abd Wahab, MA and Mohd Khalid, MKN}, title = {A SNP-based phylogenetic analysis of Corynebacterium diphtheriae in Malaysia.}, journal = {BMC research notes}, volume = {11}, number = {1}, pages = {760}, doi = {10.1186/s13104-018-3868-6}, pmid = {30359301}, issn = {1756-0500}, support = {NMRR id: 16-1421-32070 (JPP-IMR: 16-056)//Ministry of Health Malaysia/ ; }, abstract = {OBJECTIVE: There is a lack of study in Corynebacterium diphtheriae isolates in Malaysia. The alarming surge of cases in year 2016 lead us to evaluate the local clinical C. diphtheriae strains in Malaysia. We conducted single nucleotide polymorphism phylogenetic analysis on the core and pan-genome as well as toxin and diphtheria toxin repressor (DtxR) genes of Malaysian C. diphtheriae isolates from the year 1986-2016.<br><br>RESULTS: The comparison between core and pan-genomic comparison showed variation in the distribution of C. diphtheriae. The local isolates portrayed a heterogenous trait and a close relationship between Malaysia's and Belarus's, Africa's and India's strains were observed. A toxigenic C. diphtheriae clone was noted to be circulating in the Malaysian population for nearly 30 years and from our study, the non-toxigenic and toxigenic C. diphtheriae strains can be differentiated significantly into two large clusters, A and B respectively. Analysis against vaccine strain, PW8 portrayed that the amino acid composition of toxin and DtxR in Malaysia's local strains are well-conserved and there was no functional defect noted. Hence, the change in efficacy of the currently used toxoid vaccine is unlikely to occur.}, }
@article {pmid30353070, year = {2018}, author = {Subedi, D and Vijay, AK and Kohli, GS and Rice, SA and Willcox, M}, title = {Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15668}, doi = {10.1038/s41598-018-34020-7}, pmid = {30353070}, issn = {2045-2322}, abstract = {The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.}, }
@article {pmid30349509, year = {2018}, author = {Chaudhari, NM and Gautam, A and Gupta, VK and Kaur, G and Dutta, C and Paul, S}, title = {PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2322}, doi = {10.3389/fmicb.2018.02322}, pmid = {30349509}, issn = {1664-302X}, abstract = {The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) - a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project. The resource allows users to explore genomic/functional diversity and genome-based phylogenetic relationships between human associated microbial genomes, not provided by any other resource. The key features implemented here include pan-genome and functional analysis of organisms based on taxonomy or body-site, and comparative analysis between groups of organisms. The first feature can also identify probable gene-loss events and significantly over/under represented KEGG/COG categories within pan-genome. The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes. The dynamic nature of this resource enables users to define parameters for orthologous clustering and to select any set of organisms for analysis. As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 Lactobacillus genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized the body-site specific genes, enzymes and pathways. Altogether, PanGFR-HM, being unique in its content and functionality, is expected to provide a platform for microbiome-based comparative functional and evolutionary genomics.}, }
@article {pmid30348668, year = {2018}, author = {Johnson, TJ and Elnekave, E and Miller, EA and Munoz-Aguayo, J and Flores Figueroa, C and Johnston, B and Nielson, DW and Logue, CM and Johnson, JR}, title = {Phylogenomic analysis of extraintestinal pathogenic Escherichia coli ST1193, an emerging multidrug-resistant clonal group.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1128/AAC.01913-18}, pmid = {30348668}, issn = {1098-6596}, abstract = {The fluoroquinolone-resistant ST1193 clonal group of Escherichia coli, from the ST14 clonal complex (STc14) within phylogenetic group B2, has appeared recently as an important cause of extraintestinal disease in humans. Although this emerging lineage has been characterized to some extent using conventional methods, it has not been studied extensively at the genomic level. Here, we used whole genome sequence analysis to compare 355 ST1193 isolates with 72 isolates from other STs within STc14. Using core genome phylogeny, the ST1193 isolates formed a tightly clustered clade with many genotypic similarities, as compared to ST14 isolates. All ST1193 isolates possessed the same set of three chromosomal mutations conferring fluoroquinolone resistance, carried the fimH64 allele, and were lactose non-fermenting. Analysis revealed an evolutionary progression from K1 to K5 capsular types and acquisition of an F-type virulence plasmid followed by changes in plasmid structure congruent with genome phylogeny. In contrast, the numerous identified antimicrobial resistance genes were distributed incongruently with the underlying phylogeny, suggesting frequent gain or loss of the corresponding resistance gene cassettes despite retention of the presumed carrier plasmids. Pangenome analysis revealed gains and losses of genetic loci occurring during the transition from ST14 to ST1193, and from the K1 to K5 capsular types. Using time-scaled phylogenetic analysis, we estimated that current ST1193 clades first emerged approximately 25 years ago. Overall, ST1193 appears to be a recently emerged clone in which both stepwise and mosaic evolution likely have contributed to epidemiologic success.}, }
@article {pmid30341495, year = {2018}, author = {Bettgenhaeuser, J and Krattinger, SG}, title = {Rapid gene cloning in cereals.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00122-018-3210-7}, pmid = {30341495}, issn = {1432-2242}, abstract = {KEY MESSAGE: The large and complex genomes of many cereals hindered cloning efforts in the past. Advances in genomics now allow the rapid cloning of genes from humanity's most valuable crops. The past two decades were characterized by a genomics revolution that entailed profound changes to crop research, plant breeding, and agriculture. Today, high-quality reference sequences are available for all major cereal crop species. Large resequencing and pan-genome projects start to reveal a more comprehensive picture of the genetic makeup and the diversity among domesticated cereals and their wild relatives. These technological advancements will have a dramatic effect on dissecting genotype-phenotype associations and on gene cloning. In this review, we will highlight the status of the genomic resources available for various cereal crops and we will discuss their implications for gene cloning. A particular focus will be given to the cereal species barley and wheat, which are characterized by very large and complex genomes that have been inaccessible to rapid gene cloning until recently. With the advancements in genomics and the development of several rapid gene-cloning methods, it has now become feasible to tackle the cloning of most agriculturally important genes, even in wheat and barley.}, }
@article {pmid30341451, year = {2018}, author = {Fraunhofer, ME and Geißler, AJ and Behr, J and Vogel, RF}, title = {Comparative Genomics of Lactobacillus brevis Reveals a Significant Plasmidome Overlap of Brewery and Insect Isolates.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-018-1581-2}, pmid = {30341451}, issn = {1432-0991}, support = {AiF 18194 N//German Ministry of Economics/ ; }, abstract = {Lactobacillus (L.) brevis represents a versatile, ubiquitistic species of lactic acid bacteria, occurring in various foods, as well as plants and intestinal tracts. The ability to deal with considerably differing environmental conditions in the respective ecological niches implies a genomic adaptation to the particular requirements to use it as a habitat beyond a transient state. Given the isolation source, 24 L. brevis genomes were analyzed via comparative genomics to get a broad view of the genomic complexity and ecological versatility of this species. This analysis showed L. brevis being a genetically diverse species possessing a remarkably large pan genome. As anticipated, it proved difficult to draw a correlation between chromosomal settings and isolation source. However, on plasmidome level, brewery- and insect-derived strains grouped into distinct clusters, referable to a noteworthy gene sharing between both groups. The brewery-specific plasmidome is characterized by several genes, which support a life in the harsh environment beer, but 40% of the brewery plasmidome were found in insect-derived strains as well. This suggests a close interaction between these habitats. Further analysis revealed the presence of a truncated horC cluster version in brewery- and insect-associated strains. This disproves horC, the major contributor to survival in beer, as brewery isolate specific. We conclude that L. brevis does not perform rigorous chromosomal changes to live in different habitats. Rather it appears that the species retains a certain genetic diversity in the plasmidome and meets the requirements of a particular ecological niche with the acquisition of appropriate plasmids.}, }
@article {pmid30335848, year = {2018}, author = {Mercante, JW and Caravas, JA and Ishaq, MK and Kozak-Muiznieks, NA and Raphael, BH and Winchell, JM}, title = {Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0206110}, doi = {10.1371/journal.pone.0206110}, pmid = {30335848}, issn = {1932-6203}, abstract = {Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations and environmental source attribution. In the United States (US), ST1 is the most prevalent clinical and environmental Lp sequence type. In order to characterize the ST1 population, we sequenced 289 outbreak and non-outbreak associated clinical and environmental ST1 and ST1-variant Lp strains from the US and, together with international isolate sequences, explored their genetic and geographic diversity. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant and environmental isolates unassociated with human disease (n = 99) contained ~65% more nucleotide diversity compared to clinical-sporadic (n = 139) or outbreak-associated (n = 28) ST1 subgroups. The accessory pangenome of environmental isolates was also ~30-60% larger than other subgroups and was enriched for transposition and conjugative transfer-associated elements. Up to ~10% of US ST1 genetic variation could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and from different decades. These findings provide new insight into the ST1 population structure and establish a foundation for interpreting genetic relationships among ST1 strains; these data may also inform future analyses for improved outbreak investigations.}, }
@article {pmid30333483, year = {2018}, author = {Kavvas, ES and Catoiu, E and Mih, N and Yurkovich, JT and Seif, Y and Dillon, N and Heckmann, D and Anand, A and Yang, L and Nizet, V and Monk, JM and Palsson, BO}, title = {Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4306}, doi = {10.1038/s41467-018-06634-y}, pmid = {30333483}, issn = {2041-1723}, support = {1-U01-AI124316-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U01GM102098//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses. Here, we develop a reference strain-agnostic computational platform that uses machine learning approaches, complemented by both genetic interaction analysis and 3D structural mutation-mapping, to identify signatures of AMR evolution to 13 antibiotics. This platform is applied to 1595 sequenced strains to yield four key results. First, a pan-genome analysis shows that M. tuberculosis is highly conserved with sequenced variation concentrated in PE/PPE/PGRS genes. Second, the platform corroborates 33 genes known to confer resistance and identifies 24 new genetic signatures of AMR. Third, 97 epistatic interactions across 10 resistance classes are revealed. Fourth, detailed structural analysis of these genes yields mechanistic bases for their selection. The platform can be used to study other human pathogens.}, }
@article {pmid30326842, year = {2018}, author = {Zoledowska, S and Motyka-Pomagruk, A and Sledz, W and Mengoni, A and Lojkowska, E}, title = {High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {751}, doi = {10.1186/s12864-018-5140-9}, pmid = {30326842}, issn = {1471-2164}, support = {2014/14/M/NZ8/00501//Narodowe Centrum Nauki/ ; }, abstract = {BACKGROUND: Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline.<br><br>RESULTS: The pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland.<br><br>CONCLUSIONS: We can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.}, }
@article {pmid30315621, year = {2018}, author = {Yu, J and Golicz, AA and Lu, K and Dossa, K and Zhang, Y and Chen, J and Wang, L and You, J and Fan, D and Edwards, D and Zhang, X}, title = {Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.13022}, pmid = {30315621}, issn = {1467-7652}, abstract = {Sesame (Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces (S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars (S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference-assisted assembly approach to improve the draft assemblies of four of the sesame varieties. We then constructed a sesame pan-genome of 554.05 Mb. The pan-genome contained 26,472 orthologous gene clusters; 15,409 (58.21%) of them were core (present across all five sesame genomes), whereas the remaining 41.79% (11,063) clusters and the 15,890 variety-specific genes were dispensable. Comparisons between varieties suggest that modern cultivars from China and India display significant genomic variation. The gene families unique to the sesame modern cultivars contain genes mainly related to yield and quality, while those unique to the landraces contain genes involved in environmental adaptation. Comparative evolutionary analysis indicates that several genes involved in plant-pathogen interaction and lipid metabolism are under positive selection, which may be associated with sesame environmental adaption and selection for high seed oil content. This study of the sesame pan-genome provides insights into the evolution and genomic characteristics of this important oilseed and constitutes a resource for further sesame crop improvement. This article is protected by copyright. All rights reserved.}, }
@article {pmid30314447, year = {2018}, author = {Bobay, LM and Ochman, H}, title = {Factors driving effective population size and pan-genome evolution in bacteria.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {153}, doi = {10.1186/s12862-018-1272-4}, pmid = {30314447}, issn = {1471-2148}, support = {R35GM118038/NH/NIH HHS/United States ; R01GM108657/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Knowledge of population-level processes is essential to understanding the efficacy of selection operating within a species. However, attempts at estimating effective population sizes (Ne) are particularly challenging in bacteria due to their extremely large census populations sizes, varying rates of recombination and arbitrary species boundaries.<br><br>RESULTS: In this study, we estimated Ne for 153 species (152 bacteria and one archaeon) defined under a common framework and found that ecological lifestyle and growth rate were major predictors of Ne; and that contrary to theoretical expectations, Ne was unaffected by recombination rate. Additionally, we found that Ne shapes the evolution and diversity of total gene repertoires of prokaryotic species.<br><br>CONCLUSION: Together, these results point to a new model of genome architecture evolution in prokaryotes, in which pan-genome sizes, not individual genome sizes, are governed by drift-barrier evolution.}, }
@article {pmid30297045, year = {2019}, author = {Chun, BH and Kim, KH and Jeong, SE and Jeon, CO}, title = {Genomic and metabolic features of the Bacillus amyloliquefaciens group- B. amyloliquefaciens, B. velezensis, and B. siamensis- revealed by pan-genome analysis.}, journal = {Food microbiology}, volume = {77}, number = {}, pages = {146-157}, doi = {10.1016/j.fm.2018.09.001}, pmid = {30297045}, issn = {1095-9998}, abstract = {The genomic and metabolic features of the Bacillus amyloliquefaciens group comprising B. amyloliquefaciens, B. velezensis, and B. siamensis were investigated through a pan-genome analysis combined with an experimental verification of some of the functions identified. All B. amyloliquefaciens group genomes were retrieved from GenBank and their phylogenetic relatedness was subsequently investigated. Genome comparisons of B. amyloliquefaciens, B. siamensis, and B. velezensis showed that their genomic and metabolic features were similar; however species-specific features were also identified. Energy metabolism-related genes are more enriched in B. amyloliquefaciens, whereas secondary metabolite biosynthesis-related genes are enriched in B. velezensis. Compared to B. amyloliquefaciens and B. siamensis, B. velezensis harbors more genes in its core-genome which are involved in the biosynthesis of antimicrobial compounds, as well as genes involved in d-galacturonate and d-fructuronate metabolism. B. amyloliquefaciens, B. siamensis, and B. velezensis all harbor a xanthine oxidase gene cluster (xoABCDE) in their core-genomes that is involved in metabolizing xanthine and uric acid to glycine and oxalureate. A reconstruction of B. amyloliquefaciens group metabolic pathways using their individual pan-genomes revealed that the B. amyloliquefaciens group strains have the ability to metabolize diverse carbon sources aerobically, or anaerobically, and can produce various metabolites such as lactate, ethanol, acetate, CO2, xylitol, diacetyl, acetoin, and 2,3-butanediol. This study therefore provides insights into the genomic and metabolic features of the B. amyloliquefaciens group.}, }
@article {pmid30285620, year = {2018}, author = {Wright, ES and Baum, DA}, title = {Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {724}, doi = {10.1186/s12864-018-5099-6}, pmid = {30285620}, issn = {1471-2164}, abstract = {BACKGROUND: The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to define taxa is based on exclusivity of relatedness, which applies when members of a taxon are more closely related to each other than they are to any outsider. It is largely unknown whether exclusive bacterial taxa exist when averaging over the genome or are rare due to rampant hybridization.<br><br>RESULTS: Here, we analyze a collection of 701 genomes representing a wide variety of environmental isolates from the family Streptomycetaceae, whose members are competent at HGT. We find that the presence/absence of auxiliary genes in the pan-genome displays a hierarchical (tree-like) structure that correlates significantly with the genealogy of the core-genome. Moreover, we identified the existence of many exclusive taxa, although individual genes often contradict these taxa. These conclusions were supported by repeating the analysis on 1,586 genomes belonging to the genus Bacillus. However, despite confirming the existence of exclusive groups (taxa), we were unable to identify an objective threshold at which to assign the rank of species.<br><br>CONCLUSIONS: The existence of bacterial taxa is justified by considering average relatedness across the entire genome, as captured by exclusivity, but is rejected if one requires unanimous agreement of all parts of the genome. We propose using exclusivity to delimit taxa and conventional genome similarity thresholds to assign bacterial taxa to the species rank. This approach recognizes species that are phylogenetically meaningful, while also establishing some degree of comparability across species-ranked taxa in different bacterial clades.}, }
@article {pmid30277499, year = {2018}, author = {Peng, Y and Tang, S and Wang, D and Zhong, H and Jia, H and Cai, X and Zhang, Z and Xiao, M and Yang, H and Wang, J and Kristiansen, K and Xu, X and Li, J}, title = {MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giy121}, pmid = {30277499}, issn = {2047-217X}, abstract = {Pangenome analyses facilitate the interpretation of genetic diversity and evolutionary history of a taxon. However, there is an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome network from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved. MetaPGN also includes a self-developed Cytoscape plugin for layout of and interaction with the resulting pangenome network, providing an intuitive and interactive interface for full exploration of genetic diversity. We demonstrate the utility of MetaPGN by constructing Escherichia coli (E. coli) pangenome networks from five E. coli pathogenic strains and 760 human gut microbiomes respectively, revealing extensive genetic diversity of E. coli within both isolates and gut microbial populations. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data, MetaPGN provides advantages in expanding pangenome analysis to uncultured microbial taxa. MetaPGN is available at https://github.com/peng-ye/MetaPGN.}, }
@article {pmid30275399, year = {2018}, author = {Sharma, V and Mobeen, F and Prakash, T}, title = {Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics.}, journal = {Genes}, volume = {9}, number = {10}, pages = {}, doi = {10.3390/genes9100477}, pmid = {30275399}, issn = {2073-4425}, abstract = {Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.}, }
@article {pmid30257645, year = {2018}, author = {Awan, F and Dong, Y and Liu, J and Wang, N and Mushtaq, MH and Lu, C and Liu, Y}, title = {Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factors.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {712}, doi = {10.1186/s12864-018-5100-4}, pmid = {30257645}, issn = {1471-2164}, support = {31372454//National Nature Science Foundation of China/ ; CX(17)2027//Independent Innovation Fund of Agricultural Science and Technology in Jiangsu Province/ ; D2017-3-1//Jiangsu fishery science and technology project/ ; }, abstract = {BACKGROUND: Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. Moreover, the potential pathogenic factors among the publicly available genomes in A. hydrophila strains of different origins have not yet been investigated.<br><br>RESULTS: To identify the valid strains of A. hydrophila and their pathogenic factors, we performed a pan-genomic study. It revealed that there were 13 mislabelled strains and 49 valid strains that were further verified by Average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and in silico multiple locus strain typing (MLST). Multiple numbers of phages were detected among the strains and among them Aeromonas phi 018 was frequently present. The diversity in type III secretion system (T3SS) and conservation of type II and type VI secretion systems (T2SS and T6SS, respectively) among all the strains are important to study for designing future strategies. The most prevalent antibiotic resistances were found to be beta-lactamase, polymyxin and colistin resistances. The comparative analyses of sequence type (ST) 251 and other ST groups revealed that there were higher numbers of virulence factors in ST-251 than in other STs group.<br><br>CONCLUSION: Publicly available genomes have 13 mislabelled organisms, and there are only 49 valid A. hydrophila strains. This valid pan-genome identifies multiple prophages that can be further utilized. Different A. hydrophila strains harbour multiple virulence factors and antibiotic resistance genes. Identification of such factors is important for designing future treatment regimes.}, }
@article {pmid30257640, year = {2018}, author = {Sheikhizadeh Anari, S and de Ridder, D and Schranz, ME and Smit, S}, title = {Efficient inference of homologs in large eukaryotic pan-proteomes.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {340}, doi = {10.1186/s12859-018-2362-4}, pmid = {30257640}, issn = {1471-2105}, support = {3184519600//Experimental Plant Sciences/ ; }, abstract = {BACKGROUND: Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, there is a need for efficient standalone tools to detect homologs in novel data.<br><br>RESULTS: To address this, we present a fast method for detecting homology groups across a large number of individuals and/or species. We adopted a k-mer based approach which considerably reduces the number of pairwise protein alignments without sacrificing sensitivity. We demonstrate accuracy, scalability, efficiency and applicability of the presented method for detecting homology in large proteomes of bacteria, fungi, plants and Metazoa.<br><br>CONCLUSIONS: We clearly observed the trade-off between recall and precision in our homology inference. Favoring recall or precision strongly depends on the application. The clustering behavior of our program can be optimized for particular applications by altering a few key parameters. The program is available for public use at https://github.com/sheikhizadeh/pantools as an extension to our pan-genomic analysis tool, PanTools.}, }
@article {pmid30233526, year = {2018}, author = {Wang, LYR and Jokinen, CC and Laing, CR and Johnson, RP and Ziebell, K and Gannon, VPJ}, title = {Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2040}, doi = {10.3389/fmicb.2018.02040}, pmid = {30233526}, issn = {1664-302X}, abstract = {In this study, fecal samples were collected from a closed beef herd in Alberta, Canada from 2012 to 2015. To limit serotype bias, which was observed in enrichment broth cultures, Verotoxigenic Escherichia coli (VTEC) were isolated directly from samples using a hydrophobic grid-membrane filter verotoxin immunoblot assay. Overall VTEC isolation rates were similar for three different cohorts of yearling heifers on both an annual (68.5 to 71.8%) and seasonal basis (67.3 to 76.0%). Across all three cohorts, O139:H19 (37.1% of VTEC-positive samples), O22:H8 (15.8%) and O?(O108):H8 (15.4%) were among the most prevalent serotypes. However, isolation rates for serotypes O139:H19, O130:H38, O6:H34, O91:H21, and O113:H21 differed significantly between cohort-years, as did isolation rates for some serotypes within a single heifer cohort. There was a high level of VTEC serotype diversity with an average of 4.3 serotypes isolated per heifer and 65.8% of the heifers classified as &quot;persistent shedders&quot; of VTEC based on the criteria of >50% of samples positive and ≥4 consecutive samples positive. Only 26.8% (90/336) of the VTEC isolates from yearling heifers belonged to the human disease-associated seropathotypes A (O157:H7), B (O26:H11, O111:NM), and C (O22:H8, O91:H21, O113:H21, O137:H41, O2:H6). Conversely, seropathotypes B (O26:NM, O111:NM) and C (O91:H21, O2:H29) strains were dominant (76.0%, 19/25) among VTEC isolates from month-old calves from this herd. Among VTEC from heifers, carriage rates of vt1, vt2, vt1+vt2, eae, and hlyA were 10.7, 20.8, 68.5, 3.9, and 88.7%, respectively. The adhesin gene saa was present in 82.7% of heifer strains but absent from all of 13 eae+ve strains (from serotypes/intimin types O157:H7/γ1, O26:H11/β1, O111:NM/θ, O84:H2/ζ, and O182:H25/ζ). Phylogenetic relationships inferred from wgMLST and pan genome-derived core SNP analysis showed that strains clustered by phylotype and serotype. Further, VTEC strains of the same serotype usually shared the same suite of antibiotic resistance and virulence genes, suggesting the circulation of dominant clones within this distinct herd. This study provides insight into the diverse and dynamic nature of VTEC populations within groups of cattle and points to a broad spectrum of human health risks associated with these E. coli strains.}, }
@article {pmid30233505, year = {2018}, author = {Golanowska, M and Potrykus, M and Motyka-Pomagruk, A and Kabza, M and Bacci, G and Galardini, M and Bazzicalupo, M and Makalowska, I and Smalla, K and Mengoni, A and Hugouvieux-Cotte-Pattat, N and Lojkowska, E}, title = {Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1940}, doi = {10.3389/fmicb.2018.01940}, pmid = {30233505}, issn = {1664-302X}, abstract = {Bacteria belonging to the genera Dickeya and Pectobacterium are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of Dickeya solani. The D. solani strains investigated so far share genetic homogeneity, although different virulence levels were observed among strains of various origins. The purpose of this study was to investigate the genetic traits possibly related to the diverse virulence levels by means of comparative genomics. First, we developed a new genome assembly pipeline which allowed us to complete the D. solani genomes. Four de novo sequenced and ten publicly available genomes were used to identify the structure of the D. solani pangenome, in which 74.8 and 25.2% of genes were grouped into the core and dispensable genome, respectively. For D. solani panregulon analysis, we performed a binding site prediction for four transcription factors, namely CRP, KdgR, PecS and Fur, to detect the regulons of these virulence regulators. Most of the D. solani potential virulence factors were predicted to belong to the accessory regulons of CRP, KdgR, and PecS. Thus, some differences in gene expression could exist between D. solani strains. The comparison between a highly and a low virulent strain, IFB0099 and IFB0223, respectively, disclosed only small differences between their genomes but significant differences in the production of virulence factors like pectinases, cellulases and proteases, and in their mobility. The D. solani strains also diverge in the number and size of prophages present in their genomes. Another relevant difference is the disruption of the adhesin gene fhaB2 in the highly virulent strain. Strain IFB0223, which has a complete adhesin gene, is less mobile and less aggressive than IFB0099. This suggests that in this case, mobility rather than adherence is needed in order to trigger disease symptoms. This study highlights the utility of comparative genomics in predicting D. solani traits involved in the aggressiveness of this emerging plant pathogen.}, }
@article {pmid30230187, year = {2018}, author = {Bayer, PE and Golicz, AA and Tirnaz, S and Chan, CK and Edwards, D and Batley, J}, title = {Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.13015}, pmid = {30230187}, issn = {1467-7652}, support = {DP1601004497//Australian Research Council/ ; FT130100604//Australian Research Council/ ; LP130100925//Australian Research Council/ ; LP140100537//Australian Research Council/ ; LP160100030//Australian Research Council/ ; //Government of Western Australia/ ; }, abstract = {Brassica oleracea is an important agricultural species encompassing many vegetable crops including cabbage, cauliflower, broccoli and kale; however, it can be susceptible to a variety of fungal diseases such as clubroot, blackleg, leaf spot and downy mildew. Resistance to these diseases is meditated by specific disease resistance genes analogs (RGAs) which are differently distributed across B. oleracea lines. The sequenced reference cultivar does not contain all B. oleracea genes due to gene presence/absence variation between individuals, which makes it necessary to search for RGA candidates in the B. oleracea pangenome. Here we present a comparative analysis of RGA candidates in the pangenome of B. oleracea. We show that the presence of RGA candidates differs between lines and suggests that in B. oleracea, SNPs and presence/absence variation drive RGA diversity using separate mechanisms. We identified 59 RGA candidates linked to Sclerotinia, clubroot, and Fusarium wilt resistance QTL, and these findings have implications for crop breeding in B. oleracea, which may also be applicable in other crops species.}, }
@article {pmid30223644, year = {2018}, author = {Checcucci, A and diCenzo, GC and Ghini, V and Bazzicalupo, M and Becker, A and Decorosi, F and Döhlemann, J and Fagorzi, C and Finan, TM and Fondi, M and Luchinat, C and Turano, P and Vignolini, T and Viti, C and Mengoni, A}, title = {Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.8b00158}, pmid = {30223644}, issn = {2161-5063}, abstract = {Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.}, }
@article {pmid30212910, year = {2018}, author = {Le, KK and Whiteside, MD and Hopkins, JE and Gannon, VPJ and Laing, CR}, title = {Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses.}, journal = {Database : the journal of biological databases and curation}, volume = {2018}, number = {}, pages = {1-10}, doi = {10.1093/database/bay086}, pmid = {30212910}, issn = {1758-0463}, abstract = {Public health laboratories are currently moving to whole-genome sequence (WGS)-based analyses, and require the rapid prediction of standard reference laboratory methods based solely on genomic data. Currently, these predictive genomics tasks rely on workflows that chain together multiple programs for the requisite analyses. While useful, these systems do not store the analyses in a genome-centric way, meaning the same analyses are often re-computed for the same genomes. To solve this problem, we created Spfy, a platform that rapidly performs the common reference laboratory tests, uses a graph database to store and retrieve the results from the computational workflows and links data to individual genomes using standardized ontologies. The Spfy platform facilitates rapid phenotype identification, as well as the efficient storage and downstream comparative analysis of tens of thousands of genome sequences. Though generally applicable to bacterial genome sequences, Spfy currently contains 10 243 Escherichia coli genomes, for which in-silico serotype and Shiga-toxin subtype, as well as the presence of known virulence factors and antimicrobial resistance determinants have been computed. Additionally, the presence/absence of the entire E. coli pan-genome was computed and linked to each genome. Owing to its database of diverse pre-computed results, and the ability to easily incorporate user data, Spfy facilitates hypothesis testing in fields ranging from population genomics to epidemiology, while mitigating the re-computation of analyses. The graph approach of Spfy is flexible, and can accommodate new analysis software modules as they are developed, easily linking new results to those already stored. Spfy provides a database and analyses approach for E. coli that is able to match the rapid accumulation of WGS data in public databases.}, }
@article {pmid30204489, year = {2018}, author = {Kavya, VNS and Tayal, K and Srinivasan, R and Sivadasan, N}, title = {Sequence Alignment on Directed Graphs.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cmb.2017.0264}, pmid = {30204489}, issn = {1557-8666}, abstract = {Genomic variations in a reference collection are naturally represented as genome variation graphs. Such graphs encode common subsequences as vertices and the variations are captured using additional vertices and directed edges. The resulting graphs are directed graphs possibly with cycles. Existing algorithms for aligning sequences on such graphs make use of partial order alignment (POA) techniques that work on directed acyclic graphs (DAGs). To achieve this, acyclic extensions of the input graphs are first constructed through expensive loop unrolling steps (DAGification). Furthermore, such graph extensions could have considerable blowup in their size and in the worst case the blow-up factor is proportional to the input sequence length. We provide a novel alignment algorithm V-ALIGN that aligns the input sequence directly on the input graph while avoiding such expensive DAGification steps. V-ALIGN is based on a novel dynamic programming (DP) formulation that allows gapped alignment directly on the input graph. It supports affine and linear gaps. We also propose refinements to V-ALIGN for better performance in practice. With the proposed refinements, the time to fill the DP table has linear dependence on the sizes of the sequence, the graph, and its feedback vertex set. We conducted experiments to compare the proposed algorithm against the existing POA-based techniques. We also performed alignment experiments on the genome variation graphs constructed from the 1000 Genomes data. For aligning short sequences, standard approaches restrict the expensive gapped alignment to small filtered subgraphs having high similarity to the input sequence. In such cases, the performance of V-ALIGN for gapped alignment on the filtered subgraph depends on the subgraph sizes.}, }
@article {pmid30186253, year = {2018}, author = {Chen, X and Zhang, Y and Zhang, Z and Zhao, Y and Sun, C and Yang, M and Wang, J and Liu, Q and Zhang, B and Chen, M and Yu, J and Wu, J and Jin, Z and Xiao, J}, title = {PGAweb: A Web Server for Bacterial Pan-Genome Analysis.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1910}, doi = {10.3389/fmicb.2018.01910}, pmid = {30186253}, issn = {1664-302X}, abstract = {An astronomical increase in microbial genome data in recent years has led to strong demand for bioinformatic tools for pan-genome analysis within and across species. Here, we present PGAweb, a user-friendly, web-based tool for bacterial pan-genome analysis, which is composed of two main pan-genome analysis modules, PGAP and PGAP-X. PGAweb provides key interactive and customizable functions that include orthologous clustering, pan-genome profiling, sequence variation and evolution analysis, and functional classification. PGAweb presents features of genomic structural dynamics and sequence diversity with different visualization methods that are helpful for intuitively understanding the dynamics and evolution of bacterial genomes. PGAweb has an intuitive interface with one-click setting of parameters and is freely available at http://PGAweb.vlcc.cn/.}, }
@article {pmid30184068, year = {2018}, author = {Syme, RA and Tan, KC and Rybak, K and Friesen, TL and McDonald, BA and Oliver, RP and Hane, JK}, title = {Pan-Parastagonospora Comparative Genome Analysis-Effector Prediction and Genome Evolution.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2443-2457}, doi = {10.1093/gbe/evy192}, pmid = {30184068}, issn = {1759-6653}, abstract = {We report a fungal pan-genome study involving Parastagonospora spp., including 21 isolates of the wheat (Triticum aestivum) pathogen Parastagonospora nodorum, 10 of the grass-infecting Parastagonospora avenae, and 2 of a closely related undefined sister species. We observed substantial variation in the distribution of polymorphisms across the pan-genome, including repeat-induced point mutations, diversifying selection and gene gains and losses. We also discovered chromosome-scale inter and intraspecific presence/absence variation of some sequences, suggesting the occurrence of one or more accessory chromosomes or regions that may play a role in host-pathogen interactions. The presence of known pathogenicity effector loci SnToxA, SnTox1, and SnTox3 varied substantially among isolates. Three P. nodorum isolates lacked functional versions for all three loci, whereas three P. avenae isolates carried one or both of the SnTox1 and SnTox3 genes, indicating previously unrecognized potential for discovering additional effectors in the P. nodorum-wheat pathosystem. We utilized the pan-genomic comparative analysis to improve the prediction of pathogenicity effector candidates, recovering the three confirmed effectors among our top-ranked candidates. We propose applying this pan-genomic approach to identify the effector repertoire involved in other host-microbe interactions involving necrotrophic pathogens in the Pezizomycotina.}, }
@article {pmid30177918, year = {2018}, author = {Yang, T and Zhong, J and Zhang, J and Li, C and Yu, X and Xiao, J and Jia, X and Ding, N and Ma, G and Wang, G and Yue, L and Liang, Q and Sheng, Y and Sun, Y and Huang, H and Chen, F}, title = {Pan-Genomic Study of Mycobacterium tuberculosis Reflecting the Primary/Secondary Genes, Generality/Individuality, and the Interconversion Through Copy Number Variations.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1886}, doi = {10.3389/fmicb.2018.01886}, pmid = {30177918}, issn = {1664-302X}, abstract = {Tuberculosis (TB) has surpassed HIV as the leading infectious disease killer worldwide since 2014. The main pathogen, Mycobacterium tuberculosis (Mtb), contains ~4,000 genes that account for ~90% of the genome. However, it is still unclear which of these genes are primary/secondary, which are responsible for generality/individuality, and which interconvert during evolution. Here we utilized a pan-genomic analysis of 36 Mtb genomes to address these questions. We identified 3,679 Mtb core (i.e., primary) genes, determining their phenotypic generality (e.g., virulence, slow growth, dormancy). We also observed 1,122 dispensable and 964 strain-specific secondary genes, reflecting partially shared and lineage-/strain-specific individualities. Among which, five L2 lineage-specific genes might be related to the increased virulence of the L2 lineage. Notably, we discovered 28 Mtb &quot;Super Core Genes&quot; (SCGs: more than a copy in at least 90% strains), which might be of increased importance, and reflected the &quot;super phenotype generality.&quot; Most SCGs encode PE/PPE, virulence factors, antigens, and transposases, and have been verified as playing crucial roles in Mtb pathogenicity. Further investigation of the 28 SCGs demonstrated the interconversion among SCGs, single-copy core, dispensable, and strain-specific genes through copy number variations (CNVs) during evolution; different mutations on different copies highlight the delicate adaptive-evolution regulation amongst Mtb lineages. This reflects that the importance of genes varied through CNVs, which might be driven by selective pressure from environment/host-adaptation. In addition, compared with Mycobacterium bovis (Mbo), Mtb possesses 48 specific single core genes that partially reflect the differences between Mtb and Mbo individuality.}, }
@article {pmid30175026, year = {2018}, author = {Asaf, S and Khan, AL and Khan, MA and Al-Harrasi, A and Lee, IJ}, title = {Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth.}, journal = {3 Biotech}, volume = {8}, number = {9}, pages = {389}, doi = {10.1007/s13205-018-1403-z}, pmid = {30175026}, issn = {2190-572X}, abstract = {Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.}, }
@article {pmid30166979, year = {2018}, author = {Kiu, R and Hall, LJ}, title = {Response: Commentary: Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1857}, doi = {10.3389/fmicb.2018.01857}, pmid = {30166979}, issn = {1664-302X}, support = {//Wellcome Trust/United Kingdom ; }, }
@article {pmid30165579, year = {2018}, author = {Inman, JM and Sutton, GG and Beck, E and Brinkac, LM and Clarke, TH and Fouts, DE}, title = {Large-Scale Comparative Analysis of Microbial Pan-genomes using PanOCT.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty744}, pmid = {30165579}, issn = {1367-4811}, support = {U19 AI110819/AI/NIAID NIH HHS/United States ; }, abstract = {Summary: The JCVI Pan-Genome Pipeline is a collection of programs to run PanOCT and tools that support and extend the capabilities of PanOCT. PanOCT (Pan-genome Ortholog Clustering Tool) is a tool for pan-genome analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invoke third-party tools such as NCBI Blast+, run PanOCT, generate a consensus pan-genome, annotate features of the pan-genome, detect sets of genes of interest such as antimicrobial resistance (AMR) genes, and generate figures, tables, and html pages to visualize the results. The pipeline can run in a hierarchical mode, lowering the RAM and compute resources used.<br><br>Availability: Source code, demo data, and detailed documentation are freely available at https://github.com/JCVenterInstitute/PanGenomePipeline.}, }
@article {pmid30154769, year = {2018}, author = {Mehdizadeh Gohari, I and Prescott, JF}, title = {Commentary: Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1856}, doi = {10.3389/fmicb.2018.01856}, pmid = {30154769}, issn = {1664-302X}, }
@article {pmid30129229, year = {2018}, author = {Ou, L and Li, D and Lv, J and Chen, W and Zhang, Z and Li, X and Yang, B and Zhou, S and Yang, S and Li, W and Gao, H and Zeng, Q and Yu, H and Ouyang, B and Li, F and Liu, F and Zheng, J and Liu, Y and Wang, J and Wang, B and Dai, X and Ma, Y and Zou, X}, title = {Pan-genome of cultivated pepper (Capsicum) and its use in gene presence-absence variation analyses.}, journal = {The New phytologist}, volume = {220}, number = {2}, pages = {360-363}, doi = {10.1111/nph.15413}, pmid = {30129229}, issn = {1469-8137}, support = {2016YFD0101704//National Key R&amp;D Program of China/ ; }, }
@article {pmid30126366, year = {2018}, author = {Argemi, X and Matelska, D and Ginalski, K and Riegel, P and Hansmann, Y and Bloom, J and Pestel-Caron, M and Dahyot, S and Lebeurre, J and Prévost, G}, title = {Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {621}, doi = {10.1186/s12864-018-4978-1}, pmid = {30126366}, issn = {1471-2164}, support = {2014/15/B/NZ1/03357//Polish National Science Centre/ ; }, abstract = {BACKGROUND: Coagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections, particularly in hospital settings. Unlike other staphylococci, it remains highly susceptible to antimicrobials, and genome-based phylogenetic studies have evidenced a highly conserved genome that distinguishes it from all other staphylococci.<br><br>RESULTS: We demonstrate that S. lugdunensis possesses a closed pan-genome with a very limited number of new genes, in contrast to other staphylococci that have an open pan-genome. Whole-genome nucleotide and amino acid identity levels are also higher than in other staphylococci. We identified numerous genetic barriers to horizontal gene transfer that might explain this result. The S. lugdunensis genome has multiple operons encoding for restriction-modification, CRISPR/Cas and toxin/antitoxin systems. We also identified a new PIN-like domain-associated protein that might belong to a larger operon, comprising a metalloprotease, that could function as a new toxin/antitoxin or detoxification system.<br><br>CONCLUSION: We show that S. lugdunensis has a unique genome profile within staphylococci, with a closed pan-genome and several systems to prevent horizontal gene transfer. Its virulence in clinical settings does not rely on its ability to acquire and exchange antibiotic resistance genes or other virulence factors as shown for other staphylococci.}, }
@article {pmid30116789, year = {2018}, author = {Pena-Gonzalez, A and Rodriguez-R, LM and Marston, CK and Gee, JE and Gulvik, CA and Kolton, CB and Saile, E and Frace, M and Hoffmaster, AR and Konstantinidis, KT}, title = {Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains.}, journal = {mSystems}, volume = {3}, number = {4}, pages = {}, doi = {10.1128/mSystems.00065-18}, pmid = {30116789}, issn = {2379-5077}, abstract = {Bacillus anthracis plasmids pXO1 and pXO2 carry the main virulence factors responsible for anthrax. However, the extent of copy number variation within the species and how the plasmids are related to pXO1/pXO2-like plasmids in other species of the Bacillus cereus sensu lato group remain unclear. To gain new insights into these issues, we sequenced 412 B. anthracis strains representing the total phylogenetic and ecological diversity of the species. Our results revealed that B. anthracis genomes carried, on average, 3.86 and 2.29 copies of pXO1 and pXO2, respectively, and also revealed a positive linear correlation between the copy numbers of pXO1 and pXO2. No correlation between the plasmid copy number and the phylogenetic relatedness of the strains was observed. However, genomes of strains isolated from animal tissues generally maintained a higher plasmid copy number than genomes of strains from environmental sources (P < 0.05 [Welch two-sample t test]). Comparisons against B. cereus genomes carrying complete or partial pXO1-like and pXO2-like plasmids showed that the plasmid-based phylogeny recapitulated that of the main chromosome, indicating limited plasmid horizontal transfer between or within these species. Comparisons of gene content revealed a closed pXO1 and pXO2 pangenome; e.g., plasmids encode <8 unique genes, on average, and a single large fragment deletion of pXO1 in one B. anthracis strain (2000031682) was detected. Collectively, our results provide a more complete view of the genomic diversity of B. anthracis plasmids, their copy number variation, and the virulence potential of other Bacillus species carrying pXO1/pXO2-like plasmids. IMPORTANCE Bacillus anthracis microorganisms are of historical and epidemiological importance and are among the most homogenous bacterial groups known, even though the B. anthracis genome is rich in mobile elements. Mobile elements can trigger the diversification of lineages; therefore, characterizing the extent of genomic variation in a large collection of strains is critical for a complete understanding of the diversity and evolution of the species. Here, we sequenced a large collection of B. anthracis strains (>400) that were recovered from human, animal, and environmental sources around the world. Our results confirmed the remarkable stability of gene content and synteny of the anthrax plasmids and revealed no signal of plasmid exchange between B. anthracis and pathogenic B. cereus isolates but rather predominantly vertical descent. These findings advance our understanding of the biology and pathogenomic evolution of B. anthracis and its plasmids.}, }
@article {pmid30115097, year = {2018}, author = {Thind, AK and Wicker, T and Müller, T and Ackermann, PM and Steuernagel, B and Wulff, BBH and Spannagl, M and Twardziok, SO and Felder, M and Lux, T and Mayer, KFX and ,  and Keller, B and Krattinger, SG}, title = {Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {104}, doi = {10.1186/s13059-018-1477-2}, pmid = {30115097}, issn = {1474-760X}, abstract = {BACKGROUND: Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the dynamics of wheat genomes on a megabase scale.<br><br>RESULTS: Here, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes-the old landrace Chinese Spring and the elite Swiss spring wheat line 'CH Campala Lr22a'. Both chromosomes were assembled into megabase-sized scaffolds. There is a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations reveals four large indels of more than 100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the molecular mechanisms that caused these indels. Three of the large indels affect copy number of NLRs, a gene family involved in plant immunity. Analysis of SNP density reveals four haploblocks of 4, 8, 9 and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Gene content across the two chromosomes was highly conserved. Ninety-nine percent of the genic sequences were present in both genotypes and the fraction of unique genes ranged from 0.4 to 0.7%.<br><br>CONCLUSIONS: This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.}, }
@article {pmid30106690, year = {2018}, author = {Cleary, A and Ramaraj, T and Kahanda, I and Mudge, J and Mumey, B}, title = {Exploring Frequented Regions in Pan-Genomic Graphs.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1109/TCBB.2018.2864564}, pmid = {30106690}, issn = {1557-9964}, abstract = {We consider the problem of identifying regions within a pan-genome De Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In this work, we formalize the FR problem and describe an efficient algorithm for finding FRs. Subsequently, we propose some applications of FRs based on machine-learning and pan-genome graph simplification. We demonstrate the effectiveness of these applications using data sets for the organisms Staphylococcus aureus (bacterium) and Saccharomyces cerevisiae (yeast). We corroborate the biological relevance of FRs such as identifying introgressions in yeast that aid in alcohol tolerance, and show that FRs are useful for classification of yeast strains by industrial use and visualizing pan-genomic space.}, }
@article {pmid30104693, year = {2018}, author = {Das, S and Pettersson, BMF and Behra, PRK and Mallick, A and Cheramie, M and Ramesh, M and Shirreff, L and DuCote, T and Dasgupta, S and Ennis, DG and Kirsebom, LA}, title = {Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12040}, doi = {10.1038/s41598-018-30152-y}, pmid = {30104693}, issn = {2045-2322}, support = {RD01-A-38//Louisiana Board of Regents (Board of Regents)/ ; 222-2012-492//Svenska Forskningsr&amp;#x00E5;det Formas (Swedish Research Council Formas)/ ; }, abstract = {Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the &quot;M&quot;- and the &quot;Aronson&quot;-type. We suggest that these two clusters should be considered to represent two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to the ability of M. marinum to occupy different ecological niches.}, }
@article {pmid30074293, year = {2018}, author = {Pluta, R and Espinosa, M}, title = {Antisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs.}, journal = {Wiley interdisciplinary reviews. RNA}, volume = {9}, number = {6}, pages = {e1500}, doi = {10.1002/wrna.1500}, pmid = {30074293}, issn = {1757-7012}, abstract = {Bacterial plasmids constitute a wealth of shared DNA amounting to about 20% of the total prokaryotic pangenome. Plasmids replicate autonomously and control their replication by maintaining a fairly constant number of copies within a given host. Plasmids should acquire a good fitness to their hosts so that they do not constitute a genetic load. Here we review some basic concepts in plasmid biology, pertaining to the control of replication and distribution of plasmid copies among daughter cells. A particular class of plasmids is constituted by those that replicate by the rolling circle mode (rolling circle-replicating [RCR]-plasmids). They are small double-stranded DNA molecules, with a rather high number of copies in the original host. RCR-plasmids control their replication by means of a small short-lived antisense RNA, alone or in combination with a plasmid-encoded transcriptional repressor protein. Two plasmid prototypes have been studied in depth, namely the staphylococcal plasmid pT181 and the streptococcal plasmid pMV158, each corresponding to the two types of replication control circuits, respectively. We further discuss possible applications of the plasmid-encoded antisense RNAs and address some future directions that, in our opinion, should be pursued in the study of these small molecules. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.}, }
@article {pmid30072959, year = {2018}, author = {González-Torres, P and Gabaldón, T}, title = {Genome Variation in the Model Halophilic Bacterium Salinibacter ruber.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1499}, doi = {10.3389/fmicb.2018.01499}, pmid = {30072959}, issn = {1664-302X}, abstract = {The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, current insights on the genomic diversity of this species is limited to the comparison of the genomes of two co-isolated strains. Here, we present a comparative genomic analysis of eight S. ruber strains isolated at two different time points in each of two different Mediterranean solar salterns. Our results show an open pangenome with contrasting evolutionary patterns in the core and accessory genomes. We found that the core genome is shaped by extensive homologous recombination (HR), which results in limited sequence variation within population clusters. In contrast, the accessory genome is modulated by horizontal gene transfer (HGT), with genomic islands and plasmids acting as gateways to the rest of the genome. In addition, both types of genetic exchange are modulated by restriction and modification (RM) or CRISPR-Cas systems. Finally, genes differentially impacted by such processes reveal functional processes potentially relevant for environmental interactions and adaptation to extremophilic conditions. Altogether, our results support scenarios that conciliate &quot;Neutral&quot; and &quot;Constant Diversity&quot; models of bacterial evolution.}, }
@article {pmid30061736, year = {2018}, author = {Springer, NM and Anderson, SN and Andorf, CM and Ahern, KR and Bai, F and Barad, O and Barbazuk, WB and Bass, HW and Baruch, K and Ben-Zvi, G and Buckler, ES and Bukowski, R and Campbell, MS and Cannon, EKS and Chomet, P and Dawe, RK and Davenport, R and Dooner, HK and Du, LH and Du, C and Easterling, KA and Gault, C and Guan, JC and Hunter, CT and Jander, G and Jiao, Y and Koch, KE and Kol, G and Köllner, TG and Kudo, T and Li, Q and Lu, F and Mayfield-Jones, D and Mei, W and McCarty, DR and Noshay, JM and Portwood, JL and Ronen, G and Settles, AM and Shem-Tov, D and Shi, J and Soifer, I and Stein, JC and Stitzer, MC and Suzuki, M and Vera, DL and Vollbrecht, E and Vrebalov, JT and Ware, D and Wei, S and Wimalanathan, K and Woodhouse, MR and Xiong, W and Brutnell, TP}, title = {The maize W22 genome provides a foundation for functional genomics and transposon biology.}, journal = {Nature genetics}, volume = {50}, number = {9}, pages = {1282-1288}, doi = {10.1038/s41588-018-0158-0}, pmid = {30061736}, issn = {1546-1718}, abstract = {The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.}, }
@article {pmid30055586, year = {2018}, author = {Wolf, IR and Paschoal, AR and Quiroga, C and Domingues, DS and de Souza, RF and Pretto-Giordano, LG and Vilas-Boas, LA}, title = {Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {556}, doi = {10.1186/s12864-018-4951-z}, pmid = {30055586}, issn = {1471-2164}, abstract = {BACKGROUND: Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae.<br><br>RESULTS: Comparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types.<br><br>CONCLUSIONS: The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen.}, }
@article {pmid30050512, year = {2018}, author = {Luo, Y and Cheng, Y and Yi, J and Zhang, Z and Luo, Q and Zhang, D and Li, Y}, title = {Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1520}, doi = {10.3389/fmicb.2018.01520}, pmid = {30050512}, issn = {1664-302X}, abstract = {Paenibacillus polymyxa (formerly known as Bacillus polymyxa) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the P. polymyxa strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on P. polymyxa for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different P. polymyxa strains. The complete genome size of HY96-2 was found to be 5.75 Mb and 5207 coding sequences were predicted. HY96-2 was compared with seven other P. polymyxa strains for which complete genome sequences have been published, using phylogenetic tree, pan-genome, and nucleic acid co-linearity analysis. In addition, the genes and gene clusters involved in biofilm formation, antibiotic synthesis, and systemic resistance inducer production were compared between strain HY96-2 and two other strains, namely, SC2 and E681. The results revealed that all three of the P. polymyxa strains have the ability to control plant diseases via the mechanisms of colonization (biofilm formation), antagonism (antibiotic production), and induced resistance (systemic resistance inducer production). However, the variation of the corresponding genes or gene clusters between the three strains may lead to different antimicrobial spectra and biocontrol efficacies. Two possible pathways of biofilm formation in P. polymyxa were reported for the first time after searching the KEGG database. This study provides a scientific basis for the further optimization of the field applications and quality standards of industrial microbial biopesticides based on HY96-2. It may also serve as a reference for studying the differences in antimicrobial spectra and biocontrol capability between different biocontrol agents.}, }
@article {pmid30042742, year = {2018}, author = {Aherfi, S and Andreani, J and Baptiste, E and Oumessoum, A and Dornas, FP and Andrade, ACDSP and Chabriere, E and Abrahao, J and Levasseur, A and Raoult, D and La Scola, B and Colson, P}, title = {A Large Open Pangenome and a Small Core Genome for Giant Pandoraviruses.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1486}, doi = {10.3389/fmicb.2018.01486}, pmid = {30042742}, issn = {1664-302X}, abstract = {Giant viruses of amoebae are distinct from classical viruses by the giant size of their virions and genomes. Pandoraviruses are the record holders in size of genomes and number of predicted genes. Three strains, P. salinus, P. dulcis, and P. inopinatum, have been described to date. We isolated three new ones, namely P. massiliensis, P. braziliensis, and P. pampulha, from environmental samples collected in Brazil. We describe here their genomes, the transcriptome and proteome of P. massiliensis, and the pangenome of the group encompassing the six pandoravirus isolates. Genome sequencing was performed with an Illumina MiSeq instrument. Genome annotation was performed using GeneMarkS and Prodigal softwares and comparative genomic analyses. The core genome and pangenome were determined using notably ProteinOrtho and CD-HIT programs. Transcriptomics was performed for P. massiliensis with the Illumina MiSeq instrument; proteomics was also performed for this virus using 1D/2D gel electrophoresis and mass spectrometry on a Synapt G2Si Q-TOF traveling wave mobility spectrometer. The genomes of the three new pandoraviruses are comprised between 1.6 and 1.8 Mbp. The genomes of P. massiliensis, P. pampulha, and P. braziliensis were predicted to harbor 1,414, 2,368, and 2,696 genes, respectively. These genes comprise up to 67% of ORFans. Phylogenomic analyses showed that P. massiliensis and P. braziliensis were more closely related to each other than to the other pandoraviruses. The core genome of pandoraviruses comprises 352 clusters of genes, and the ratio core genome/pangenome is less than 0.05. The extinction curve shows clearly that the pangenome is still open. A quarter of the gene content of P. massiliensis was detected by transcriptomics. In addition, a product for a total of 162 open reading frames were found by proteomic analysis of P. massiliensis virions, including notably the products of 28 ORFans, 99 hypothetical proteins, and 90 core genes. Further analyses should allow to gain a better knowledge and understanding of the evolution and origin of these giant pandoraviruses, and of their relationships with viruses and cellular microorganisms.}, }
@article {pmid30035711, year = {2018}, author = {Fleshman, A and Mullins, K and Sahl, J and Hepp, C and Nieto, N and Wiggins, K and Hornstra, H and Kelly, D and Chan, TC and Phetsouvanh, R and Dittrich, S and Panyanivong, P and Paris, D and Newton, P and Richards, A and Pearson, T}, title = {Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity.}, journal = {Microbial genomics}, volume = {4}, number = {9}, pages = {}, doi = {10.1099/mgen.0.000199}, pmid = {30035711}, issn = {2057-5858}, abstract = {Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.}, }
@article {pmid30033331, year = {2018}, author = {Zhou, Z and Lundstrøm, I and Tran-Dien, A and Duchêne, S and Alikhan, NF and Sergeant, MJ and Langridge, G and Fotakis, AK and Nair, S and Stenøien, HK and Hamre, SS and Casjens, S and Christophersen, A and Quince, C and Thomson, NR and Weill, FX and Ho, SYW and Gilbert, MTP and Achtman, M}, title = {Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.}, journal = {Current biology : CB}, volume = {28}, number = {15}, pages = {2420-2428.e10}, doi = {10.1016/j.cub.2018.05.058}, pmid = {30033331}, issn = {1879-0445}, support = {//Wellcome Trust/United Kingdom ; MR/M50161X/1//Medical Research Council/United Kingdom ; }, abstract = {Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20th-century observations in Eastern Europe [3, 4] suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here, we describe a draft Paratyphi C genome (Ragna) recovered from the 800-year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C lineage, which also includes serovars Choleraesuis, Typhisuis, and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar [5] (and occasionally humans), and Typhisuis causes epidemic swine salmonellosis (chronic paratyphoid) in domestic pigs [2, 3]. These different host specificities likely evolved in Europe over the last ∼4,000 years since the time of their most recent common ancestor (tMRCA) and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe [6].}, }
@article {pmid30026808, year = {2018}, author = {Zhong, C and Han, M and Yu, S and Yang, P and Li, H and Ning, K}, title = {Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway.}, journal = {Biotechnology for biofuels}, volume = {11}, number = {}, pages = {193}, doi = {10.1186/s13068-018-1201-1}, pmid = {30026808}, issn = {1754-6834}, support = {R34 AA021502/AA/NIAAA NIH HHS/United States ; }, abstract = {Background: Shewanella strains are important dissimilatory metal-reducing bacteria which are widely distributed in diverse habitats. Despite efforts to genomically characterize Shewanella, knowledge of the molecular components, functional information and evolutionary patterns remain lacking, especially for their compatibility in the metal-reducing pathway. The increasing number of genome sequences of Shewanella strains offers a basis for pan-genome studies.<br><br>Results: A comparative pan-genome analysis was conducted to study genomic diversity and evolutionary relationships among 24 Shewanella strains. Results revealed an open pan-genome of 13,406 non-redundant genes and a core-genome of 1878 non-redundant genes. Selective pressure acted on the invariant members of core genome, in which purifying selection drove evolution in the housekeeping mechanisms. Shewanella strains exhibited extensive genome variability, with high levels of gene gain and loss during the evolution, which affected variable gene sets and facilitated the rapid evolution. Additionally, genes related to metal reduction were diversely distributed in Shewanella strains and evolved under purifying selection, which highlighted the basic conserved functionality and specificity of respiratory systems.<br><br>Conclusions: The diversity of genes present in the accessory and specific genomes of Shewanella strains indicates that each strain uses different strategies to adapt to diverse environments. Horizontal gene transfer is an important evolutionary force in shaping Shewanella genomes. Purifying selection plays an important role in the stability of the core-genome and also drives evolution in mtr-omc cluster of different Shewanella strains.}, }
@article {pmid30013519, year = {2018}, author = {Collins, FWJ and Mesa-Pereira, B and O'Connor, PM and Rea, MC and Hill, C and Ross, RP}, title = {Reincarnation of Bacteriocins From the Lactobacillus Pangenomic Graveyard.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1298}, doi = {10.3389/fmicb.2018.01298}, pmid = {30013519}, issn = {1664-302X}, abstract = {Bacteria commonly produce narrow spectrum bacteriocins as a means of inhibiting closely related species competing for similar resources in an environment. The increasing availability of genomic data means that it is becoming easier to identify bacteriocins encoded within genomes. Often, however, the presence of bacteriocin genes in a strain does not always translate into biological antimicrobial activity. For example, when analysing the Lactobacillus pangenome we identified strains encoding ten pediocin-like bacteriocin structural genes which failed to display inhibitory activity. Nine of these bacteriocins were novel whilst one was identified as the previously characterized bacteriocin &quot;penocin A.&quot; The composition of these bacteriocin operons varied between strains, often with key components missing which are required for bacteriocin production, such as dedicated bacteriocin transporters and accessory proteins. In an effort to functionally express these bacteriocins, the structural genes for the ten pediocin homologs were cloned alongside the dedicated pediocin PA-1 transporter in both Escherichia coli and Lactobacillus paracasei heterologous hosts. Each bacteriocin was cloned with its native leader sequence and as a fusion protein with the pediocin PA-1 leader sequence. Several of these bacteriocins displayed a broader spectrum of inhibition than the original pediocin PA-1. We show how potentially valuable bacteriocins can easily be &quot;reincarnated&quot; from in silico data and produced in vitro despite often lacking the necessary accompanying machinery. Moreover, the study demonstrates how genomic datasets such as the Lactobacilus pangenome harbor a potential &quot;arsenal&quot; of antimicrobial activity with the possibility of being activated when expressed in more genetically amenable hosts.}, }
@article {pmid30011247, year = {2018}, author = {Holley, G and Wittler, R and Stoye, J and Hach, F}, title = {Dynamic Alignment-Free and Reference-Free Read Compression.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {25}, number = {7}, pages = {825-836}, doi = {10.1089/cmb.2018.0068}, pmid = {30011247}, issn = {1557-8666}, abstract = {The advent of high throughput sequencing (HTS) technologies raises a major concern about storage and transmission of data produced by these technologies. In particular, large-scale sequencing projects generate an unprecedented volume of genomic sequences ranging from tens to several thousands of genomes per species. These collections contain highly similar and redundant sequences, also known as pangenomes. The ideal way to represent and transfer pangenomes is through compression. A number of HTS-specific compression tools have been developed to reduce the storage and communication costs of HTS data, yet none of them is designed to process a pangenome. In this article, we present dynamic alignment-free and reference-free read compression (DARRC), a new alignment-free and reference-free compression method. It addresses the problem of pangenome compression by encoding the sequences of a pangenome as a guided de Bruijn graph. The novelty of this method is its ability to incrementally update DARRC archives with new genome sequences without full decompression of the archive. DARRC can compress both single-end and paired-end read sequences of any length using all symbols of the IUPAC nucleotide code. On a large Pseudomonas aeruginosa data set, our method outperforms all other tested tools. It provides a 30% compression ratio improvement in single-end mode compared with the best performing state-of-the-art HTS-specific compression method in our experiments.}, }
@article {pmid30005805, year = {2018}, author = {Driscoll, CB and Meyer, KA and Šulčius, S and Brown, NM and Dick, GJ and Cao, H and Gasiūnas, G and Timinskas, A and Yin, Y and Landry, ZC and Otten, TG and Davis, TW and Watson, SB and Dreher, TW}, title = {A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales.}, journal = {Harmful algae}, volume = {77}, number = {}, pages = {93-107}, doi = {10.1016/j.hal.2018.05.009}, pmid = {30005805}, issn = {1878-1470}, abstract = {In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N2-fixing heterocysts, and the uptake and incorporation of the major nutrients P, N and S, we identified several gene pathways in the pangenome that may contribute to niche partitioning. Genes for problematic secondary metabolites-cyanotoxins and taste-and-odor compounds-were sporadically present, as were other polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. By contrast, genes predicted to encode the ribosomally generated bacteriocin peptides were found in all genomes.}, }
@article {pmid29994032, year = {2018}, author = {Rizzi, R and Cairo, M and Makinen, V and Tomescu, AI and Valenzuela, D}, title = {Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1109/TCBB.2018.2831691}, pmid = {29994032}, issn = {1557-9964}, abstract = {Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence analysis. In this paper, we show that the computational complexity will change for natural extensions of alignments to pan-genome representations and to diploid genomes. More broadly, our approach can also be seen as a minimal extension of sequence alignment to labelled directed acyclic graphs (labeled DAGs). Namely, we show that finding a covering alignment of two labeled DAGs is NP-hard even on binary alphabets. A covering alignment asks for two paths (red) and (green) in DAG and two paths (red) and (green) in DAG that cover the nodes of the graphs and maximize the sum of the global alignment scores: , where is the concatenation of labels on the path P. Pair-wise alignment of haplotype sequences forming a diploid chromosome can be converted to a two-path coverable labelled DAG, and then the covering alignment models the similarity of two diploids over arbitrary recombinations. Reduction to the other direction shows that problem NP-hard on alphabets of size 3.}, }
@article {pmid29978435, year = {2018}, author = {Tetz, G and Tetz, V}, title = {Tetz's theory and law of longevity.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12064-018-0267-4}, pmid = {29978435}, issn = {1611-7530}, abstract = {Here, we present new theory and law of longevity intended to evaluate fundamental factors that control lifespan. This theory is based on the fact that genes affecting host organism longevity are represented by subpopulations: genes of host eukaryotic cells, commensal microbiota, and non-living genetic elements. Based on Tetz's theory of longevity, we propose that lifespan and aging are defined by the accumulation of alterations over all genes of macroorganism and microbiome and the non-living genetic elements associated with them. Tetz's law of longevity states that longevity is limited by the accumulation of alterations to the limiting value that is not compatible with life. Based on theory and law, we also propose a novel model to calculate several parameters, including the rate of aging and the remaining lifespan of individuals. We suggest that this theory and model have explanatory and predictive potential to eukaryotic organisms, allowing the influence of diseases, medication, and medical procedures to be re-examined in relation to longevity. Such estimates also provide a framework to evaluate new fundamental aspects that control aging and lifespan.}, }
@article {pmid29975997, year = {2018}, author = {Choi, S and Jin, GD and Park, J and You, I and Kim, EB}, title = {Pan-Genomics of Lactobacillus plantarum Revealed Group-Specific Genomic Profiles without Habitat Association.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {8}, pages = {1352-1359}, doi = {10.4014/jmb.1803.03029}, pmid = {29975997}, issn = {1738-8872}, abstract = {Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (L-arabinose, L-rhamnose, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restriction-modification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.}, }
@article {pmid29961804, year = {2018}, author = {Lemos Junior, WJF and da Silva Duarte, V and Treu, L and Campanaro, S and Nadai, C and Giacomini, A and Corich, V}, title = {Whole genome comparison of two Starmerella bacillaris strains with other wine yeasts uncovers genes involved in modulating important winemaking traits.}, journal = {FEMS yeast research}, volume = {18}, number = {7}, pages = {}, doi = {10.1093/femsyr/foy069}, pmid = {29961804}, issn = {1567-1364}, abstract = {Starmerella bacillaris is an osmotolerant yeast with interesting winemaking traits such as low-ethanol and high-glycerol production, previously considered as wine spoilage and recently proposed to improve the sensory quality of wine. This is the first work performing a whole-genome analysis of the variants identified by comparing two S. bacillaris strains (PAS13 and FRI751). Additionally, an extensive search for orthologous genes against Saccharomyces and non-Saccharomyces yeasts produced a detailed reconstruction of the pan-genome for yeast species used in winemaking. Starmerella bacillaris PAS13 was able to produce 36% more glycerol than S. bacillaris FRI751 without increasing ethanol level over 5% (v/v). Orthologous genes revealed new insights in the response to osmotic stress determined by the mitogen-activated protein kinase (MAPK) from S. bacillaris strains. The comparison between the two S. bacillaris genomes revealed 33 771 high-quality variants that were ranked considering their predicted impact on gene functions. Furthermore, analysis of structural variations in the genome revealed five translocations. The absence of some transcriptional factors involved in the regulation of GPD (glycerol-3-phosphate dehydrogenase), like the protein kinases YpK1p and YpK2p, and the identification of a tandem duplication increasing the GPP1 (glycerol-3-phosphate phosphatase) gene copy number suggest a remarkably different regulation of the glycerol pathway for S. bacillaris in comparison to S. cerevisiae.}, }
@article {pmid29949970, year = {2018}, author = {Her, HL and Wu, YW}, title = {A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {13}, pages = {i89-i95}, doi = {10.1093/bioinformatics/bty276}, pmid = {29949970}, issn = {1367-4811}, abstract = {Motivation: Antimicrobial resistance (AMR) is becoming a huge problem in both developed and developing countries, and identifying strains resistant or susceptible to certain antibiotics is essential in fighting against antibiotic-resistant pathogens. Whole-genome sequences have been collected for different microbial strains in order to identify crucial characteristics that allow certain strains to become resistant to antibiotics; however, a global inspection of the gene content responsible for AMR activities remains to be done.<br><br>Results: We propose a pan-genome-based approach to characterize antibiotic-resistant microbial strains and test this approach on the bacterial model organism Escherichia coli. By identifying core and accessory gene clusters and predicting AMR genes for the E. coli pan-genome, we not only showed that certain classes of genes are unevenly distributed between the core and accessory parts of the pan-genome but also demonstrated that only a portion of the identified AMR genes belong to the accessory genome. Application of machine learning algorithms to predict whether specific strains were resistant to antibiotic drugs yielded the best prediction accuracy for the set of AMR genes within the accessory part of the pan-genome, suggesting that these gene clusters were most crucial to AMR activities in E. coli. Selecting subsets of AMR genes for different antibiotic drugs based on a genetic algorithm (GA) achieved better prediction performances than the gene sets established in the literature, hinting that the gene sets selected by the GA may warrant further analysis in investigating more details about how E. coli fight against antibiotics.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid29946138, year = {2018}, author = {Gemmell, MR and Berry, S and Mukhopadhya, I and Hansen, R and Nielsen, HL and Bajaj-Elliott, M and Nielsen, H and Hold, GL}, title = {Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential.}, journal = {Emerging microbes &amp; infections}, volume = {7}, number = {1}, pages = {116}, doi = {10.1038/s41426-018-0118-x}, pmid = {29946138}, issn = {2222-1751}, abstract = {In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. Campylobacter concisus, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from C. concisus strains and undertook a comprehensive pangenome assessment to identify C. concisus virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new C. concisus strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn's disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the Campylobacter genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that C. concisus strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.}, }
@article {pmid29945570, year = {2018}, author = {Clarke, TH and Brinkac, LM and Inman, JM and Sutton, G and Fouts, DE}, title = {PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {246}, doi = {10.1186/s12859-018-2250-y}, pmid = {29945570}, issn = {1471-2105}, support = {U19 AI110819/AI/NIAID NIH HHS/United States ; U19AI110819//National Institute of Allergy and Infectious Diseases (US)/ ; }, abstract = {BACKGROUND: Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to locate and analyze these regions. Multiple software packages are available to visualize pan-genomes, but currently their ability to address these concerns are limited by using only pre-computed data sets, prioritizing core over variable gene clusters, or by not accounting for pan-chromosome positioning in the viewer.<br><br>RESULTS: We introduce PanACEA (Pan-genome Atlas with Chromosome Explorer and Analyzer), which utilizes locally-computed interactive web-pages to view ordered pan-genome data. It consists of multi-tiered, hierarchical display pages that extend from pan-chromosomes to both core and variable regions to single genes. Regions and genes are functionally annotated to allow for rapid searching and visual identification of regions of interest with the option that user-supplied genomic phylogenies and metadata can be incorporated. PanACEA's memory and time requirements are within the capacities of standard laptops. The capability of PanACEA as a research tool is demonstrated by highlighting a variable region important in differentiating strains of Enterobacter hormaechei.<br><br>CONCLUSIONS: PanACEA can rapidly translate the results of pan-chromosome programs into an intuitive and interactive visual representation. It will empower researchers to visually explore and identify regions of the pan-chromosome that are most biologically interesting, and to obtain publication quality images of these regions.}, }
@article {pmid29940840, year = {2018}, author = {Matey-Hernandez, ML and ,  and Brunak, S and Izarzugaza, JMG}, title = {Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {239}, doi = {10.1186/s12859-018-2239-6}, pmid = {29940840}, issn = {1471-2105}, support = {NNF14CC0001//Novo Nordisk Fonden (DK)/ ; NNF17OC0027594//Novo Nordisk Fonden (DK)/ ; 5184-00102B//Innovationsfonden (DK)/ ; }, abstract = {BACKGROUND: The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods.<br><br>RESULTS: We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles.<br><br>CONCLUSIONS: Although current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.}, }
@article {pmid29939210, year = {2018}, author = {Cislak, A and Grabowski, S and Holub, J}, title = {SOPanG: online text searching over a pan-genome.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty506}, pmid = {29939210}, issn = {1367-4811}, abstract = {Motivation: The many thousands of high-quality genomes available nowadays imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such a scenario is online search over a collection of similar texts, a problem with surprisingly few solutions presented so far.<br><br>Results: We present SOPanG, a simple tool for exact pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome. Thanks to bit-parallelism, it achieves pattern matching speeds above 400MB/s, more than an order of magnitude higher than of other software.<br><br>Availability: SOPanG is available for free from: https://github.com/MrAlexSee/sopang.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid29937764, year = {2018}, author = {Zhang, X and Liu, Z and Wei, G and Yang, F and Liu, X}, title = {In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1255}, doi = {10.3389/fmicb.2018.01255}, pmid = {29937764}, issn = {1664-302X}, abstract = {The coinage &quot;pan-genome&quot; was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species' basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species' core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H2ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H2ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.}, }
@article {pmid29925429, year = {2018}, author = {Tschitschko, B and Erdmann, S and DeMaere, MZ and Roux, S and Panwar, P and Allen, MA and Williams, TJ and Brazendale, S and Hancock, AM and Eloe-Fadrosh, EA and Cavicchioli, R}, title = {Genomic variation and biogeography of Antarctic haloarchaea.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {113}, doi = {10.1186/s40168-018-0495-3}, pmid = {29925429}, issn = {2049-2618}, support = {DP150100244//Australian Research Council/ ; 4031//Australian Antarctic Division/ ; DE-AC02-05CH11231//Office of Science/ ; }, abstract = {BACKGROUND: The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised.<br><br>RESULTS: The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica.<br><br>CONCLUSION: The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea.}, }
@article {pmid29915568, year = {2018}, author = {Yu, J and Zhao, J and Song, Y and Zhang, J and Yu, Z and Zhang, H and Sun, Z}, title = {Comparative Genomics of the Herbivore Gut Symbiont Lactobacillus reuteri Reveals Genetic Diversity and Lifestyle Adaptation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1151}, doi = {10.3389/fmicb.2018.01151}, pmid = {29915568}, issn = {1664-302X}, abstract = {Lactobacillus reuteri is a catalase-negative, Gram-positive, non-motile, obligately heterofermentative bacterial species that has been used as a model to describe the ecology and evolution of vertebrate gut symbionts. However, the genetic features and evolutionary strategies of L. reuteri from the gastrointestinal tract of herbivores remain unknown. Therefore, 16 L. reuteri strains isolated from goat, sheep, cow, and horse in Inner Mongolia, China were sequenced in this study. A comparative genomic approach was used to assess genetic diversity and gain insight into the distinguishing features related to the different hosts based on 21 published genomic sequences. Genome size, G + C content, and average nucleotide identity values of the L. reuteri strains from different hosts indicated that the strains have broad genetic diversity. The pan-genome of 37 L. reuteri strains contained 8,680 gene families, and the core genome contained 726 gene families. A total of 92,270 nucleotide mutation sites were discovered among 37 L. reuteri strains, and all core genes displayed a Ka/Ks ratio much lower than 1, suggesting strong purifying selective pressure (negative selection). A highly robust maximum likelihood tree based on the core genes shown in the herbivore isolates were divided into three clades; clades A and B contained most of the herbivore isolates and were more closely related to human isolates and vastly distinct from clade C. Some functional genes may be attributable to host-specific of the herbivore, omnivore, and sourdough groups. Moreover, the numbers of genes encoding cell surface proteins and active carbohydrate enzymes were host-specific. This study provides new insight into the adaptation of L. reuteri to the intestinal habitat of herbivores, suggesting that the genomic diversity of L. reuteri from different ecological origins is closely associated with their living environment.}, }
@article {pmid29915429, year = {2018}, author = {Sibbesen, JA and Maretty, L and ,  and Krogh, A}, title = {Accurate genotyping across variant classes and lengths using variant graphs.}, journal = {Nature genetics}, volume = {50}, number = {7}, pages = {1054-1059}, doi = {10.1038/s41588-018-0145-5}, pmid = {29915429}, issn = {1546-1718}, abstract = {Genotype estimates from short-read sequencing data are typically based on the alignment of reads to a linear reference, but reads originating from more complex variants (for example, structural variants) often align poorly, resulting in biased genotype estimates. This bias can be mitigated by first collecting a set of candidate variants across discovery methods, individuals and databases, and then realigning the reads to the variants and reference simultaneously. However, this realignment problem has proved computationally difficult. Here, we present a new method (BayesTyper) that uses exact alignment of read k-mers to a graph representation of the reference and variants to efficiently perform unbiased, probabilistic genotyping across the variation spectrum. We demonstrate that BayesTyper generally provides superior variant sensitivity and genotyping accuracy relative to existing methods when used to integrate variants across discovery approaches and individuals. Finally, we demonstrate that including a 'variation-prior' database containing already known variants significantly improves sensitivity.}, }
@article {pmid29915111, year = {2018}, author = {Kawasaki, M and Delamare-Deboutteville, J and Bowater, RO and Walker, MJ and Beatson, S and Ben Zakour, NL and Barnes, AC}, title = {Microevolution of Streptococcus agalactiae ST-261 from Australia Indicates Dissemination via Imported Tilapia and Ongoing Adaptation to Marine Hosts or Environment.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {16}, pages = {}, doi = {10.1128/AEM.00859-18}, pmid = {29915111}, issn = {1098-5336}, abstract = {Streptococcus agalactiae (group B Streptococcus [GBS]) causes disease in a wide range of animals. The serotype Ib lineage is highly adapted to aquatic hosts, exhibiting substantial genome reduction compared with terrestrial conspecifics. Here, we sequence genomes from 40 GBS isolates, including 25 isolates from wild fish and captive stingrays in Australia, six local veterinary or human clinical isolates, and nine isolates from farmed tilapia in Honduras, and compared them with 42 genomes from public databases. Phylogenetic analysis based on nonrecombinant core-genome single nucleotide polymorphisms (SNPs) indicated that aquatic serotype Ib isolates from Queensland were distantly related to local veterinary and human clinical isolates. In contrast, Australian aquatic isolates are most closely related to a tilapia isolate from Israel, differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on core-genome SNPs indicates the dissemination of sequence type 261 (ST-261) from an ancestral tilapia strain, which is congruent with several introductions of tilapia into Australia from Israel during the 1970s and 1980s. Pangenome analysis identified 1,440 genes as core, with the majority being dispensable or strain specific, with non-protein-coding intergenic regions (IGRs) divided among core and strain-specific genes. Aquatic serotype Ib strains have lost many virulence factors during adaptation, but six adhesins were well conserved across the aquatic isolates and might be critical for virulence in fish and for targets in vaccine development. The close relationship among recent ST-261 isolates from Ghana, the United States, and China with the Israeli tilapia isolate from 1988 implicates the global trade in tilapia seed for aquaculture in the widespread dissemination of serotype Ib fish-adapted GBS.IMPORTANCEStreptococcus agalactiae (GBS) is a significant pathogen of humans and animals. Some lineages have become adapted to particular hosts, and serotype Ib is highly specialized to fish. Here, we show that this lineage is likely to have been distributed widely by the global trade in tilapia for aquaculture, with probable introduction into Australia in the 1970s and subsequent dissemination in wild fish populations. We report here the variability in the polysaccharide capsule among this lineage but identify a cohort of common surface proteins that may be a focus of future vaccine development to reduce the biosecurity risk in international fish trade.}, }
@article {pmid29905870, year = {2018}, author = {Rodriguez-R, LM and Gunturu, S and Harvey, WT and Rosselló-Mora, R and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.}, journal = {Nucleic acids research}, volume = {46}, number = {W1}, pages = {W282-W288}, doi = {10.1093/nar/gky467}, pmid = {29905870}, issn = {1362-4962}, abstract = {The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.}, }
@article {pmid29895899, year = {2018}, author = {Mahfouz, N and Caucci, S and Achatz, E and Semmler, T and Guenther, S and Berendonk, TU and Schroeder, M}, title = {High genomic diversity of multi-drug resistant wastewater Escherichia coli.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8928}, doi = {10.1038/s41598-018-27292-6}, pmid = {29895899}, issn = {2045-2322}, abstract = {Wastewater treatment plants play an important role in the emergence of antibiotic resistance. They provide a hot spot for exchange of resistance within and between species. Here, we analyse and quantify the genomic diversity of the indicator Escherichia coli in a German wastewater treatment plant and we relate it to isolates' antibiotic resistance. Our results show a surprisingly large pan-genome, which mirrors how rich an environment a treatment plant is. We link the genomic analysis to a phenotypic resistance screen and pinpoint genomic hot spots, which correlate with a resistance phenotype. Besides well-known resistance genes, this forward genomics approach generates many novel genes, which correlated with resistance and which are partly completely unknown. A surprising overall finding of our analyses is that we do not see any difference in resistance and pan genome size between isolates taken from the inflow of the treatment plant and from the outflow. This means that while treatment plants reduce the amount of bacteria released into the environment, they do not reduce the potential for antibiotic resistance of these bacteria.}, }
@article {pmid29891839, year = {2018}, author = {Legendre, M and Fabre, E and Poirot, O and Jeudy, S and Lartigue, A and Alempic, JM and Beucher, L and Philippe, N and Bertaux, L and Christo-Foroux, E and Labadie, K and Couté, Y and Abergel, C and Claverie, JM}, title = {Diversity and evolution of the emerging Pandoraviridae family.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2285}, doi = {10.1038/s41467-018-04698-4}, pmid = {29891839}, issn = {2041-1723}, abstract = {With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now the most complex viruses since their discovery in 2013. Our isolation of three new strains from distant locations and environments is now used to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses reveals many non-coding transcripts and significantly reduces the former set of predicted protein-coding genes. Here we show that the pandoraviruses exhibit an open pan-genome, the enormous size of which is not adequately explained by gene duplications or horizontal transfers. As most of the strain-specific genes have no extant homolog and exhibit statistical features comparable to intergenic regions, we suggest that de novo gene creation could contribute to the evolution of the giant pandoravirus genomes.}, }
@article {pmid29890970, year = {2018}, author = {Fang, X and Monk, JM and Mih, N and Du, B and Sastry, AV and Kavvas, E and Seif, Y and Smarr, L and Palsson, BO}, title = {Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.}, journal = {BMC systems biology}, volume = {12}, number = {1}, pages = {66}, doi = {10.1186/s12918-018-0587-5}, pmid = {29890970}, issn = {1752-0509}, support = {U01 AI124316/AI/NIAID NIH HHS/United States ; Microbial Science Initiative Graduate Research Fellowship//UC San Diego Center for Microbiome Innovation/ ; 1-U01-AI124316-01//National Institutes of Health/ ; NNF10CC1016517//Novo Nordisk/ ; }, abstract = {BACKGROUND: Escherichia coli is considered a leading bacterial trigger of inflammatory bowel disease (IBD). E. coli isolates from IBD patients primarily belong to phylogroup B2. Previous studies have focused on broad comparative genomic analysis of E. coli B2 isolates, and identified virulence factors that allow B2 strains to reside within human intestinal mucosa. Metabolic capabilities of E. coli strains have been shown to be related to their colonization site, but remain unexplored in IBD-associated strains.<br><br>RESULTS: In this study, we utilized pan-genome analysis and genome-scale models (GEMs) of metabolism to study metabolic capabilities of IBD-associated E. coli B2 strains. The study yielded three results: i) Pan-genome analysis of 110 E. coli strains (including 53 isolates from IBD studies) revealed discriminating metabolic genes between B2 strains and other strains; ii) Both comparative genomic analysis and GEMs suggested that B2 strains have an advantage in degrading and utilizing sugars derived from mucus glycan, and iii) GEMs revealed distinct metabolic features in B2 strains that potentially allow them to utilize energy more efficiently. For example, B2 strains lack the enzymes to degrade amadori products, but instead rely on neighboring bacteria to convert these substrates into a more readily usable and potentially less sought after product.<br><br>CONCLUSIONS: Taken together, these results suggest that the metabolic capabilities of B2 strains vary significantly from those of other strains, enabling B2 strains to colonize intestinal mucosa.The results from this study motivate a broad experimental assessment of the nutritional effects on E. coli B2 pathophysiology in IBD patients.}, }
@article {pmid29867794, year = {2018}, author = {de Moraes, MH and Soto, EB and Salas González, I and Desai, P and Chu, W and Porwollik, S and McClelland, M and Teplitski, M}, title = {Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {877}, doi = {10.3389/fmicb.2018.00877}, pmid = {29867794}, issn = {1664-302X}, abstract = {Outbreaks of salmonellosis linked to the consumption of vegetables have been disproportionately associated with strains of serovar Newport. We tested the hypothesis that strains of sv. Newport have evolved unique adaptations to persistence in plants that are not shared by strains of other Salmonella serovars. We used a genome-wide mutant screen to compare growth in tomato fruit of a sv. Newport strain from an outbreak traced to tomatoes, and a sv. Typhimurium strain from animals. Most genes in the sv. Newport strain that were selected during persistence in tomatoes were shared with, and similarly selected in, the sv. Typhimurium strain. Many of their functions are linked to central metabolism, including amino acid biosynthetic pathways, iron acquisition, and maintenance of cell structure. One exception was a greater need for the core genes involved in purine metabolism in sv. Typhimurium than in sv. Newport. We discovered a gene, papA, that was unique to sv. Newport and contributed to the strain's fitness in tomatoes. The papA gene was present in about 25% of sv. Newport Group III genomes and generally absent from other Salmonella genomes. Homologs of papA were detected in the genomes of Pantoea, Dickeya, and Pectobacterium, members of the Enterobacteriacea family that can colonize both plants and animals.}, }
@article {pmid29859036, year = {2018}, author = {Adamek, M and Alanjary, M and Sales-Ortells, H and Goodfellow, M and Bull, AT and Winkler, A and Wibberg, D and Kalinowski, J and Ziemert, N}, title = {Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {426}, doi = {10.1186/s12864-018-4809-4}, pmid = {29859036}, issn = {1471-2164}, support = {TTU 9.704//Deutsches Zentrum für Infektionsforschung/ ; 031A533//Bielefeld-Gießen Center for Microbial Bioinformatics/ ; Emeritus Fellowship//Leverhulme Trust/ ; }, abstract = {BACKGROUND: Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary.<br><br>RESULTS: Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis' strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes.<br><br>CONCLUSIONS: Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.}, }
@article {pmid29858585, year = {2018}, author = {Zhao, Q and Feng, Q and Lu, H and Li, Y and Wang, A and Tian, Q and Zhan, Q and Lu, Y and Zhang, L and Huang, T and Wang, Y and Fan, D and Zhao, Y and Wang, Z and Zhou, C and Chen, J and Zhu, C and Li, W and Weng, Q and Xu, Q and Wang, ZX and Wei, X and Han, B and Huang, X}, title = {Publisher Correction: Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.}, journal = {Nature genetics}, volume = {50}, number = {8}, pages = {1196}, doi = {10.1038/s41588-018-0136-6}, pmid = {29858585}, issn = {1546-1718}, abstract = {When published, this article did not initially appear open access. This error has been corrected, and the open access status of the paper is noted in all versions of the paper.}, }
@article {pmid29857590, year = {2018}, author = {Angermeyer, A and Das, MM and Singh, DV and Seed, KD}, title = {Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period.}, journal = {Viruses}, volume = {10}, number = {6}, pages = {}, doi = {10.3390/v10060299}, pmid = {29857590}, issn = {1999-4915}, support = {R01 AI127652/AI/NIAID NIH HHS/United States ; }, abstract = {The Vibrio cholerae biotype &quot;El Tor&quot; is responsible for all of the current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal, and it is hypothesized that they originate from the coastal areas near the Bay of Bengal, where the lytic bacteriophage ICP1 (International Centre for Diarrhoeal Disease Research, Bangladesh cholera phage 1) specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stools since 2001. However, little is known about the genomic differences between the ICP1 strains that have been collected over time. Here, we elucidate the pan-genome and the phylogeny of the ICP1 strains by aligning, annotating, and analyzing the genomes of 19 distinct isolates that were collected between 2001 and 2012. Our results reveal that the ICP1 isolates are highly conserved and possess a large core-genome as well as a smaller, somewhat flexible accessory-genome. Despite its overall conservation, ICP1 strains have managed to acquire a number of unknown genes, as well as a CRISPR-Cas system which is known to be critical for its ongoing struggle for co-evolutionary dominance over its host. This study describes a foundation on which to construct future molecular and bioinformatic studies of these V. cholerae-associated bacteriophages.}, }
@article {pmid29855598, year = {2018}, author = {Bulagonda, EP and Manivannan, B and Mahalingam, N and Lama, M and Chanakya, PP and Khamari, B and Jadhao, S and Vasudevan, M and Nagaraja, V}, title = {Comparative genomic analysis of a naturally competent Elizabethkingia anophelis isolated from an eye infection.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8447}, doi = {10.1038/s41598-018-26874-8}, pmid = {29855598}, issn = {2045-2322}, abstract = {Elizabethkingia anophelis has now emerged as an opportunistic human pathogen. However, its mechanisms of transmission remain unexplained. Comparative genomic (CG) analysis of E. anopheles endophthalmitis strain surprisingly found from an eye infection patient with twenty-five other E. anophelis genomes revealed its potential to participate in horizontal gene transfer. CG analysis revealed that the study isolate has an open pan genome and has undergone extensive gene rearrangements. We demonstrate that the strain is naturally competent, hitherto not reported in any members of Elizabethkingia. Presence of competence related genes, mobile genetic elements, Type IV, VI secretory systems and a unique virulence factor arylsulfatase suggests a different lineage of the strain. Deciphering the genome of E. anophelis having a reservoir of antibiotic resistance genes and virulence factors associated with diverse human infections may open up avenues to deal with the myriad of its human infections and devise strategies to combat the pathogen.}, }
@article {pmid29850478, year = {2018}, author = {Oyedara, OO and Segura-Cabrera, A and Guo, X and Elufisan, TO and Cantú González, RA and Rodríguez Pérez, MA}, title = {Whole-Genome Sequencing and Comparative Genome Analysis Provided Insight into the Predatory Features and Genetic Diversity of Two Bdellovibrio Species Isolated from Soil.}, journal = {International journal of genomics}, volume = {2018}, number = {}, pages = {9402073}, doi = {10.1155/2018/9402073}, pmid = {29850478}, issn = {2314-436X}, abstract = {Bdellovibrio spp. are predatory bacteria with great potential as antimicrobial agents. Studies have shown that members of the genus Bdellovibrio exhibit peculiar characteristics that influence their ecological adaptations. In this study, whole genomes of two different Bdellovibrio spp. designated SKB1291214 and SSB218315 isolated from soil were sequenced. The core genes shared by all the Bdellovibrio spp. considered for the pangenome analysis including the epibiotic B. exovorus were 795. The number of unique genes identified in Bdellovibrio spp. SKB1291214, SSB218315, W, and B. exovorus JJS was 1343, 113, 857, and 1572, respectively. These unique genes encode hydrolytic, chemotaxis, and transporter proteins which might be useful for predation in the Bdellovibrio strains. Furthermore, the two Bdellovibrio strains exhibited differences based on the % GC content, amino acid identity, and 16S rRNA gene sequence. The 16S rRNA gene sequence of Bdellovibrio sp. SKB1291214 shared 99% identity with that of an uncultured Bdellovibrio sp. clone 12L 106 (a pairwise distance of 0.008) and 95-97% identity (a pairwise distance of 0.043) with that of other culturable terrestrial Bdellovibrio spp., including strain SSB218315. In Bdellovibrio sp. SKB1291214, 174 bp sequence was inserted at the host interaction (hit) locus region usually attributed to prey attachment, invasion, and development of host independent Bdellovibrio phenotypes. Also, a gene equivalent to Bd0108 in B. bacteriovorus HD100 was not conserved in Bdellovibrio sp. SKB1291214. The results of this study provided information on the genetic characteristics and diversity of the genus Bdellovibrio that can contribute to their successful applications as a biocontrol agent.}, }
@article {pmid29806079, year = {2018}, author = {Gias, E and Brosnahan, CL and Orr, D and Binney, B and Ha, HJ and Preece, MA and Jones, B}, title = {In vivo growth and genomic characterization of rickettsia-like organisms isolated from farmed Chinook salmon (Oncorhynchus tshawytscha) in New Zealand.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfd.12817}, pmid = {29806079}, issn = {1365-2761}, abstract = {A rickettsia-like organism, designated NZ-RLO2, was isolated from Chinook salmon (Oncorhynchus tshawytscha) farmed in the South Island, New Zealand. In vivo growth showed NZ-RLO2 was able to grow in CHSE-214, EPC, BHK-21, C6/36 and Sf21 cell lines, while Piscirickettsia salmonis LF-89T grew in all but BHK-21 and Sf21. NZ-RLO2 grew optimally in EPC at 15°C, CHSE-214 and EPC at 18°C. The growth of LF-89 T was optimal at 15°C, 18°C and 22°C in CHSE-24, but appeared less efficient in EPC cells at all temperatures. Pan-genome comparison of predicted proteomes shows that available Chilean strains of P. salmonis grouped into two clusters (p-value = 94%). NZ-RLO2 was genetically different from previously described NZ-RLO1, and both strains grouped separately from the Chilean strains in one of the two clusters (p-value = 88%), but were closely related to each other. TaqMan and Sybr Green real-time PCR targeting RNA polymerase (rpoB) and DNA primase (dnaG), respectively, were developed to detect NZ-RLO2. This study indicates that the New Zealand strains showed a closer genetic relationship to one of the Chilean P. salmonis clusters; however, more Piscirickettsia genomes from wider geographical regions and diverse hosts are needed to better understand the classification within this genus.}, }
@article {pmid29802996, year = {2018}, author = {Hurtado, R and Carhuaricra, D and Soares, S and Viana, MVC and Azevedo, V and Maturrano, L and Aburjaile, F}, title = {Pan-genomic approach shows insight of genetic divergence and pathogenic-adaptation of Pasteurella multocida.}, journal = {Gene}, volume = {670}, number = {}, pages = {193-206}, doi = {10.1016/j.gene.2018.05.084}, pmid = {29802996}, issn = {1879-0038}, mesh = {Animals ; Gene Transfer, Horizontal ; Genetic Drift ; Genome, Bacterial ; Genomics/*methods ; Pasteurella Infections/*microbiology ; Pasteurella multocida/*classification/genetics/isolation &amp; purification/pathogenicity ; Phylogeny ; }, abstract = {Pasteurella multocida is a gram-negative, non-motile bacterial pathogen, which is associated with chronic and acute infections as snuffles, pneumonia, atrophic rhinitis, fowl cholera and hemorrhagic septicemia. These diseases affect a wide range of domestic animals, leading to significant morbidity and mortality and causing significant economic losses worldwide. Due to the interest in deciphering the genetic diversity and process adaptive between P. multocida strains, this work aimed was to perform a pan-genome analysis to evidence horizontal gene transfer and positive selection among 23 P. multocida strains isolated from distinct diseases and hosts. The results revealed an open pan-genome containing 3585 genes and an accessory genome presenting 1200 genes. The phylogenomic analysis based on the presence/absence of genes and islands exhibit high levels of plasticity, which reflects a high intraspecific diversity and a possible adaptive mechanism responsible for the specific disease manifestation between the established groups (pneumonia, fowl cholera, hemorrhagic septicemia and snuffles). Additionally, we identified differences in accessory genes among groups, which are involved in sugar metabolism and transport systems, virulence-related genes and a high concentration of hypothetical proteins. However, there was no specific indispensable functional mechanism to decisively correlate the presence of genes and their adaptation to a specific host/disease. Also, positive selection was found only for two genes from sub-group hemorrhagic septicemia, serotype B. This comprehensive comparative genome analysis will provide new insights of horizontal gene transfers that play an essential role in the diversification and adaptation mechanism into P. multocida species to a specific disease.}, }
@article {pmid29795803, year = {2018}, author = {Abreu, VAC and Popin, RV and Alvarenga, DO and Schaker, PDC and Hoff-Risseti, C and Varani, AM and Fiore, MF}, title = {Corrigendum: Genomic and Genotypic Characterization of Cylindrospermopsis raciborskii: Toward an Intraspecific Phylogenetic Evaluation by Comparative Genomics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {979}, doi = {10.3389/fmicb.2018.00979}, pmid = {29795803}, issn = {1664-302X}, abstract = {[This corrects the article on p. 306 in vol. 9, PMID: 29535689.].}, }
@article {pmid29795552, year = {2018}, author = {Jiao, J and Ni, M and Zhang, B and Zhang, Z and Young, JPW and Chan, TF and Chen, WX and Lam, HM and Tian, CF}, title = {Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii.}, journal = {PLoS genetics}, volume = {14}, number = {5}, pages = {e1007428}, doi = {10.1371/journal.pgen.1007428}, pmid = {29795552}, issn = {1553-7404}, mesh = {Adaptation, Biological/*genetics ; Bacterial Proteins/genetics ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial/genetics ; Genome, Bacterial ; Nitrogen Fixation/genetics ; Plasmids/*genetics ; Replicon/genetics ; Sinorhizobium fredii/*genetics ; Soybeans/microbiology ; Symbiosis/*genetics ; Transcriptome ; }, abstract = {Prokaryotes benefit from having accessory genes, but it is unclear how accessory genes can be linked with the core regulatory network when developing adaptations to new niches. Here we determined hierarchical core/accessory subsets in the multipartite pangenome (composed of genes from the chromosome, chromid and plasmids) of the soybean microsymbiont Sinorhizobium fredii by comparing twelve Sinorhizobium genomes. Transcriptomes of two S. fredii strains at mid-log and stationary growth phases and in symbiotic conditions were obtained. The average level of gene expression, variation of expression between different conditions, and gene connectivity within the co-expression network were positively correlated with the gene conservation level from strain-specific accessory genes to genus core. Condition-dependent transcriptomes exhibited adaptive transcriptional changes in pangenome subsets shared by the two strains, while strain-dependent transcriptomes were enriched with accessory genes on the chromid. Proportionally more chromid genes than plasmid genes were co-expressed with chromosomal genes, while plasmid genes had a higher within-replicon connectivity in expression than chromid ones. However, key nitrogen fixation genes on the symbiosis plasmid were characterized by high connectivity in both within- and between-replicon analyses. Among those genes with host-specific upregulation patterns, chromosomal znu and mdt operons, encoding a conserved high-affinity zinc transporter and an accessory multi-drug efflux system, respectively, were experimentally demonstrated to be involved in host-specific symbiotic adaptation. These findings highlight the importance of integrative regulation of hierarchical core/accessory components in the multipartite genome of bacteria during niche adaptation and in shaping the prokaryotic pangenome in the long run.}, }
@article {pmid29792377, year = {2018}, author = {Satti, M and Tanizawa, Y and Endo, A and Arita, M}, title = {Comparative analysis of probiotic bacteria based on a new definition of core genome.}, journal = {Journal of bioinformatics and computational biology}, volume = {16}, number = {3}, pages = {1840012}, doi = {10.1142/S0219720018400127}, pmid = {29792377}, issn = {1757-6334}, abstract = {The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of &quot;core genome&quot;, core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes. Functional comparison of the core genes of the two genera revealed a significant difference in the categories &quot;amino acid transport and metabolism&quot; representing their difference in niche specificity. Over-represented Bifidobacterium protein families were primarily involved in host interactions, the complex compound metabolism, and in stress responses. These findings coincide with the published information and validate our bias-resilient definition of the core genome.}, }
@article {pmid29788909, year = {2018}, author = {Lacey, JA and Allnutt, TR and Vezina, B and Van, TTH and Stent, T and Han, X and Rood, JI and Wade, B and Keyburn, AL and Seemann, T and Chen, H and Haring, V and Johanesen, PA and Lyras, D and Moore, RJ}, title = {Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {379}, doi = {10.1186/s12864-018-4771-1}, pmid = {29788909}, issn = {1471-2164}, support = {1.1.2//Poultry Cooperative Research Centre/ ; }, abstract = {BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome.<br><br>RESULTS: Distinct pathogenic clades of necrotic enteritis-causing C. perfringens were identified. They were characterised by variable regions encoded on the chromosome, with predicted roles in capsule production, adhesion, inhibition of related strains, phage integration, and metabolism. Some strains have almost identical genomes, even though they were isolated from different geographic regions at various times, while other highly distant genomes appear to result in similar outcomes with regard to virulence and pathogenesis.<br><br>CONCLUSIONS: The high level of diversity in chicken isolates suggests there is no reliable factor that defines a chicken strain of C. perfringens, however, disease-causing strains can be defined by the presence of netB-encoding plasmids. This study reveals that horizontal gene transfer appears to play a significant role in genetic variation of the C. perfringens chromosome as well as the plasmid content within strains.}, }
@article {pmid29785479, year = {2018}, author = {Kulsum, U and Kapil, A and Singh, H and Kaur, P}, title = {NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads.}, journal = {Advances in experimental medicine and biology}, volume = {1052}, number = {}, pages = {39-49}, doi = {10.1007/978-981-10-7572-8_4}, pmid = {29785479}, issn = {0065-2598}, abstract = {Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species. It can also assist in identifying drug targets and proposing vaccine candidates. The effective analysis of these large genome datasets necessitates the development of robust tools. Current methods to develop pan-genome do not support direct input of raw reads from the sequencer machine but require preprocessing of reads as an assembled protein/gene sequence file or the binary matrix of orthologous genes/proteins. We have designed an easy-to-use integrated pipeline, NGSPanPipe, which can directly identify the pan-genome from short reads. The output from the pipeline is compatible with other pan-genome analysis tools. We evaluated our pipeline with other methods for developing pan-genome, i.e. reference-based assembly and de novo assembly using simulated reads of Mycobacterium tuberculosis. The single script pipeline (pipeline.pl) is applicable for all bacterial strains. It integrates multiple in-house Perl scripts and is freely accessible from https://github.com/Biomedinformatics/NGSPanPipe .}, }
@article {pmid29773867, year = {2018}, author = {Kim, YB and Kim, JY and Song, HS and Lee, C and Ahn, SW and Lee, SH and Jung, MY and Rhee, JK and Kim, J and Hyun, DW and Bae, JW and Roh, SW}, title = {Novel haloarchaeon Natrinema thermophila having the highest growth temperature among haloarchaea with a large genome size.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7777}, doi = {10.1038/s41598-018-25887-7}, pmid = {29773867}, issn = {2045-2322}, abstract = {Environmental temperature is one of the most important factors for the growth and survival of microorganisms. Here we describe a novel extremely halophilic archaeon (haloarchaea) designated as strain CBA1119T isolated from solar salt. Strain CBA1119T had the highest maximum and optimal growth temperatures (66 °C and 55 °C, respectively) and one of the largest genome sizes among haloarchaea (5.1 Mb). It also had the largest number of strain-specific pan-genome orthologous groups and unique pathways among members of the genus Natrinema in the class Halobacteria. A dendrogram based on the presence/absence of genes and a phylogenetic tree constructed based on OrthoANI values highlighted the particularities of strain CBA1119T as compared to other Natrinema species and other haloarchaea members. The large genome of strain CBA1119T may provide information on genes that confer tolerance to extreme environmental conditions, which may lead to the discovery of other thermophilic strains with potential applications in industrial biotechnology.}, }
@article {pmid29768136, year = {2018}, author = {Sánchez-Vallet, A and Fouché, S and Fudal, I and Hartmann, FE and Soyer, JL and Tellier, A and Croll, D}, title = {The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens.}, journal = {Annual review of phytopathology}, volume = {56}, number = {}, pages = {21-40}, doi = {10.1146/annurev-phyto-080516-035303}, pmid = {29768136}, issn = {1545-2107}, abstract = {Filamentous pathogens, including fungi and oomycetes, pose major threats to global food security. Crop pathogens cause damage by secreting effectors that manipulate the host to the pathogen's advantage. Genes encoding such effectors are among the most rapidly evolving genes in pathogen genomes. Here, we review how the major characteristics of the emergence, function, and regulation of effector genes are tightly linked to the genomic compartments where these genes are located in pathogen genomes. The presence of repetitive elements in these compartments is associated with elevated rates of point mutations and sequence rearrangements with a major impact on effector diversification. The expression of many effectors converges on an epigenetic control mediated by the presence of repetitive elements. Population genomics analyses showed that rapidly evolving pathogens show high rates of turnover at effector loci and display a mosaic in effector presence-absence polymorphism among strains. We conclude that effective pathogen containment strategies require a thorough understanding of the effector genome biology and the pathogen's potential for rapid adaptation.}, }
@article {pmid29765358, year = {2018}, author = {Vinuesa, P and Ochoa-Sánchez, LE and Contreras-Moreira, B}, title = {GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {771}, doi = {10.3389/fmicb.2018.00771}, pmid = {29765358}, issn = {1664-302X}, abstract = {The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.}, }
@article {pmid29764365, year = {2018}, author = {Valenzuela, D and Norri, T and Välimäki, N and Pitkänen, E and Mäkinen, V}, title = {Towards pan-genome read alignment to improve variation calling.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 2}, pages = {87}, doi = {10.1186/s12864-018-4465-8}, pmid = {29764365}, issn = {1471-2164}, abstract = {BACKGROUND: Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation.<br><br>RESULTS: We propose a new unified framework for variant calling with short-read data utilizing a representation of human genetic variation - a pan-genomic reference. We provide a modular pipeline that can be seamlessly incorporated into existing sequencing data analysis workflows. Our tool is open source and available online: https://gitlab.com/dvalenzu/PanVC .<br><br>CONCLUSIONS: Our experiments show that by replacing a standard human reference with a pan-genomic one we achieve an improvement in single-nucleotide variant calling accuracy and in short indel calling accuracy over the widely adopted Genome Analysis Toolkit (GATK) in difficult genomic regions.}, }
@article {pmid29755426, year = {2018}, author = {Howat, AM and Vollmers, J and Taubert, M and Grob, C and Dixon, JL and Todd, JD and Chen, Y and Kaster, AK and Murrell, JC}, title = {Comparative Genomics and Mutational Analysis Reveals a Novel XoxF-Utilizing Methylotroph in the Roseobacter Group Isolated From the Marine Environment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {766}, doi = {10.3389/fmicb.2018.00766}, pmid = {29755426}, issn = {1664-302X}, abstract = {The Roseobacter group comprises a significant group of marine bacteria which are involved in global carbon and sulfur cycles. Some members are methylotrophs, using one-carbon compounds as a carbon and energy source. It has recently been shown that methylotrophs generally require a rare earth element when using the methanol dehydrogenase enzyme XoxF for growth on methanol. Addition of lanthanum to methanol enrichments of coastal seawater facilitated the isolation of a novel methylotroph in the Roseobacter group: Marinibacterium anthonyi strain La 6. Mutation of xoxF5 revealed the essential nature of this gene during growth on methanol and ethanol. Physiological characterization demonstrated the metabolic versatility of this strain. Genome sequencing revealed that strain La 6 has the largest genome of all Roseobacter group members sequenced to date, at 7.18 Mbp. Multilocus sequence analysis (MLSA) showed that whilst it displays the highest core gene sequence similarity with subgroup 1 of the Roseobacter group, it shares very little of its pangenome, suggesting unique genetic adaptations. This research revealed that the addition of lanthanides to isolation procedures was key to cultivating novel XoxF-utilizing methylotrophs from the marine environment, whilst genome sequencing and MLSA provided insights into their potential genetic adaptations and relationship to the wider community.}, }
@article {pmid29743119, year = {2018}, author = {Zolfo, M and Asnicar, F and Manghi, P and Pasolli, E and Tett, A and Segata, N}, title = {Profiling microbial strains in urban environments using metagenomic sequencing data.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {9}, doi = {10.1186/s13062-018-0211-z}, pmid = {29743119}, issn = {1745-6150}, abstract = {BACKGROUND: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. It is thus currently unclear whether such methods, that have proven successful at distinguishing even closely related strains in human microbiomes, are also effective in urban settings for tasks such as cultivation-free pathogen detection and microbial surveillance. Here, we aimed at a) testing the currently available metagenomic profiling tools on urban metagenomics; b) characterizing the organisms in urban environment at the resolution of single strain and c) discussing the biological insights that can be inferred from such methods.<br><br>RESULTS: We applied three complementary methods on the 1614 metagenomes of the CAMDA 2017 challenge. With MetaMLST we identified 121 known sequence-types from 15 species of clinical relevance. For instance, we identified several Acinetobacter strains that were close to the nosocomial opportunistic pathogen A. nosocomialis. With StrainPhlAn, a generalized version of the MetaMLST approach, we inferred the phylogenetic structure of Pseudomonas stutzeri strains and suggested that the strain-level heterogeneity in environmental samples is higher than in the human microbiome. Finally, we also probed the functional potential of the different strains with PanPhlAn. We further showed that SNV-based and pangenome-based profiling provide complementary information that can be combined to investigate the evolutionary trajectories of microbes and to identify specific genetic determinants of virulence and antibiotic resistances within closely related strains.<br><br>CONCLUSION: We show that strain-level methods developed primarily for the analysis of human microbiomes can be effective for city-associated microbiomes. In fact, (opportunistic) pathogens can be tracked and monitored across many hundreds of urban metagenomes. However, while more effort is needed to profile strains of currently uncharacterized species, this work poses the basis for high-resolution analyses of microbiomes sampled in city and mass transportation environments.<br><br>REVIEWERS: This article was reviewed by Alexandra Bettina Graf, Daniel Huson and Trevor Cickovski.}, }
@article {pmid29721151, year = {2018}, author = {Kumar, R and Acharya, V and Singh, D and Kumar, S}, title = {Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01.}, journal = {Standards in genomic sciences}, volume = {13}, number = {}, pages = {11}, doi = {10.1186/s40793-018-0313-3}, pmid = {29721151}, issn = {1944-3277}, abstract = {A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus and also to decipher its survival strategy at the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes. Whole genome-based multilocus sequence analysis clustering, in silico DDH similarity value of 95.1% and, the ANI value of 99.25% established the identity of the strain ERGS5:01 (MCC 2953) as a non-violacein producing J. lividum. The genome comparisons across genus Janthinobacterium revealed an open pan-genome with the scope of the addition of new orthologous cluster to complete the genomic inventory. The genomic insight provided the genetic basis of freezing and frequent freeze-thaw cycle tolerance and, for industrially important enzymes. Extended insight into the genome provided clues of crucial genes associated with adaptation in the harsh aquatic ecosystem of high altitude.}, }
@article {pmid29716534, year = {2018}, author = {Oliver, A and Kay, M and Cooper, KK}, title = {Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {310}, doi = {10.1186/s12864-018-4635-8}, pmid = {29716534}, issn = {1471-2164}, support = {P30 CA062203/CA/NCI NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; S10 RR025496/RR/NCRR NIH HHS/United States ; }, abstract = {BACKGROUND: Cocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements.<br><br>RESULTS: For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world. We generated the first six complete genomes and methylomes utilizing PacBio sequencing, and an additional 22 draft genomes using Illumina sequencing. Genomic analysis revealed that cocci-shaped Sporosarcina strains contained an average genome of 3.3 Mb comprised of 3222 CDS, 54 tRNAs and 6 rRNAs, while only two strains contained plasmids. The cocci-shaped Sporosarcina genome on average contained 2.3 prophages and 15.6 IS elements, while methylome analysis supported the diversity of these strains as only one of 31 methylation motifs were shared under identical growth conditions. Analysis with a 90% identity cut-off revealed 221 core genes or ~ 7% of the genome, while a 30% identity cut-off generated a pan-genome of 8610 genes. The phylogenetic relationship of the cocci-shaped Sporosarcina strains based on either core genes, accessory genes or spore-related genes consistently resulted in the 29 strains being divided into eight clades.<br><br>CONCLUSIONS: This study begins to unravel the phylogenetic relationship of cocci-shaped Sporosarcina strains, and the comparative genomics of these strains supports identification of several new species.}, }
@article {pmid29695866, year = {2018}, author = {Wang, W and Mauleon, R and Hu, Z and Chebotarov, D and Tai, S and Wu, Z and Li, M and Zheng, T and Fuentes, RR and Zhang, F and Mansueto, L and Copetti, D and Sanciangco, M and Palis, KC and Xu, J and Sun, C and Fu, B and Zhang, H and Gao, Y and Zhao, X and Shen, F and Cui, X and Yu, H and Li, Z and Chen, M and Detras, J and Zhou, Y and Zhang, X and Zhao, Y and Kudrna, D and Wang, C and Li, R and Jia, B and Lu, J and He, X and Dong, Z and Xu, J and Li, Y and Wang, M and Shi, J and Li, J and Zhang, D and Lee, S and Hu, W and Poliakov, A and Dubchak, I and Ulat, VJ and Borja, FN and Mendoza, JR and Ali, J and Li, J and Gao, Q and Niu, Y and Yue, Z and Naredo, MEB and Talag, J and Wang, X and Li, J and Fang, X and Yin, Y and Glaszmann, JC and Zhang, J and Li, J and Hamilton, RS and Wing, RA and Ruan, J and Zhang, G and Wei, C and Alexandrov, N and McNally, KL and Li, Z and Leung, H}, title = {Genomic variation in 3,010 diverse accessions of Asian cultivated rice.}, journal = {Nature}, volume = {557}, number = {7703}, pages = {43-49}, doi = {10.1038/s41586-018-0063-9}, pmid = {29695866}, issn = {1476-4687}, mesh = {Asia ; Crops, Agricultural/*classification/*genetics ; Evolution, Molecular ; Genes, Plant/genetics ; *Genetic Variation ; Genetics, Population ; Genome, Plant/*genetics ; Genomics ; Haplotypes ; INDEL Mutation/genetics ; Oryza/*classification/*genetics ; Phylogeny ; Plant Breeding ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.}, }
@article {pmid29695424, year = {2018}, author = {Rodrigues, RAL and Andreani, J and Andrade, ACDSP and Machado, TB and Abdi, S and Levasseur, A and Abrahão, JS and La Scola, B}, title = {Morphologic and Genomic Analyses of New Isolates Reveal a Second Lineage of Cedratviruses.}, journal = {Journal of virology}, volume = {92}, number = {13}, pages = {}, doi = {10.1128/JVI.00372-18}, pmid = {29695424}, issn = {1098-5514}, mesh = {Acanthamoeba castellanii/*virology ; DNA, Viral ; *Evolution, Molecular ; *Genome, Viral ; Genomics/*methods ; Giant Viruses/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Virion/*genetics ; }, abstract = {Giant viruses have been isolated and characterized in different environments, expanding our knowledge about the biology of these unique microorganisms. In the last 2 years, a new group was discovered, the cedratviruses, currently composed of only two isolates and members of a putative new family, &quot;Pithoviridae,&quot; along with previously known pithoviruses. Here we report the isolation and biological and genomic characterization of two novel cedratviruses isolated from samples collected in France and Brazil. Both viruses were isolated using Acanthamoeba castellanii as a host cell and exhibit ovoid particles with corks at either extremity of the particle. Curiously, the Brazilian cedratvirus is ∼20% smaller and presents a shorter genome of 460,038 bp, coding for fewer proteins than other cedratviruses. In addition, it has a completely asyntenic genome and presents a lower amino acid identity of orthologous genes (∼73%). Pangenome analysis comprising the four cedratviruses revealed an increase in the pangenome concomitant with a decrease in the core genome with the addition of the two novel viruses. Finally, phylogenetic analyses clustered the Brazilian virus in a separate branch within the group of cedratviruses, while the French isolate is closer to the previously reported Cedratvirus lausannensis Taking all together, we propose the existence of a second lineage of this emerging viral genus and provide new insights into the biodiversity and ubiquity of these giant viruses.IMPORTANCE Various giant viruses have been described in recent years, revealing a unique part of the virosphere. A new group among the giant viruses has recently been described, the cedratviruses, which is currently composed of only two isolates. In this paper, we describe two novel cedratviruses isolated from French and Brazilian samples. Biological and genomic analyses showed viruses with different particle sizes, genome lengths, and architecture, revealing the existence of a second lineage of this new group of giant viruses. Our results provide new insights into the biodiversity of cedratviruses and highlight the importance of ongoing efforts to prospect for and characterize new giant viruses.}, }
@article {pmid29695124, year = {2018}, author = {Nguyen, TL and Kim, DH}, title = {Genome-Wide Comparison Reveals a Probiotic Strain Lactococcus Lactis WFLU12 Isolated from the Gastrointestinal Tract of Olive Flounder (Paralichthys Olivaceus) Harboring Genes Supporting Probiotic Action.}, journal = {Marine drugs}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/md16050140}, pmid = {29695124}, issn = {1660-3397}, mesh = {Animals ; Chromosome Mapping ; Chromosomes, Bacterial ; Flounder/*microbiology ; Gene Expression Regulation, Bacterial/*physiology ; *Genome, Bacterial ; Lactococcus lactis/*genetics/*metabolism ; *Probiotics ; }, abstract = {Our previous study has shown that dietary supplementation with Lactococcus lactis WFLU12 can enhance the growth of olive flounder and its resistance against streptococcal infection. The objective of the present study was to use comparative genomics tools to investigate genomic characteristics of strain WFLU12 and the presence of genes supporting its probiotic action using sequenced genomes of L. lactis strains. Dispensable and singleton genes of strain WFLU12 were found to be more enriched in genes associated with metabolism (e.g., energy production and conversion, and carbohydrate transport and metabolism) than pooled dispensable and singleton genes in other L. lactis strains, reflecting WFLU12 strain-specific ecosystem origin and its ability to metabolize different energy sources. Strain WFLU12 produced antimicrobial compounds that could inhibit several bacterial fish pathogens. It possessed the nisin gene cluster (nisZBTCIPRKFEG) and genes encoding lysozyme and colicin V. However, only three other strains (CV56, IO-1, and SO) harbor a complete nisin gene cluster. We also found that L. lactis WFLU12 possessed many other important functional genes involved in stress responses to the gastrointestinal tract environment, dietary energy extraction, and metabolism to support the probiotic action of this strain found in our previous study. This strongly indicates that not all L. lactis strains can be used as probiotics. This study highlights comparative genomics approaches as very useful and powerful tools to select probiotic candidates and predict their probiotic effects.}, }
@article {pmid29694430, year = {2018}, author = {Chen, C and Wu, L and Cao, Q and Shao, H and Li, X and Zhang, Y and Wang, H and Tan, X}, title = {Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195994}, doi = {10.1371/journal.pone.0195994}, pmid = {29694430}, issn = {1932-6203}, mesh = {Ethanol/metabolism ; Evolution, Molecular ; Genome Size ; *Genome, Bacterial ; Hydrogen-Ion Concentration ; Phylogeny ; Sequence Analysis, DNA/*methods ; Zymomonas/*classification/genetics/metabolism ; }, abstract = {Zymomonas mobilis has the special Entner-Doudoroff (ED) pathway and it has excellent industrial characteristics, including low cell mass formation, high-specific productivity,ethanol yield, notable ethanol tolerance and wide pH range, a relatively small genome size. In this study, the genome sequences of NRRL B-14023 and NRRL B-12526 were sequenced and compared with other strains to explore their evolutionary relationships and the genetic basis of Z. mobilis. The comparative genomic analyses revealed that the 8 strains share a conserved core chromosomal backbone. ZM4, NRRL B-12526, NRRL B-14023, NCIMB 11163 and NRRL B-1960 share 98% sequence identity across the whole genome sequences. Highly similar plasmids and CRISPR repeats were detected in these strains. A whole-genome phylogenetic tree of the 8 strains indicated that NRRL B-12526, NRRL B-14023 and ATCC 10988 had a close evolutionary relationship with the strain ZM4. Furthermore, strains ATCC29191 and ATCC29192 had distinctive CRISPR with a far distant relationship. The size of the pan-genome was 1945 genes, including 1428 core genes and 517 accessory genes. The genomes of Z. mobilis were highly conserved; particularly strains ZM4, NRRL B-12526, NRRL B-14023, NCIMB 11163 and NRRL B-1960 had a close genomic relationship. This comparative study of Z. mobilis presents a foundation for future functional analyses and applications.}, }
@article {pmid29690879, year = {2018}, author = {Inglin, RC and Meile, L and Stevens, MJA}, title = {Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {284}, doi = {10.1186/s12864-018-4601-5}, pmid = {29690879}, issn = {1471-2164}, support = {145214//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, abstract = {BACKGROUND: Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events.<br><br>RESULTS: We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class &quot;genetic information processing&quot; is conserved in the core-genome but that &quot;signaling and cellular processes&quot; is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation.<br><br>CONCLUSIONS: Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed by the environment and HGT.}, }
@article {pmid29688542, year = {2018}, author = {Kupczok, A and Neve, H and Huang, KD and Hoeppner, MP and Heller, KJ and Franz, CMAP and Dagan, T}, title = {Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades.}, journal = {Molecular biology and evolution}, volume = {35}, number = {5}, pages = {1147-1159}, doi = {10.1093/molbev/msy027}, pmid = {29688542}, issn = {1537-1719}, support = {281357//European Research Council/International ; }, abstract = {The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years. We estimate a constant substitution rate of 1.9 × 10-4 substitutions per site per year due to mutation that is within the range of estimates for eukaryotic RNA and DNA viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5 × 10-3 nucleotide alterations due to recombination per site per year. Thus, the recombination rate exceeds the substitution rate, resulting in a relative effect of recombination to mutation (r/m) of ∼24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with phages of the 936 group, demonstrating the role of the 936 group pangenome as a reservoir of genetic variation. The observed substitution rate homogeneity conforms to the neutral theory of evolution; hence, the neutral theory can be applied to phage genome evolution and also to genetic variation brought about by recombination.}, }
@article {pmid29680695, year = {2018}, author = {Parry-Hanson Kunadu, A and Holmes, M and Miller, EL and Grant, AJ}, title = {Microbiological quality and antimicrobial resistance characterization of Salmonella spp. in fresh milk value chains in Ghana.}, journal = {International journal of food microbiology}, volume = {277}, number = {}, pages = {41-49}, doi = {10.1016/j.ijfoodmicro.2018.04.025}, pmid = {29680695}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cheese/*microbiology ; Ciprofloxacin/pharmacology ; *Drug Resistance, Bacterial ; Escherichia coli O157/drug effects/*isolation &amp; purification ; Food Microbiology ; Ghana ; Listeria monocytogenes/drug effects/*isolation &amp; purification ; Microbial Sensitivity Tests ; Milk/*microbiology ; Phylogeny ; Salmonella enterica/classification/drug effects/*isolation &amp; purification ; Staphylococcus aureus/drug effects/*isolation &amp; purification ; }, abstract = {Consumer perception of poor hygiene of fresh milk products is a major barrier to promotion of milk consumption as an intervention to alleviate the burden of malnutrition in Ghana. Fresh milk is retailed raw, boiled, or processed into unfermented cheese and spontaneously fermented products in unlicensed outlets. In this study, we have determined microbiological quality of informally retailed fresh milk products and characterized the genomic diversity and antimicrobial resistance (AMR) patterns of non-typhoidal Salmonella (NTS) in implicated products. A total of 159 common dairy products were purchased from five traditional milk markets in Accra. Samples were analysed for concentrations of aerobic bacteria, total and fecal coliforms, Escherichia coli, staphylococci, lactic acid bacteria and yeast and moulds. The presence of Salmonella, E. coli O157:H7, Listeria monocytogenes and Staphylococcus aureus were determined. AMR of Salmonella against 18 antibiotics was experimentally determined. Genome sequencing of 19 Salmonella isolates allowed determination of serovars, antigenic profiles, prediction of AMR genes in silico and inference of phylogenetic relatedness between strains. Raw and heat-treated milk did not differ significantly in overall bacterial quality (P = 0.851). E. coli O157:H7 and Staphylococcus aureus were present in 34.3% and 12.9% of dairy products respectively. Multidrug resistant (MDR) Salmonella enterica serovars Muenster and Legon were identified in 11.8% and 5.9% of unfermented cheese samples respectively. Pan genome analysis revealed a total of 3712 core genes. All Salmonella strains were resistant to Trimethoprim/Sulfamethoxazole, Cefoxitin, Cefuroxime Axetil and Cefuroxime. Resistance to Chloramphenicol (18%) and Ciprofloxacin (100%), which are first line antibiotics used in treatment of NTS bacteremia in Ghana, was evident. AMR was attributed to presence and/or mutations in the following genes: golS, sdiA for cephalosporins, aac(6')-Iy, ant(9) for aminoglycosides, mdtK, gyrA, gyrB, parC, parE for quinolones and cat1, cat4 for phenicols. Phylogenetic analysis based on accessory genes clustered S. Legon strains separately from the S. Muenster strains. These strains were from different markets suggesting local circulation of related strains. Our study justifies consumer resistance to consumption of unripened soft cheese without further lethal heat treatment, and provides evidence that supports the Ghana Health Service recommendation for use of 3rd generation cephalosporins for the treatment of MDR NTS infections.}, }
@article {pmid29657968, year = {2018}, author = {Baby, V and Lachance, JC and Gagnon, J and Lucier, JF and Matteau, D and Knight, T and Rodrigue, S}, title = {Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSystems.00198-17}, pmid = {29657968}, issn = {2379-5077}, support = {27307C0010/ES/NIEHS NIH HHS/United States ; }, abstract = {The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. IMPORTANCE The last years have witnessed the development of whole-genome cloning and transplantation methods and the complete synthesis of entire chromosomes. Recently, the first minimal cell, Mycoplasma mycoides JCVI-syn3.0, was created. Despite these milestone achievements, several questions remain to be answered. For example, is the composition of minimal genomes virtually identical in phylogenetically related species? On the basis of comparative genomics and transposon mutagenesis, we investigated this question by using an alternative model, Mesoplasma florum, that is also amenable to genome reduction efforts. Our results suggest that the creation of additional minimal genomes could help reveal different gene compositions and strategies that can support life, even within closely related species.}, }
@article {pmid29636744, year = {2018}, author = {Zhang, X and Liu, X and Yang, F and Chen, L}, title = {Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {577}, doi = {10.3389/fmicb.2018.00577}, pmid = {29636744}, issn = {1664-302X}, abstract = {Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.}, }
@article {pmid29635365, year = {2018}, author = {Holm, KO and Bækkedal, C and Söderberg, JJ and Haugen, P}, title = {Complete Genome Sequences of Seven Vibrio anguillarum Strains as Derived from PacBio Sequencing.}, journal = {Genome biology and evolution}, volume = {10}, number = {4}, pages = {1127-1131}, doi = {10.1093/gbe/evy074}, pmid = {29635365}, issn = {1759-6653}, mesh = {DNA Transposable Elements/*genetics ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; Vibrio/*genetics ; *Whole Genome Sequencing ; }, abstract = {We report here the complete genome sequences of seven Vibrio anguillarum strains isolated from multiple geographic locations, thus increasing the total number of genomes of finished quality to 11. The genomes were de novo assembled from long-sequence PacBio reads. Including draft genomes, a total of 44 V. anguillarum genomes are currently available in the genome databases. They represent an important resource in the study of, for example, genetic variations and for identifying virulence determinants. In this article, we present the genomes and basic genome comparisons of the 11 complete genomes, including a BRIG analysis, and pan genome calculation. We also describe some structural features of superintegrons on chromosome 2 s, and associated insertion sequence (IS) elements, including 18 new ISs (ISVa3 - ISVa20), both of importance in the complement of V. anguillarum genomes.}, }
@article {pmid29635296, year = {2018}, author = {Thorpe, HA and Bayliss, SC and Sheppard, SK and Feil, EJ}, title = {Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria.}, journal = {GigaScience}, volume = {7}, number = {4}, pages = {1-11}, doi = {10.1093/gigascience/giy015}, pmid = {29635296}, issn = {2047-217X}, support = {MR/L015080/1//Medical Research Council/United Kingdom ; G1000803//Medical Research Council/United Kingdom ; }, abstract = {Background: The concept of the &quot;pan-genome,&quot; which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences.<br><br>Findings: To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent (&quot;switched&quot;) intergenic regions (IGRs) upstream of genes. We demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli.<br><br>Conclusions: For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).}, }
@article {pmid29629856, year = {2018}, author = {Croxen, MA and Lee, TD and Azana, R and Hoang, LM}, title = {Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae.}, journal = {Microbial genomics}, volume = {4}, number = {7}, pages = {}, doi = {10.1099/mgen.0.000175}, pmid = {29629856}, issn = {2057-5858}, abstract = {Distinuishing the species of mitis group streptococci is challenging due to ambiguous phenotypic characteristics and high degree of genetic similarity. This has been particularly true for resolving atypical Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We used phylogenetic clustering to demonstrate specific and separate clades for both S. pneumoniae and S. pseudopneumoniae genomes. The genomes that clustered within these defined clades were used to extract species-specific genes from the pan-genome. The S. pneumoniae marker was detected in 8027 out of 8051 (>99.7 %) S. pneumoniae genomes. The S. pseudopneumoniae marker was specific for all genomes that clustered in the S. pseudopneumoniae clade, including unresolved species of the genus Streptococcus sequenced by the BC Centre for Disease Control Public Health Laboratory that previously could not be distinguished by other methods. Other than the presence of the S. pseudopneumoniae marker in six of 8051 (<0.08 %) S. pneumoniae genomes, both the S. pneumoniae and S. pseudopneumoniae markers showed little to no detectable cross-reactivity to the genomes of any other species of the genus Streptococcus or to a panel of over 46 000 genomes from viral, fungal, bacterial pathogens and microbiota commonly found in the respiratory tract. A real-time PCR assay was designed targeting these two markers. Genomics provides a useful technique for PCR assay design and development.}, }
@article {pmid29617810, year = {2018}, author = {Murillo, T and Ramírez-Vargas, G and Riedel, T and Overmann, J and Andersen, JM and Guzmán-Verri, C and Chaves-Olarte, E and Rodríguez, C}, title = {Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms.}, journal = {Genome biology and evolution}, volume = {10}, number = {3}, pages = {982-998}, doi = {10.1093/gbe/evy059}, pmid = {29617810}, issn = {1759-6653}, mesh = {Clostridium Infections/*genetics/microbiology ; Clostridium difficile/*genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Genome, Bacterial ; Genotype ; Humans ; Mutation ; Virulence/genetics ; }, abstract = {Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0.54/kb; NAP1/ST01 = 0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301-8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes). Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role.}, }
@article {pmid29617440, year = {2018}, author = {Azarian, T and Grant, LR and Arnold, BJ and Hammitt, LL and Reid, R and Santosham, M and Weatherholtz, R and Goklish, N and Thompson, CM and Bentley, SD and O'Brien, KL and Hanage, WP and Lipsitch, M}, title = {The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.}, journal = {PLoS pathogens}, volume = {14}, number = {4}, pages = {e1006966}, doi = {10.1371/journal.ppat.1006966}, pmid = {29617440}, issn = {1553-7374}, support = {R01 AI048935/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Child ; Genetics, Population ; *Genome, Bacterial ; Heptavalent Pneumococcal Conjugate Vaccine/*administration &amp; dosage ; Humans ; Middle Aged ; Nasopharynx/microbiology ; Phylogeny ; Pneumococcal Infections/epidemiology/immunology/microbiology/*prevention &amp; control ; Pneumococcal Vaccines/*administration &amp; dosage ; Population Dynamics ; Prospective Studies ; *Serogroup ; Serotyping ; Streptococcus pneumoniae/genetics/*immunology ; Vaccination ; Young Adult ; }, abstract = {In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use. To investigate the evolutionary impact of vaccination, we assessed recombination, evolution, and pathogen demographic history of 937 pneumococci collected from 1998-2012 among Navajo and White Mountain Apache Native American communities. We analyzed changes in the pneumococcal pangenome, focusing on metabolic loci and 19 polymorphic protein antigens. We found the impact of PCV on the pneumococcal population could be observed in reduced diversity, a smaller pangenome, and changing frequencies of accessory clusters of orthologous groups (COGs). Post-PCV7, diversity rebounded through clonal expansion of NVT lineages and inferred in-migration of two previously unobserved lineages. Accessory COGs frequencies trended toward pre-PCV7 values with increasing time since vaccine introduction. Contemporary frequencies of protein antigen variants are better predicted by pre-PCV7 values (1998-2000) than the preceding period (2006-2008), suggesting balancing selection may have acted in maintaining variant frequencies in this population. Overall, we present the largest genomic analysis of pneumococcal carriage in the United States to date, which includes a snapshot of a true vaccine-naïve community prior to the introduction of PCV7. These data improve our understanding of pneumococcal evolution and emphasize the need to consider pangenome composition when inferring the impact of vaccination and developing future protein-based pneumococcal vaccines.}, }
@article {pmid29610707, year = {2018}, author = {Åvall-Jääskeläinen, S and Taponen, S and Kant, R and Paulin, L and Blom, J and Palva, A and Koort, J}, title = {Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4560}, doi = {10.7717/peerj.4560}, pmid = {29610707}, issn = {2167-8359}, abstract = {Non-aureus staphylococci (NAS) are most commonly isolated from subclinical mastitis. Different NAS species may, however, have diverse effects on the inflammatory response in the udder. We determined the genome sequences of 20 staphylococcal isolates from clinical or subclinical bovine mastitis, belonging to the NAS species Staphylococcus agnetis, S. chromogenes, and S. simulans, and focused on the putative virulence factor genes present in the genomes. For comparison we used our previously published genome sequences of four S. aureus isolates from bovine mastitis. The pan-genome and core genomes of the non-aureus isolates were characterized. After that, putative virulence factor orthologues were searched in silico. We compared the presence of putative virulence factors in the NAS species and S. aureus and evaluated the potential association between bacterial genotype and type of mastitis (clinical vs. subclinical). The NAS isolates had much less virulence gene orthologues than the S. aureus isolates. One third of the virulence genes were detected only in S. aureus. About 100 virulence genes were present in all S. aureus isolates, compared to about 40 to 50 in each NAS isolate. S. simulans differed the most. Several of the virulence genes detected among NAS were harbored only by S. simulans, but it also lacked a number of genes present both in S. agnetis and S. chromogenes. The type of mastitis was not associated with any specific virulence gene profile. It seems that the virulence gene profiles or cumulative number of different virulence genes are not directly associated with the type of mastitis (clinical or subclinical), indicating that host derived factors such as the immune status play a pivotal role in the manifestation of mastitis.}, }
@article {pmid29593678, year = {2018}, author = {Moldovan, MA and Gelfand, MS}, title = {Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {428}, doi = {10.3389/fmicb.2018.00428}, pmid = {29593678}, issn = {1664-302X}, abstract = {The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria Prochlorococcus marinus should be divided into two species. As a control we have confirmed the paraphyletic origin of Yersinia pseudotuberculosis (with embedded, monophyletic Y. pestis) and Burkholderia pseudomallei (with B. mallei). We also demonstrate that by our definition and in accordance with recent studies Escherichia coli and Shigella spp. are one species.}, }
@article {pmid29584736, year = {2018}, author = {Kelly, AC and Ward, TJ}, title = {Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194616}, doi = {10.1371/journal.pone.0194616}, pmid = {29584736}, issn = {1932-6203}, mesh = {Bacterial Toxins/classification/metabolism ; Bayes Theorem ; *Biological Evolution ; Fusarium/classification/*genetics/isolation &amp; purification ; Genetic Variation ; Genetics, Population ; *Genome, Bacterial ; Haplotypes ; Phylogeny ; Plant Diseases/microbiology ; Polymorphism, Single Nucleotide ; Trichothecenes/biosynthesis/classification ; Triticum/metabolism/*microbiology ; }, abstract = {The cereal pathogen Fusarium graminearum is the primary cause of Fusarium head blight (FHB) and a significant threat to food safety and crop production. To elucidate population structure and identify genomic targets of selection within major FHB pathogen populations in North America we sequenced the genomes of 60 diverse F. graminearum isolates. We also assembled the first pan-genome for F. graminearum to clarify population-level differences in gene content potentially contributing to pathogen diversity. Bayesian and phylogenomic analyses revealed genetic structure associated with isolates that produce the novel NX-2 mycotoxin, suggesting a North American population that has remained genetically distinct from other endemic and introduced cereal-infecting populations. Genome scans uncovered distinct signatures of selection within populations, focused in high diversity, frequently recombining regions. These patterns suggested selection for genomic divergence at the trichothecene toxin gene cluster and thirteen additional regions containing genes potentially involved in pathogen specialization. Gene content differences further distinguished populations, in that 121 genes showed population-specific patterns of conservation. Genes that differentiated populations had predicted functions related to pathogenesis, secondary metabolism and antagonistic interactions, though a subset had unique roles in temperature and light sensitivity. Our results indicated that F. graminearum populations are distinguished by dozens of genes with signatures of selection and an array of dispensable accessory genes, suggesting that FHB pathogen populations may be equipped with different traits to exploit the agroecosystem. These findings provide insights into the evolutionary processes and genomic features contributing to population divergence in plant pathogens, and highlight candidate genes for future functional studies of pathogen specialization across evolutionarily and ecologically diverse fungi.}, }
@article {pmid29575852, year = {2018}, author = {Dutkiewicz, J and Zając, V and Sroka, J and Wasiński, B and Cisak, E and Sawczyn, A and Kloc, A and Wójcik-Fatla, A}, title = {Streptococcus suis: a re-emerging pathogen associated with occupational exposure to pigs or pork products. Part II - Pathogenesis.}, journal = {Annals of agricultural and environmental medicine : AAEM}, volume = {25}, number = {1}, pages = {186-203}, doi = {10.26444/aaem/85651}, pmid = {29575852}, issn = {1898-2263}, mesh = {Agricultural Workers' Diseases/*microbiology ; Animals ; Humans ; Occupational Exposure/*adverse effects ; Streptococcal Infections/*microbiology/transmission ; Streptococcus suis/genetics/isolation &amp; purification/pathogenicity/*physiology ; Swine ; Swine Diseases/*microbiology ; Virulence ; Virulence Factors/genetics/metabolism ; Zoonoses/*microbiology/transmission ; }, abstract = {Streptococcus suis is a re-emerging zoonotic pathogen that may cause severe disease, mostly meningitis, in pigs and in humans having occupational contact with pigs and pork, such as farmers, slaughterhose workers and butchers. The first stage of the pathogenic process, similar in pigs and humans, is adherence to and colonisation of mucosal and/or epithelial surface(s) of the host. The second stage is invasion into deeper tissue and extracellular translocation of bacterium in the bloodstream, either free in circulation or attached to the surface of monocytes. If S. suis present in blood fails to cause fatal septicaemia, it is able to progress into the third stage comprising penetration into host's organs, mostly by crossing the blood-brain barrier and/or blood-cerebrospinal fluid barrier to gain access to the central nervous system (CNS) and cause meningitis. The fourth stage is inflammation that plays a key role in the pathogen esis of both systemic and CNS infections caused by S. suis. The pathogen may induce the overproduction of pro-inflammatory cytokines that cause septic shock and/or the recruitment and activation of different leukocyte populations, causing acute inflammation of the CNS. Streptococcus suis can also evoke - through activation of microglial cells, astrocytes and possibly other cell types - a fulminant inflammatory reaction of the brain which leads to intracranial complications, including brain oedema, increased intracranial pressure, cerebrovascular insults, and deafness, as a result of cochlear sepsis. In all stages of the pathogenic process, S. suis interacts with many types of immunocompetent host's cells, such as polymorphonuclear leukocytes, mononuclear macrophages, lymphocytes, dendritic cells and microglia, using a range of versatile virulence factors for evasion of the innate and adaptive immune defence of the host, and for overcoming environmental stress. It is estimated that S. suis produces more than 100 different virulence factors that could be classified into 4 groups: surface components or secreted elements, enzymes, transcription factors or regulatory systems and transporter factors or secretion systems. A major virulence factor is capsular polysaccharide (CPS) that protects bacteria from phagocytosis. However, it hampers adhesion to and invasion of host's cells, release of inflammatory cytokines and formation of the resistant biofilm which, in many cases, is vital for the persistence of bacteria. It has been demonstrated that the arising by mutation unencapsulated S. suis clones, which are more successful in penetration to and propagation within the host's cells, may coexist in the organism of a single host together with those that are encapsulated. Both 'complementary' clones assist each other in the successful colonization of host's tissues and persistence therein. S. suis has an open pan-genome characterized by a frequent gene transfer and a large diversity. Of the genetic determinants of S. suis pathogenicity, the most important are pathogenicity islands (PAI), in particular, a novel DNA segment of 89 kb length with evident pathogenic traits that has been designated as 89K PAI. It has been estimated that more than one-third of the S. suis virulence factors is associated with this PAI. It has been proved that the virulent S. suis strains possess smaller genomes, compared to avirulent ones, but more genes associated with virulence. Overall, the evolution of the species most probably aims towards increased pathogenicity, and hence the most significant task of the current research is an elaboration of a vaccine, efficient both for humans and pigs.}, }
@article {pmid29551444, year = {2018}, author = {Cundon, CC and Ameal, A and Maubecín, E and Bentancor, A}, title = {[Characterization of extraintestinal pathogenic Escherichia coli strains isolated from household dogs and cats in Buenos Aires, Argentina].}, journal = {Revista Argentina de microbiologia}, volume = {50}, number = {3}, pages = {290-294}, doi = {10.1016/j.ram.2017.11.003}, pmid = {29551444}, issn = {0325-7541}, abstract = {The pangenome of Escherichia coli is composed of a conserved core and variable genomic regions. The constant genetic component allows to determine the phylogeny of the microorganism, while genetic variability promoted the emergence of intestinal pathogenic strains and extraintestinal strains. In this study we characterized 85 extraintestinal pathogenic isolates genetically isolated from canines and felines. We used the Clermont scheme that includes intestinal (A and B1) and extraintestinal (B2 and D) phylogroups, virulence markers (pap1-2, pap3-4, sfa, afa, hlyA, aer and cnf) and hybrid pathogens. A percentage of 69.4% of the isolates belonged to phylogroup A; 1.2% to phylogroup B1; 16.5% to phylogroup B2 and 12.9% to phylogroup D. The most commonly found gene was sfa (21/85), followed by pap1-2 and cnf (20/85) and pap3-4 (19/85). No hybrids were detected. Animal isolates should be studied due to the zoonotic potential of the microorganism.}, }
@article {pmid29535689, year = {2018}, author = {Abreu, VAC and Popin, RV and Alvarenga, DO and Schaker, PDC and Hoff-Risseti, C and Varani, AM and Fiore, MF}, title = {Genomic and Genotypic Characterization of Cylindrospermopsis raciborskii: Toward an Intraspecific Phylogenetic Evaluation by Comparative Genomics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {306}, doi = {10.3389/fmicb.2018.00306}, pmid = {29535689}, issn = {1664-302X}, abstract = {Cylindrospermopsis raciborskii is a freshwater cyanobacterial species with increasing bloom reports worldwide that are likely due to factors related to climate change. In addition to the deleterious effects of blooms on aquatic ecosystems, the majority of ecotypes can synthesize toxic secondary metabolites causing public health issues. To overcome the harmful effects of C. raciborskii blooms, it is important to advance knowledge of diversity, genetic variation, and evolutionary processes within populations. An efficient approach to exploring this diversity and understanding the evolution of C. raciborskii is to use comparative genomics. Here, we report two new draft genomes of C. raciborskii (strains CENA302 and CENA303) from Brazilian isolates of different origins and explore their molecular diversity, phylogeny, and evolutionary diversification by comparing their genomes with sequences from other strains available in public databases. The results obtained by comparing seven C. raciborskii and the Raphidiopsis brookii D9 genomes revealed a set of conserved core genes and a variable set of accessory genes, such as those involved in the biosynthesis of natural products, heterocyte glycolipid formation, and nitrogen fixation. Gene cluster arrangements related to the biosynthesis of the antifungal cyclic glycosylated lipopeptide hassallidin were identified in four C. raciborskii genomes, including the non-nitrogen fixing strain CENA303. Shifts in gene clusters involved in toxin production according to geographic origins were observed, as well as a lack of nitrogen fixation (nif) and heterocyte glycolipid (hgl) gene clusters in some strains. Single gene phylogeny (16S rRNA sequences) was congruent with phylogeny based on 31 concatenated housekeeping protein sequences, and both analyses have shown, with high support values, that the species C. raciborskii is monophyletic. This comparative genomics study allowed a species-wide view of the biological diversity of C. raciborskii and in some cases linked genome differences to phenotype.}, }
@article {pmid29522508, year = {2018}, author = {Beck, C and Knoop, H and Steuer, R}, title = {Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes.}, journal = {PLoS genetics}, volume = {14}, number = {3}, pages = {e1007239}, doi = {10.1371/journal.pgen.1007239}, pmid = {29522508}, issn = {1553-7404}, mesh = {Bacterial Proteins/*genetics/metabolism ; Cyanobacteria/*genetics ; Gene Regulatory Networks ; *Genome, Bacterial ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; }, abstract = {Cyanobacteria are a monophyletic phylogenetic group of global importance and have received considerable attention as potential host organisms for the renewable synthesis of chemical bulk products from atmospheric CO2. The cyanobacterial phylum exhibits enormous metabolic diversity with respect to morphology, lifestyle and habitat. As yet, however, research has mostly focused on few model strains and cyanobacterial diversity is insufficiently understood. In this respect, the increasing availability of fully sequenced bacterial genomes opens new and unprecedented opportunities to investigate the genetic inventory of organisms in the context of their pan-genome. Here, we seek understand cyanobacterial diversity using a comparative genome analysis of 77 fully sequenced and assembled cyanobacterial genomes. We use phylogenetic profiling to analyze the co-occurrence of clusters of likely ortholog genes (CLOGs) and reveal novel functional associations between CLOGs that are not captured by co-localization of genes. Going beyond pair-wise co-occurrences, we propose a network approach that allows us to identify modules of co-occurring CLOGs. The extracted modules exhibit a high degree of functional coherence and reveal known as well as previously unknown functional associations. We argue that the high functional coherence observed for the modules is a consequence of the similar-yet-diverse nature of cyanobacteria. Our approach highlights the importance of a multi-strain analysis to understand gene functions and environmental adaptations, with implications beyond the cyanobacterial phylum. The analysis is augmented with a simple toolbox that facilitates further analysis to investigate the co-occurrence neighborhood of specific CLOGs of interest.}, }
@article {pmid29515533, year = {2018}, author = {Dias, GM and Bidault, A and Le Chevalier, P and Choquet, G and Der Sarkissian, C and Orlando, L and Medigue, C and Barbe, V and Mangenot, S and Thompson, CC and Thompson, FL and Jacq, A and Pichereau, V and Paillard, C}, title = {Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {227}, doi = {10.3389/fmicb.2018.00227}, pmid = {29515533}, issn = {1664-302X}, abstract = {The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam Venerupis philippinarum introduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium, Vibrio tapetis, which is also pathogenic to fish. Here we report the first assembly of the complete genome of V. tapetis CECT4600T, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan- and core genomes and to identify putative virulence factors. The V. tapetis core genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I restriction modification system, GGDEF domain proteins, several conjugative plasmids, and a Type IV secretion system. Future research on the coevolutionary arms race between V. tapetis virulence factors and host resistance mechanisms will improve our understanding of how pathogenicity develops in this emerging pathogen.}, }
@article {pmid29509989, year = {2018}, author = {Méric, G and Mageiros, L and Pascoe, B and Woodcock, DJ and Mourkas, E and Lamble, S and Bowden, R and Jolley, KA and Raymond, B and Sheppard, SK}, title = {Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group.}, journal = {Molecular ecology}, volume = {27}, number = {7}, pages = {1524-1540}, doi = {10.1111/mec.14546}, pmid = {29509989}, issn = {1365-294X}, support = {MR/L015080/1//Medical Research Council/United Kingdom ; MR/M501608/1//Medical Research Council/United Kingdom ; }, abstract = {Bacterial plasmids can vary from small selfish genetic elements to large autonomous replicons that constitute a significant proportion of total cellular DNA. By conferring novel function to the cell, plasmids may facilitate evolution but their mobility may be opposed by co-evolutionary relationships with chromosomes or encouraged via the infectious sharing of genes encoding public goods. Here, we explore these hypotheses through large-scale examination of the association between plasmids and chromosomal DNA in the phenotypically diverse Bacillus cereus group. This complex group is rich in plasmids, many of which encode essential virulence factors (Cry toxins) that are known public goods. We characterized population genomic structure, gene content and plasmid distribution to investigate the role of mobile elements in diversification. We analysed coding sequence within the core and accessory genome of 190 B. cereus group isolates, including 23 novel sequences and genes from 410 reference plasmid genomes. While cry genes were widely distributed, those with invertebrate toxicity were predominantly associated with one sequence cluster (clade 2) and phenotypically defined Bacillus thuringiensis. Cry toxin plasmids in clade 2 showed evidence of recent horizontal transfer and variable gene content, a pattern of plasmid segregation consistent with transfer during infectious cooperation. Nevertheless, comparison between clades suggests that co-evolutionary interactions may drive association between plasmids and chromosomes and limit wider transfer of key virulence traits. Proliferation of successful plasmid and chromosome combinations is a feature of specialized pathogens with characteristic niches (Bacillus anthracis, B. thuringiensis) and has occurred multiple times in the B. cereus group.}, }
@article {pmid29495323, year = {2018}, author = {Argemi, X and Nanoukon, C and Affolabi, D and Keller, D and Hansmann, Y and Riegel, P and Baba-Moussa, L and Prévost, G}, title = {Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains.}, journal = {Toxins}, volume = {10}, number = {3}, pages = {}, doi = {10.3390/toxins10030093}, pmid = {29495323}, issn = {2072-6651}, abstract = {Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC) similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8-89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes (hsrA and dfrG, respectively), and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus. Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis.}, }
@article {pmid29491851, year = {2018}, author = {Stice, SP and Stumpf, SD and Gitaitis, RD and Kvitko, BH and Dutta, B}, title = {Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {184}, doi = {10.3389/fmicb.2018.00184}, pmid = {29491851}, issn = {1664-302X}, abstract = {Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA) and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study.}, }
@article {pmid29475869, year = {2018}, author = {Lee, LL and Blumer-Schuette, SE and Izquierdo, JA and Zurawski, JV and Loder, AJ and Conway, JM and Elkins, JG and Podar, M and Clum, A and Jones, PC and Piatek, MJ and Weighill, DA and Jacobson, DA and Adams, MWW and Kelly, RM}, title = {Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, doi = {10.1128/AEM.02694-17}, pmid = {29475869}, issn = {1098-5336}, support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; }, abstract = {Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. strain Rt8.B8 (renamed here Caldicellulosiruptor morganii), Thermoanaerobacter cellulolyticus strain NA10 (renamed here Caldicellulosiruptor naganoensis), and Caldicellulosiruptor sp. strain Wai35.B1 (renamed here Caldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than Caldicellulosiruptor bescii in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of Caldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter, Fervidobacterium, Caloramator, and Clostridium). One enrichment, containing 89.8% Caldicellulosiruptor and 9.7% Caloramator, had a capacity for switchgrass solubilization comparable to that of C. bescii These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.IMPORTANCE The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.}, }
@article {pmid29472910, year = {2018}, author = {Castillo, D and Pérez-Reytor, D and Plaza, N and Ramírez-Araya, S and Blondel, CJ and Corsini, G and Bastías, R and Loyola, DE and Jaña, V and Pavez, L and García, K}, title = {Exploring the Genomic Traits of Non-toxigenic Vibrio parahaemolyticus Strains Isolated in Southern Chile.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {161}, doi = {10.3389/fmicb.2018.00161}, pmid = {29472910}, issn = {1664-302X}, abstract = {Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. As reported in other countries, after the rise and fall of the pandemic strain in Chile, other post-pandemic strains have been associated with clinical cases, including strains lacking the major toxins TDH and TRH. Since the presence or absence of tdh and trh genes has been used for diagnostic purposes and as a proxy of the virulence of V. parahaemolyticus isolates, the understanding of virulence in V. parahaemolyticus strains lacking toxins is essential to detect these strains present in water and marine products to avoid possible food-borne infection. In this study, we characterized the genome of four environmental and two clinical non-toxigenic strains (tdh-, trh-, and T3SS2-). Using whole-genome sequencing, phylogenetic, and comparative genome analysis, we identified the core and pan-genome of V. parahaemolyticus of strains of southern Chile. The phylogenetic tree based on the core genome showed low genetic diversity but the analysis of the pan-genome revealed that all strains harbored genomic islands carrying diverse virulence and fitness factors or prophage-like elements that encode toxins like Zot and RTX. Interestingly, the three strains carrying Zot-like toxin have a different sequence, although the alignment showed some conserved areas with the zot sequence found in V. cholerae. In addition, we identified an unexpected diversity in the genetic architecture of the T3SS1 gene cluster and the presence of the T3SS2 gene cluster in a non-pandemic environmental strain. Our study sheds light on the diversity of V. parahaemolyticus strains from the southern Pacific which increases our current knowledge regarding the global diversity of this organism.}, }
@article {pmid29467746, year = {2018}, author = {Duchaud, E and Rochat, T and Habib, C and Barbier, P and Loux, V and Guérin, C and Dalsgaard, I and Madsen, L and Nilsen, H and Sundell, K and Wiklund, T and Strepparava, N and Wahli, T and Caburlotto, G and Manfrin, A and Wiens, GD and Fujiwara-Nagata, E and Avendaño-Herrera, R and Bernardet, JF and Nicolas, P}, title = {Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {138}, doi = {10.3389/fmicb.2018.00138}, pmid = {29467746}, issn = {1664-302X}, abstract = {Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout (Oncorhynchus mykiss) worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless &quot;open&quot; according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of F. psychrophilum, a particular attention was also paid to plasmids. Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities.}, }
@article {pmid29433445, year = {2018}, author = {Lin, H and Yu, M and Wang, X and Zhang, XH}, title = {Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {135}, doi = {10.1186/s12864-018-4531-2}, pmid = {29433445}, issn = {1471-2164}, support = {41730530//National Natural Science Foundation of China/International ; 41476112//National Natural Science Foundation of China/International ; 41521064//National Natural Science Foundation of China/International ; 41506154//National Natural Science Foundation of China/International ; }, mesh = {Adaptation, Physiological/*genetics ; *Evolution, Molecular ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Seawater/microbiology ; Species Specificity ; Vibrio/classification/*genetics ; }, abstract = {BACKGROUND: Vibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level.<br><br>RESULTS: Two Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal gene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the genus. The chitinase A genes were estimated to have evolved along with the genus, and have undergone significant purifying selective force to conserve the ancestral state.<br><br>CONCLUSIONS: Vibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches.}, }
@article {pmid29429564, year = {2018}, author = {Viver, T and Orellana, L and González-Torres, P and Díaz, S and Urdiain, M and Farías, ME and Benes, V and Kaempfer, P and Shahinpei, A and Ali Amoozegar, M and Amann, R and Antón, J and Konstantinidis, KT and Rosselló-Móra, R}, title = {Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {3}, pages = {198-212}, doi = {10.1016/j.syapm.2017.12.004}, pmid = {29429564}, issn = {1618-0984}, abstract = {The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability. Altogether, the results indicated an open pan-genome for the family Salinibacteraceae, as well as the codification of relevant traits such as diverse rhodopsin genes, CRISPR-Cas systems and spacers, and one T6SS secretion system that could give ecological advantages to an EHB-2 isolate. For the new Salinibacter species, we propose the name Salinibacter altiplanensis sp. nov. (the designated type strain is AN15T=CECT 9105T=IBRC-M 11031T).}, }
@article {pmid29423345, year = {2018}, author = {Delmont, TO and Eren, AM}, title = {Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4320}, doi = {10.7717/peerj.4320}, pmid = {29423345}, issn = {2167-8359}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, abstract = {Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.}, }
@article {pmid29419787, year = {2018}, author = {Heavner, GLW and Mansfeldt, CB and Debs, GE and Hellerstedt, ST and Rowe, AR and Richardson, RE}, title = {Biomarkers' Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM.}, journal = {Microorganisms}, volume = {6}, number = {1}, pages = {}, doi = {10.3390/microorganisms6010013}, pmid = {29419787}, issn = {2076-2607}, support = {T32 GM008283/GM/NIGMS NIH HHS/United States ; }, abstract = {Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM, including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10-12 to 5.9 × 10-10 microelectron equivalents per cell per hour (μeeq/cell∙h). Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R² = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1TM. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1TM. The addition of oxygen induced cell stress that caused respiration rates to decline immediately (>95% decline within one hour). Although transcript levels did decline, they did so more slowly than the respiration rate observed (transcript decay rates between 0.02 and 0.03 per hour). Data from strain-specific probes on the pangenome array strains suggest that a minor DMC strain in KB-1™ that harbors a bvcA homolog preferentially recovered following oxygen stress relative to the dominant, vcrA-containing strain.}, }
@article {pmid29403020, year = {2018}, author = {Wilkinson, DA and O'Donnell, AJ and Akhter, RN and Fayaz, A and Mack, HJ and Rogers, LE and Biggs, PJ and French, NP and Midwinter, AC}, title = {Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2393}, doi = {10.1038/s41598-018-20889-x}, pmid = {29403020}, issn = {2045-2322}, abstract = {Campylobacter hyointestinalis is a member of an emerging group of zoonotic Campylobacter spp. that are increasingly identified in both gastric and non-gastric disease in humans. Here, we discovered C. hyointestinalis in three separate classes of New Zealand ruminant livestock; cattle, sheep and deer. To investigate the relevance of these findings we performed a systematic literature review on global C. hyointestinalis epidemiology and used comparative genomics to better understand and classify members of the species. We found that C. hyointestinalis subspecies hyointestinalis has an open pangenome, with accessory gene contents involved in many essential processes such as metabolism, virulence and defence. We observed that horizontal gene transfer is likely to have played an overwhelming role in species diversification, favouring a public-goods-like mechanism of gene 'acquisition and resampling' over a tree-of-life-like vertical inheritance model of evolution. As a result, simplistic gene-based inferences of taxonomy by similarity are likely to be misleading. Such genomic plasticity will also mean that local evolutionary histories likely influence key species characteristics, such as host-association and virulence. This may help explain geographical differences in reported C. hyointestinalis epidemiology and limits what characteristics may be generalised, requiring further genomic studies of C. hyointestinalis in areas where it causes disease.}, }
@article {pmid29402214, year = {2018}, author = {Darracq, A and Vitte, C and Nicolas, S and Duarte, J and Pichon, JP and Mary-Huard, T and Chevalier, C and Bérard, A and Le Paslier, MC and Rogowsky, P and Charcosset, A and Joets, J}, title = {Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {119}, doi = {10.1186/s12864-018-4490-7}, pmid = {29402214}, issn = {1471-2164}, support = {ANR-10-GENM-0003//Agence Nationale de la Recherche/International ; ANR-10-BTBR-01-01//Agence Nationale de la Recherche/International ; }, mesh = {*Chromosomes, Plant ; Computational Biology/methods ; DNA Copy Number Variations ; DNA Transposable Elements ; Evolution, Molecular ; *Genetic Variation ; *Genome, Plant ; Genomics/methods ; *Inbreeding ; Linkage Disequilibrium ; Poaceae/genetics ; Sequence Analysis, DNA ; Zea mays/*genetics ; }, abstract = {BACKGROUND: Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, they have been only scarcely characterized at the sequence level and the extent of presence/absence variation and relative chromosomal landscape of inbred-specific regions remain to be elucidated.<br><br>RESULTS: De novo genome sequencing of the French F2 maize inbred line revealed 10,044 novel genomic regions larger than 1 kb, making up 88 Mb of DNA, that are present in F2 but not in B73 (PAV). This set of maize PAV sequences allowed us to annotate PAV content and to analyze sequence breakpoints. Using PAV genotyping on a collection of 25 temperate lines, we also analyzed Linkage Disequilibrium in PAVs and flanking regions, and PAV frequencies within maize genetic groups.<br><br>CONCLUSIONS: We highlight the possible role of MMEJ-type double strand break repair in maize PAV formation and discover 395 new genes with transcriptional support. Pattern of linkage disequilibrium within PAVs strikingly differs from this of flanking regions and is in accordance with the intuition that PAVs may recombine less than other genomic regions. We show that most PAVs are ancient, while some are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Characterization of such PAVs will provide useful material for further association genetic studies in European and temperate maize.}, }
@article {pmid29382867, year = {2018}, author = {Kirk, KF and Méric, G and Nielsen, HL and Pascoe, B and Sheppard, SK and Thorlacius-Ussing, O and Nielsen, H}, title = {Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1902}, doi = {10.1038/s41598-018-20135-4}, pmid = {29382867}, issn = {2045-2322}, abstract = {Campylobacter concisus is an emerging pathogen associated with inflammatory bowel disease (IBD), yet little is known about the genetic diversity of C. concisus in relation to host niches and disease. We isolated 104 C. concisus isolates from saliva, mucosal biopsies and faecal samples from 41 individuals (26 IBD, 3 Gastroenteritis (GE), 12 Healthy controls (HC)). Whole genomes were sequenced and the dataset pan-genome examined, and genomic information was used for typing using multi-locus-sequence typing (MLST). C. concisus isolates clustered into two main groups/genomospecies (GS) with 71 distinct sequence types (STs) represented. Sampling site (p < 0.001), rather than disease phenotype (p = 1.00) was associated with particular GS. We identified 97 candidate genes associated with increase or decrease in prevalence during the anatomical descent from the oral cavity to mucosal biopsies to faeces. Genes related to cell wall/membrane biogenesis were more common in oral isolates, whereas genes involved in cell transport, metabolism and secretory pathways were more prevalent in enteric isolates. Furthermore, there was no correlation between individual genetic diversity and clinical phenotype. This study confirms the genetic heterogeneity of C. concisus and provides evidence that genomic variation is related to the source of isolation, but not clinical phenotype.}, }
@article {pmid29371424, year = {2018}, author = {Doron, S and Melamed, S and Ofir, G and Leavitt, A and Lopatina, A and Keren, M and Amitai, G and Sorek, R}, title = {Systematic discovery of antiphage defense systems in the microbial pangenome.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6379}, pages = {}, doi = {10.1126/science.aar4120}, pmid = {29371424}, issn = {1095-9203}, support = {//European Research Council/International ; }, mesh = {Bacillus subtilis/genetics/*immunology/*virology ; Bacteriophages/*immunology/*pathogenicity ; Escherichia coli/genetics/*immunology/*virology ; Genes, Bacterial/*physiology ; Genome, Bacterial ; Multigene Family ; }, abstract = {The arms race between bacteria and phages led to the development of sophisticated antiphage defense systems, including CRISPR-Cas and restriction-modification systems. Evidence suggests that known and unknown defense systems are located in &quot;defense islands&quot; in microbial genomes. Here, we comprehensively characterized the bacterial defensive arsenal by examining gene families that are clustered next to known defense genes in prokaryotic genomes. Candidate defense systems were systematically engineered and validated in model bacteria for their antiphage activities. We report nine previously unknown antiphage systems and one antiplasmid system that are widespread in microbes and strongly protect against foreign invaders. These include systems that adopted components of the bacterial flagella and condensin complexes. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria.}, }
@article {pmid29363431, year = {2018}, author = {Zhao, Y and Sun, C and Zhao, D and Zhang, Y and You, Y and Jia, X and Yang, J and Wang, L and Wang, J and Fu, H and Kang, Y and Chen, F and Yu, J and Wu, J and Xiao, J}, title = {PGAP-X: extension on pan-genome analysis pipeline.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 1}, pages = {36}, doi = {10.1186/s12864-017-4337-7}, pmid = {29363431}, issn = {1471-2164}, mesh = {Chlamydia trachomatis/classification/*genetics ; Computer Graphics ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Software ; Streptococcus pneumoniae/classification/*genetics ; }, abstract = {BACKGROUND: Since PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properly and effectively interpret and visualize the results data is still a challenge.<br><br>RESULT: To well present bacterial genomic characteristics, a novel cross-platform software was developed, named PGAP-X. Four kinds of data analysis modules were developed and integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile analysis, and genetic variants analysis. The results from these analyses can be directly visualized in PGAP-X. The modules for data visualization in PGAP-X include: comparison of genome structure, gene distribution by conservation, pan-genome profile curve and variation on genic and genomic region. Meanwhile, result data produced by other programs with similar function can be imported to be further analyzed and visualized in PGAP-X. To test the performance of PGAP-X, we comprehensively analyzed 14 Streptococcus pneumonia strains and 14 Chlamydia trachomatis. The results show that, S. pneumonia strains have higher diversity on genome structure and gene contents than C. trachomatis strains. In addition, S. pneumonia strains might have suffered many evolutionary events, such genomic rearrangements, frequent horizontal gene transfer, homologous recombination, and other evolutionary process.<br><br>CONCLUSION: Briefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com .}, }
@article {pmid29358148, year = {2018}, author = {Xu, H and Wang, X and Yu, X and Zhang, J and Guo, L and Huang, C and Jiang, X and Li, X and Feng, Y and Zheng, B}, title = {First detection and genomics analysis of KPC-2-producing Citrobacter isolates from river sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {235}, number = {}, pages = {931-937}, doi = {10.1016/j.envpol.2017.12.084}, pmid = {29358148}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*biosynthesis ; China ; Citrobacter/drug effects/enzymology/genetics/*isolation &amp; purification ; DNA, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/genetics ; Genomics ; Genotype ; Geologic Sediments/*microbiology ; Klebsiella pneumoniae ; Multilocus Sequence Typing ; Plasmids ; Polymerase Chain Reaction ; Rivers/microbiology ; beta-Lactamases/*biosynthesis ; }, abstract = {The wide spread of carbapenemase-producing Enterobacteriaceae (CPE) in the environment is an emerging environmental issue with potentially-serious public health implications. However, carbapenemase-producing Citrobacter from environment has rarely been investigated. Here we report the isolation and comparative genomics of carbapenemase-producing Citrobacter isolates from river sediment in China. Potential CPE was isolated by selective MacConkey agar plates containing 2 mg/L meropenem. The presence of carbapenemase genes was detected by PCR and sequencing. The clonal relatedness of Klebsiella pneumoniae carbapenemase (KPC-2)-producing Citrobacter isolates was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Plasmid analysis of KPC-2-producing Citrobacter isolates was performed by S1-PFGE, Southern blotting, and whole genome sequencing. A total of four KPC-2-producing Citrobacter and three Aeromonas isolates were recovered from 54 sediment cultures of Shifeng River. Notably, all KPC-producing isolates were isolated from sampling sites near a waste water treatment plant. Antimicrobial susceptibility testing showed that three of the four sequenced isolates (C1710, C191, and C196) resistant to multiple antibiotics. Genotyping and pan-genome analyses revealed that the C191 and C196 C. freundii isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaKPC-2 gene is located on either IncF or IncN3 plasmids in all isolates. The blaKPC-2 gene of C1710, C181 and C191 was successfully transferred with E. coli EC600 as the recipient strain. In silico analysis further suggested that pKPC-191 is a novel IncF plasmid, with 99% identity to two previously described IncFII plasmids at 71% coverage. We report here the presence of diverse conjugative blaKPC-2 plasmids from environmental Citrobacter isolates, which poses the possible dissemination of antimicrobial resistance into clinical isolates. To our knowledge, this is the first study to culture and characterize KPC-2-producing Citrobacter isolates from river sediments in China.}, }
@article {pmid29355972, year = {2018}, author = {Chen, ECH and Morin, E and Beaudet, D and Noel, J and Yildirir, G and Ndikumana, S and Charron, P and St-Onge, C and Giorgi, J and Krüger, M and Marton, T and Ropars, J and Grigoriev, IV and Hainaut, M and Henrissat, B and Roux, C and Martin, F and Corradi, N}, title = {High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.14989}, pmid = {29355972}, issn = {1469-8137}, abstract = {Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.}, }
@article {pmid29347966, year = {2018}, author = {Zhou, W and Gay, N and Oh, J}, title = {ReprDB and panDB: minimalist databases with maximal microbial representation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {15}, doi = {10.1186/s40168-018-0399-2}, pmid = {29347966}, issn = {2049-2618}, support = {K22 AI119231/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes.<br><br>RESULTS: We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets.<br><br>CONCLUSIONS: reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.}, }
@article {pmid29335547, year = {2018}, author = {Zhao, Q and Feng, Q and Lu, H and Li, Y and Wang, A and Tian, Q and Zhan, Q and Lu, Y and Zhang, L and Huang, T and Wang, Y and Fan, D and Zhao, Y and Wang, Z and Zhou, C and Chen, J and Zhu, C and Li, W and Weng, Q and Xu, Q and Wang, ZX and Wei, X and Han, B and Huang, X}, title = {Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.}, journal = {Nature genetics}, volume = {50}, number = {2}, pages = {278-284}, doi = {10.1038/s41588-018-0041-z}, pmid = {29335547}, issn = {1546-1718}, abstract = {The rich genetic diversity in Oryza sativa and Oryza rufipogon serves as the main sources in rice breeding. Large-scale resequencing has been undertaken to discover allelic variants in rice, but much of the information for genetic variation is often lost by direct mapping of short sequence reads onto the O. sativa japonica Nipponbare reference genome. Here we constructed a pan-genome dataset of the O. sativa-O. rufipogon species complex through deep sequencing and de novo assembly of 66 divergent accessions. Intergenomic comparisons identified 23 million sequence variants in the rice genome. This catalog of sequence variations includes many known quantitative trait nucleotides and will be helpful in pinpointing new causal variants that underlie complex traits. In particular, we systemically investigated the whole set of coding genes using this pan-genome data, which revealed extensive presence and absence of variation among rice accessions. This pan-genome resource will further promote evolutionary and functional studies in rice.}, }
@article {pmid29335226, year = {2018}, author = {Stanborough, T and Fegan, N and Powell, SM and Singh, T and Tamplin, M and Chandry, PS}, title = {Genomic and metabolic characterization of spoilage-associated Pseudomonas species.}, journal = {International journal of food microbiology}, volume = {268}, number = {}, pages = {61-72}, doi = {10.1016/j.ijfoodmicro.2018.01.005}, pmid = {29335226}, issn = {1879-3460}, mesh = {Acetates/metabolism ; Animals ; Cattle ; Esters/metabolism ; Food Contamination/*analysis ; Food Microbiology ; Genome, Bacterial/*genetics ; Genomics ; Meat/*analysis/microbiology ; Polymorphism, Single Nucleotide/genetics ; Pseudomonas fragi/*classification/genetics/isolation &amp; purification/*metabolism ; Volatile Organic Compounds/*analysis ; }, abstract = {Pseudomonas are common spoilage agents of aerobically stored fresh foods. Their ability to cause spoilage is species- and may be strain-specific. To improve our understanding of the meat and milk spoilage agents Pseudomonas fragi and Pseudomonas lundensis, we sequenced the genomes of 12 P. fragi and seven P. lundensis isolates. These genomes provided a dataset for genomic analyses. Key volatile organic compounds (VOCs) produced or metabolised by the isolates were determined during their growth on a beef paste and where possible, metabolic activity was associated with gene repertoire. Genome analyses showed that the isolates included in this work may belong to more than two Pseudomonas species with possible spoilage potential. Pan-genome analyses demonstrated a high degree of diversity among the P. fragi and genetic flexibility and diversity may be traits of both species. Growth of the P. lundensis isolates was characterised by the production of large amounts of 1-undecene, 5-methyl-2-hexanone and methyl-2-butenoic acid. P. fragi isolates produced extensive amounts of methyl and ethyl acetate and the production of methyl esters predominated over ethyl esters. Some of the P. fragi produced extremely low levels of VOCs, highlighting the importance of strain-specific studies in food matrices. Furthermore, although usually not considered to be denitrifiers, all isolates generated molecular nitrogen, indicating that at least some steps of this pathway are intact.}, }
@article {pmid29334898, year = {2018}, author = {Jandrasits, C and Dabrowski, PW and Fuchs, S and Renard, BY}, title = {seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {47}, doi = {10.1186/s12864-017-4401-3}, pmid = {29334898}, issn = {1471-2164}, mesh = {Genomics/*methods ; Phylogeny ; Sequence Alignment/*methods ; Software ; }, abstract = {BACKGROUND: The increasing application of next generation sequencing technologies has led to the availability of thousands of reference genomes, often providing multiple genomes for the same or closely related species. The current approach to represent a species or a population with a single reference sequence and a set of variations cannot represent their full diversity and introduces bias towards the chosen reference. There is a need for the representation of multiple sequences in a composite way that is compatible with existing data sources for annotation and suitable for established sequence analysis methods. At the same time, this representation needs to be easily accessible and extendable to account for the constant change of available genomes.<br><br>RESULTS: We introduce seq-seq-pan, a framework that provides methods for adding or removing new genomes from a set of aligned genomes and uses these to construct a whole genome alignment. Throughout the sequential workflow the alignment is optimized for generating a representative linear presentation of the aligned set of genomes, that enables its usage for annotation and in downstream analyses.<br><br>CONCLUSIONS: By providing dynamic updates and optimized processing, our approach enables the usage of whole genome alignment in the field of pan-genomics. In addition, the sequential workflow can be used as a fast alternative to existing whole genome aligners for aligning closely related genomes. seq-seq-pan is freely available at https://gitlab.com/rki_bioinformatics.}, }
@article {pmid29331569, year = {2018}, author = {López-Hermoso, C and de la Haba, RR and Sánchez-Porro, C and Ventosa, A}, title = {Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {3}, pages = {159-166}, doi = {10.1016/j.syapm.2017.12.001}, pmid = {29331569}, issn = {1618-0984}, abstract = {Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99.6-98.2% 16S rRNA gene sequence similarity) and Salinivibrio costicola subsp. costicola ATCC 35508T (99.0-98.1%). According to the MLSA analyses based on four (gyrB, recA, rpoA and rpoD) and eight (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) concatenated gene sequences, the most closely relatives were S. siamensis JCM 14472T (96.8-95.4% and 94.9-94.7%, respectively) and S. sharmensis DSM 18182T (94.0-92.6% and 92.9-92.7%, respectively). In silico DNA-DNA hybridization (GGDC) and average nucleotide identity (ANI) showed values of 23.3-44.8% and 80.2-91.8%, respectively with the related species demonstrating that the ten isolates constituted a single novel species of the genus Salinivibrio. Its pangenome and core genome consist of 6041 and 1230 genes, respectively. The phylogeny based on the concatenated orthologous core genes revealed that the ten strains form a coherent phylogroup well separated from the rest of the species of the genus Salinivibrio. The major cellular fatty acids of strain AL184T were C16:0 and C18:1. The DNA G+C content range was 51.9-52.5mol% (Tm) and 50.2-50.9mol% (genome). Based on the phylogenetic-phylogenomic, phenotypic and chemotaxonomic data, the ten isolates represent a novel species of the genus Salinivibrio, for which the name Salinivibrio kushneri sp. nov. is proposed. The type strain is AL184T (=CECT 9177T=LMG 29817T).}, }
@article {pmid29325559, year = {2018}, author = {Plissonneau, C and Hartmann, FE and Croll, D}, title = {Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome.}, journal = {BMC biology}, volume = {16}, number = {1}, pages = {5}, doi = {10.1186/s12915-017-0457-4}, pmid = {29325559}, issn = {1741-7007}, support = {12-03//ETH Zurich/ ; 31003A_173265//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)/ ; }, abstract = {BACKGROUND: Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence.<br><br>RESULTS: We constructed and analyzed the pangenome of Zymoseptoria tritici, a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes.<br><br>CONCLUSIONS: The pangenome construction of a highly polymorphic eukaryotic pathogen showed that a single reference genome significantly underestimates the gene space of a species. The substantial accessory genome provides a cradle for adaptive evolution.}, }
@article {pmid29324905, year = {2018}, author = {Sela, U and Euler, CW and Correa da Rosa, J and Fischetti, VA}, title = {Strains of bacterial species induce a greatly varied acute adaptive immune response: The contribution of the accessory genome.}, journal = {PLoS pathogens}, volume = {14}, number = {1}, pages = {e1006726}, doi = {10.1371/journal.ppat.1006726}, pmid = {29324905}, issn = {1553-7374}, support = {8 UL1 TR000043/NH/NIH HHS/United States ; }, mesh = {*Adaptive Immunity ; Adult ; B-Lymphocytes/cytology/*immunology/metabolism/microbiology ; Biomarkers/metabolism ; Cell Proliferation ; Cells, Cultured ; Gene Knockout Techniques ; *Genome, Bacterial ; Humans ; Leukocytes, Mononuclear/cytology/immunology/metabolism/microbiology ; Methicillin Resistance ; Methicillin-Resistant Staphylococcus aureus/genetics/immunology/metabolism/pathogenicity ; Reproducibility of Results ; Species Specificity ; Staphylococcus aureus/genetics/*immunology/metabolism/pathogenicity ; Streptococcus pyogenes/genetics/*immunology/metabolism/pathogenicity ; T-Lymphocytes/cytology/*immunology/metabolism/microbiology ; Th1 Cells/cytology/immunology/metabolism/microbiology ; Th17 Cells/cytology/immunology/metabolism/microbiology ; Vancomycin Resistance ; }, abstract = {A fundamental question in human susceptibility to bacterial infections is to what extent variability is a function of differences in the pathogen species or in individual humans. To focus on the pathogen species, we compared in the same individual the human adaptive T and B cell immune response to multiple strains of two major human pathogens, Staphylococcus aureus and Streptococcus pyogenes. We found wide variability in the acute adaptive immune response induced by various strains of a species, with a unique combination of activation within the two arms of the adaptive response. Further, this was also accompanied by a dramatic difference in the intensity of the specific protective T helper (Th) response. Importantly, the same immune response differences induced by the individual strains were maintained across multiple healthy human donors. A comparison of isogenic phage KO strains, demonstrated that of the pangenome, prophages were the major contributor to inter-strain immune heterogeneity, as the T cell response to the remaining &quot;core genome&quot; was noticeably blunted. Therefore, these findings extend and modify the notion of an adaptive response to a pathogenic bacterium, by implying that the adaptive immune response signature of a bacterial species should be defined either per strain or alternatively to the species' 'core genome', common to all of its strains. Further, our results demonstrate that the acquired immune response variation is as wide among different strains within a single pathogenic species as it is among different humans, and therefore may explain in part the clinical heterogeneity observed in patients infected with the same species.}, }
@article {pmid29321769, year = {2017}, author = {Cortés, MP and Mendoza, SN and Travisany, D and Gaete, A and Siegel, A and Cambiazo, V and Maass, A}, title = {Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2462}, doi = {10.3389/fmicb.2017.02462}, pmid = {29321769}, issn = {1664-302X}, abstract = {Piscirickettsia salmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with highly adverse impact in the Chilean salmon farming industry. The development of effective treatment and control methods for piscireckttsiosis is still a challenge. To meet it the number of studies on P. salmonis has grown in the last couple of years but many aspects of the pathogen's biology are still poorly understood. Studies on its metabolism are scarce and only recently a metabolic model for reference strain LF-89 was developed. We present a new genome-scale model for P. salmonis LF-89 with more than twice as many genes as in the previous model and incorporating specific elements of the fish pathogen metabolism. Comparative analysis with models of different bacterial pathogens revealed a lower flexibility in P. salmonis metabolic network. Through constraint-based analysis, we determined essential metabolites required for its growth and showed that it can benefit from different carbon sources tested experimentally in new defined media. We also built an additional model for strain A1-15972, and together with an analysis of P. salmonis pangenome, we identified metabolic features that differentiate two main species clades. Both models constitute a knowledge-base for P. salmonis metabolism and can be used to guide the efficient culture of the pathogen and the identification of specific drug targets.}, }
@article {pmid29321635, year = {2018}, author = {Brüggemann, H and Jensen, A and Nazipi, S and Aslan, H and Meyer, RL and Poehlein, A and Brzuszkiewicz, E and Al-Zeer, MA and Brinkmann, V and Söderquist, B}, title = {Pan-genome analysis of the genus Finegoldia identifies two distinct clades, strain-specific heterogeneity, and putative virulence factors.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {266}, doi = {10.1038/s41598-017-18661-8}, pmid = {29321635}, issn = {2045-2322}, abstract = {Finegoldia magna, a Gram-positive anaerobic coccus, is an opportunistic pathogen, associated with medical device-related infections. F. magna is the only described species of the genus Finegoldia. We report the analysis of 17 genomes of Finegoldia isolates. Phylogenomic analyses showed that the Finegoldia population can be divided into two distinct clades, with an average nucleotide identity of 90.7%. One clade contains strains of F. magna, whereas the other clade includes more heterogeneous strains, hereafter tentatively named &quot;Finegoldia nericia&quot;. The latter species appears to be more abundant in the human microbiome. Surface structure differences between strains of F. magna and &quot;F. nericia&quot; were detected by microscopy. Strain-specific heterogeneity is high and previously identified host-interacting factors are present only in subsets of &quot;F. nericia&quot; and F. magna strains. However, all genomes encode multiple host factor-binding proteins such as albumin-, collagen-, and immunoglobulin-binding proteins, and two to four copies of CAMP (Christie-Atkins-Munch-Petersen) factors; in accordance, most strains show a positive CAMP reaction for co-hemolysis. Our work sheds new light of the genus Finegoldia and its ability to bind host components. Future research should explore if the genomic differences identified here affect the potential of different Finegoldia species and strains to cause opportunistic infections.}, }
@article {pmid29315617, year = {2018}, author = {Rouleau, FD and Vincent, AT and Charette, SJ}, title = {Genomic and phenotypic characterization of an atypical Aeromonas salmonicida strain isolated from a lumpfish and producing unusual granular structures.}, journal = {Journal of fish diseases}, volume = {41}, number = {4}, pages = {673-681}, doi = {10.1111/jfd.12769}, pmid = {29315617}, issn = {1365-2761}, mesh = {Aeromonas salmonicida/genetics/*physiology ; Animals ; Fish Diseases/*microbiology ; *Fishes ; *Genotype ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; *Phenotype ; Phylogeny ; Quebec ; Sequence Analysis, DNA/veterinary ; }, abstract = {Aeromonas salmonicida strains are roughly classified into two categories, typical and atypical strains. The latter mainly regroup isolates that present unusual phenotypes or hosts, comparatively to the typical strains that belong to the salmonicida subspecies. This study focuses on an uncharacterized atypical strain, M18076-11, isolated from lumpfish (Cyclopterus lumpus) and not part of the four recognized Aeromonas salmonicida subspecies. This isolate presents an unreported phenotype in the A. salmonicida species: the formation of large granular aggregates. Granules are formed of a heterogeneous mix of live and dead cells, with live cells composing the majority of the population. Even if no mechanism was determined to cause cellular aggregation, small globular structures at the cell surface were observed, which might affect granular formation. Pan-genome phylogenetic analysis indicated that this strain groups alongside the masoucida subspecies. However, phenotypic tests showed that these strains have diverging phenotypes, suggesting that M18076-11 might belong to a new subspecies. Also, a pAsal1-like plasmid, which was only reported in strains of the subspecies salmonicida, was discovered in M18076-11. This study sheds light on unsuspected diversity in A. salmonicida subspecies and stresses the need of thorough identification when a new strain is encountered, as unique traits might be discovered.}, }
@article {pmid29312269, year = {2017}, author = {Liu, Y and Zhang, DF and Zhou, X and Xu, L and Zhang, L and Shi, X}, title = {Comprehensive Analysis Reveals Two Distinct Evolution Patterns of Salmonella Flagellin Gene Clusters.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2604}, doi = {10.3389/fmicb.2017.02604}, pmid = {29312269}, issn = {1664-302X}, abstract = {Salmonella is one of the primary causes of foodborne disease, especially Salmonella enterica subsp. enterica (I) which has caused ~99% of clinical salmonellosis cases for humans and domestic mammals. The flagella genes, fliC and fljB, which encode the Salmonella phase 1 and phase 2 antigens respectively, are considered as the Salmonella serotype determinant genes, and contribute to the virulence of Salmonella. However, the evolution of the two flagellin genes is still not well-understood. In this study, the fliC and fljB gene clusters were analyzed among 205 S. enterica subspecies I genomes. The dataset covered 87 different serovars of S. enterica subsp. enterica and included 9 genomes (six serovars) of four other Salmonella subspecies. Based on a pan-genome definition and flanked gene linkages, the fliC and fljB gene clusters were identified in 207 (91 serovars) and 138 (61 serovars) genomes, respectively. A phylogenetic tree constructed based on SNPs (Single Nucleotide Polymorphisms) of core genes were used to reflect the essential evolutionary relationships among various serovars. Congruence analysis was performed among the core genome and each gene of fliC and fljB gene clusters, with only fliA and fliS showing congruence to Salmonella core genome. Congruence was also observed among fliB, fliC/fljB, and fliD genes, and their phylogeny revealed a division into two major groups, which strongly corresponded to monophasic and biphasic serovars. Besides, homologous recombination events referring fliB, fliC, and fliD were found to have mainly occurred within each group. These results suggested two distinct evolutionary patterns of Salmonella flagellin gene clusters. Further insight on the evolutionary implication of the two patterns and a framework for phase variation mechanism are needed to be further processed.}, }
@article {pmid29312242, year = {2017}, author = {Assis, FL and Franco-Luiz, APM and Dos Santos, RN and Campos, FS and Dornas, FP and Borato, PVM and Franco, AC and Abrahao, JS and Colson, P and Scola, B}, title = {Genome Characterization of the First Mimiviruses of Lineage C Isolated in Brazil.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2562}, doi = {10.3389/fmicb.2017.02562}, pmid = {29312242}, issn = {1664-302X}, abstract = {The family Mimiviridae, comprised by giant DNA viruses, has been increasingly studied since the isolation of the Acanthamoeba polyphaga mimivirus (APMV), in 2003. In this work, we describe the genome analysis of two new mimiviruses, each isolated from a distinct Brazilian environment. Furthermore, for the first time, we are reporting the genomic characterization of mimiviruses of group C in Brazil (Br-mimiC), where a predominance of mimiviruses from group A has been previously reported. The genomes of the Br-mimiC isolates Mimivirus gilmour (MVGM) and Mimivirus golden (MVGD) are composed of double-stranded DNA molecules of ∼1.2 Mb, each encoding more than 1,100 open reading frames. Genome functional annotations highlighted the presence of mimivirus group C hallmark genes, such as the set of seven aminoacyl-tRNA synthetases. However, the set of tRNA encoded by the Br-mimiC was distinct from those of other group C mimiviruses. Differences could also be observed in a genome synteny analysis, which demonstrated the presence of inversions and loci translocations at both extremities of Br-mimiC genomes. Both phylogenetic and phyletic analyses corroborate previous results, undoubtedly grouping the new Brazilian isolates into mimivirus group C. Finally, an updated pan-genome analysis of genus Mimivirus was performed including all new genomes available until the present moment. This last analysis showed a slight increase in the number of clusters of orthologous groups of proteins among mimiviruses of group A, with a larger increase after addition of sequences from mimiviruses of groups B and C, as well as a plateau tendency after the inclusion of the last four mimiviruses of group C, including the Br-mimiC isolates. Future prospective studies will help us to understand the genetic diversity among mimiviruses.}, }
@article {pmid29312194, year = {2017}, author = {Kiu, R and Caim, S and Alexander, S and Pachori, P and Hall, LJ}, title = {Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2485}, doi = {10.3389/fmicb.2017.02485}, pmid = {29312194}, issn = {1664-302X}, support = {//Wellcome Trust/United Kingdom ; }, abstract = {Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an &quot;open&quot; pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc), enterotoxin (cpe), and Perfringolysin O (pfo or pfoA), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet) and anti-defensins genes (mprF) were consistently detected in silico (tet: 75%; mprF: 100%). However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.}, }
@article {pmid29310748, year = {2018}, author = {Thibeaux, R and Iraola, G and Ferrés, I and Bierque, E and Girault, D and Soupé-Gilbert, ME and Picardeau, M and Goarant, C}, title = {Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence.}, journal = {Microbial genomics}, volume = {4}, number = {1}, pages = {}, doi = {10.1099/mgen.0.000144}, pmid = {29310748}, issn = {2057-5858}, abstract = {Despite recent advances in our understanding of the genomics of members of the genus Leptospira, little is known on how virulence has emerged in this heterogeneous bacterial genus as well as on the lifestyle of pathogenic members of the genus Leptospira outside animal hosts. Here, we isolated 12 novel species of the genus Leptospira from tropical soils, significantly increasing the number of known species to 35 and finding evidence of highly unexplored biodiversity in the genus. Extended comparative phylogenomics and pan-genome analyses at the genus level by incorporating 26 novel genomes, revealed that, the traditional leptospiral 'pathogens' cluster, as defined by their phylogenetic position, can be split in two groups with distinct virulence potential and accessory gene patterns. These genomic distinctions are strongly linked to the ability to cause or not severe infections in animal models and humans. Our results not only provide new insights into virulence evolution in the members of the genus Leptospira, but also lay the foundations for refining the classification of the pathogenic species.}, }
@article {pmid29310579, year = {2018}, author = {Arboleya, S and Bottacini, F and O'Connell-Motherway, M and Ryan, CA and Ross, RP and van Sinderen, D and Stanton, C}, title = {Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {33}, doi = {10.1186/s12864-017-4388-9}, pmid = {29310579}, issn = {1471-2164}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; 10FDairy//Department of Agriculture, Food and the Marine/International ; }, mesh = {Bifidobacterium longum/*genetics/*metabolism ; Biodiversity ; *Carbohydrate Metabolism ; Databases, Genetic ; Gastrointestinal Microbiome ; *Genes, Bacterial ; *Genome, Bacterial ; Humans ; Infant ; Infant, Newborn ; Phylogeny ; Probiotics ; Quantitative Trait Loci ; *Quantitative Trait, Heritable ; }, abstract = {BACKGROUND: Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach.<br><br>RESULTS: We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO).<br><br>CONCLUSIONS: The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.}, }
@article {pmid29309930, year = {2018}, author = {Schürch, AC and Arredondo-Alonso, S and Willems, RJL and Goering, RV}, title = {Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {24}, number = {4}, pages = {350-354}, doi = {10.1016/j.cmi.2017.12.016}, pmid = {29309930}, issn = {1469-0691}, mesh = {Bacterial Infections/*diagnosis/*epidemiology ; Bacteriological Techniques/methods ; Genotyping Techniques/*methods ; Humans ; Molecular Epidemiology/*methods ; Molecular Typing/*methods ; Polymorphism, Single Nucleotide ; Sequence Homology ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings.<br><br>AIMS: This minireview describes methodologic approaches that have been explored for WGS-based epidemiologic analysis and considers the challenges and pitfalls of data interpretation.<br><br>SOURCES: Personal collection of relevant publications.<br><br>CONTENT: When applying WGS to study the molecular epidemiology of bacterial pathogens, genomic variability between strains is translated into measures of distance by determining single nucleotide polymorphisms in core genome alignments or by indexing allelic variation in hundreds to thousands of core genes, assigning types to unique allelic profiles. Interpreting isolate relatedness from these distances is highly organism specific, and attempts to establish species-specific cutoffs are unlikely to be generally applicable. In cases where single nucleotide polymorphism or core gene typing do not provide the resolution necessary for accurate assessment of the epidemiology of bacterial pathogens, inclusion of accessory gene or plasmid sequences may provide the additional required discrimination.<br><br>IMPLICATIONS: As with all epidemiologic analysis, realizing the full potential of the revolutionary advances in WGS-based approaches requires understanding and dealing with issues related to the fundamental steps of data generation and interpretation.}, }
@article {pmid29298677, year = {2018}, author = {Gámez, G and Castro, A and Gómez-Mejia, A and Gallego, M and Bedoya, A and Camargo, M and Hammerschmidt, S}, title = {The variome of pneumococcal virulence factors and regulators.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {10}, doi = {10.1186/s12864-017-4376-0}, pmid = {29298677}, issn = {1471-2164}, support = {CIEMB-097-13//Committee for Development of Research (CODI)/International ; }, mesh = {Bacterial Proteins/genetics ; Chromosome Mapping ; Genes, Bacterial ; Genes, Regulator ; *Genetic Variation ; Genome, Bacterial ; Phylogeny ; Streptococcus pneumoniae/classification/*genetics/pathogenicity ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: In recent years, the idea of a highly immunogenic protein-based vaccine to combat Streptococcus pneumoniae and its severe invasive infectious diseases has gained considerable interest. However, the target proteins to be included in a vaccine formulation have to accomplish several genetic and immunological characteristics, (such as conservation, distribution, immunogenicity and protective effect), in order to ensure its suitability and effectiveness. This study aimed to get comprehensive insights into the genomic organization, population distribution and genetic conservation of all pneumococcal surface-exposed proteins, genetic regulators and other virulence factors, whose important function and role in pathogenesis has been demonstrated or hypothesized.<br><br>RESULTS: After retrieving the complete set of DNA and protein sequences reported in the databases GenBank, KEGG, VFDB, P2CS and Uniprot for pneumococcal strains whose genomes have been fully sequenced and annotated, a comprehensive bioinformatic analysis and systematic comparison has been performed for each virulence factor, stand-alone regulator and two-component regulatory system (TCS) encoded in the pan-genome of S. pneumoniae. A total of 25 S. pneumoniae strains, representing different pneumococcal phylogenetic lineages and serotypes, were considered. A set of 92 different genes and proteins were identified, classified and studied to construct a pan-genomic variability map (variome) for S. pneumoniae. Both, pneumococcal virulence factors and regulatory genes, were well-distributed in the pneumococcal genome and exhibited a conserved feature of genome organization, where replication and transcription are co-oriented. The analysis of the population distribution for each gene and protein showed that 49 of them are part of the core genome in pneumococci, while 43 belong to the accessory-genome. Estimating the genetic variability revealed that pneumolysin, enolase and Usp45 (SP_2216 in S. p. TIGR4) are the pneumococcal virulence factors with the highest conservation, while TCS08, TCS05, and TCS02 represent the most conserved pneumococcal genetic regulators.<br><br>CONCLUSIONS: The results identified well-distributed and highly conserved pneumococcal virulence factors as well as regulators, representing promising candidates for a new generation of serotype-independent protein-based vaccine(s) to combat pneumococcal infections.}, }
@article {pmid29277863, year = {2018}, author = {Setubal, JC and Almeida, NF and Wattam, AR}, title = {Comparative Genomics for Prokaryotes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {55-78}, doi = {10.1007/978-1-4939-7463-4_3}, pmid = {29277863}, issn = {1940-6029}, support = {HHSN272201400027C/AI/NIAID NIH HHS/United States ; }, abstract = {Bacteria and archaea, collectively known as prokaryotes, have in general genomes that are much smaller than those of eukaryotes. As a result, thousands of these genomes have been sequenced. In prokaryotes, gene architecture lacks the intron-exon structure of eukaryotic genes (with an occasional exception). These two facts mean that there is an abundance of data for prokaryotic genomes, and that they are easier to study than the more complex eukaryotic genomes. In this chapter, we provide an overview of genome comparison tools that have been developed primarily (sometimes exclusively) for prokaryotic genomes. We cover methods that use only the DNA sequences, methods that use only the gene content, and methods that use both data types.}, }
@article {pmid29277862, year = {2018}, author = {Zekic, T and Holley, G and Stoye, J}, title = {Pan-Genome Storage and Analysis Techniques.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {29-53}, doi = {10.1007/978-1-4939-7463-4_2}, pmid = {29277862}, issn = {1940-6029}, abstract = {Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the concept has spread to a variety of species, such as plants or viruses. Characterizing a pan-genome provides insights into intra-species evolution, functions, and diversity. However, researchers face challenges such as processing and maintaining large datasets while providing accurate and efficient analysis approaches. Comparative genomics methods are required for detecting conserved and unique regions between a set of genomes. This chapter gives an overview of tools available for indexing pan-genomes, identifying the sub-regions of a pan-genome and offering a variety of downstream analysis methods. These tools are categorized into two groups, gene-based and sequence-based, according to the pan-genome identification method. We highlight the differences, advantages, and disadvantages between the tools, and provide information about the general workflow, methodology of pan-genome identification, covered functionalities, usability and availability of the tools.}, }
@article {pmid29277352, year = {2017}, author = {Valeriano, VDV and Oh, JK and Bagon, BB and Kim, H and Kang, DK}, title = {Comparative genomic analysis of Lactobacillus mucosae LM1 identifies potential niche-specific genes and pathways for gastrointestinal adaptation.}, journal = {Genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ygeno.2017.12.009}, pmid = {29277352}, issn = {1089-8646}, abstract = {Lactobacillus mucosae is currently of interest as putative probiotics due to their metabolic capabilities and ability to colonize host mucosal niches. L. mucosae LM1 has been studied in its functions in cell adhesion and pathogen inhibition, etc. It demonstrated unique abilities to use energy from carbohydrate and non-carbohydrate sources. Due to these functions, we report the first complete genome sequence of an L. mucosae strain, L. mucosae LM1. Analysis of the pan-genome in comparison with closely-related Lactobacillus species identified a complete glycogen metabolism pathway, as well as folate biosynthesis, complementing previous proteomic data on the LM1 strain. It also revealed common and unique niche-adaptation genes among the various L. mucosae strains. The aim of this study was to derive genomic information that would reveal the probable mechanisms underlying the probiotic effect of L. mucosae LM1, and provide a better understanding of the nature of L. mucosae sp.}, }
@article {pmid29272410, year = {2018}, author = {Brito, PH and Chevreux, B and Serra, CR and Schyns, G and Henriques, AO and Pereira-Leal, JB}, title = {Genetic Competence Drives Genome Diversity in Bacillus subtilis.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {108-124}, doi = {10.1093/gbe/evx270}, pmid = {29272410}, issn = {1759-6653}, abstract = {Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them.}, }
@article {pmid29270248, year = {2017}, author = {Birkeland, NK and Schönheit, P and Poghosyan, L and Fiebig, A and Klenk, HP}, title = {Complete genome sequence analysis of Archaeoglobus fulgidus strain 7324 (DSM 8774), a hyperthermophilic archaeal sulfate reducer from a North Sea oil field.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {79}, doi = {10.1186/s40793-017-0296-5}, pmid = {29270248}, issn = {1944-3277}, abstract = {Archaeoglobus fulgidus is the type species of genus Archaeoglobus Stetter 1998, a hyperthermophilic sulfate reducing group within the Archaeoglobi class of the euryarchaeota phylum. Members of this genus grow heterotrophically or chemolithoautotrophically with sulfate or thiosulfate as electron acceptors. Except for A. fulgidus strain 7324 and the candidate species &quot;Archaeoglobus lithotrophicus&quot;, which both originate from deep oil-fields, the other members of this genus have been recovered from marine hydrothermal systems. Here we describe the features of the A. fulgidus strain 7324 genome as compared to the A. fulgidus VC16 type strain. The 2.3 Mbp genome sequence of strain 7324 shares about 93.5% sequence identity with that of strain VC16T but is about 138 Kbp longer, which is mostly due to two large 'insertions' carrying one extra cdc6 (cell-cycle control protein 6) gene, extra CRISPR elements and mobile genetic elements, a high-GC ncRNA gene (hgcC) and a large number of hypothetical gene functions. A comparison with four other Archaeoglobus spp. genomes identified 1001 core Archaeoglobus genes and more than 2900 pan-genome orthologous genes.}, }
@article {pmid29270162, year = {2017}, author = {Gomila, M and Busquets, A and Mulet, M and García-Valdés, E and Lalucat, J}, title = {Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2422}, doi = {10.3389/fmicb.2017.02422}, pmid = {29270162}, issn = {1664-302X}, abstract = {The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that &quot;P. coronafaciens&quot; should be revived as a nomenspecies.}, }
@article {pmid29259172, year = {2017}, author = {Gordon, SP and Contreras-Moreira, B and Woods, DP and Des Marais, DL and Burgess, D and Shu, S and Stritt, C and Roulin, AC and Schackwitz, W and Tyler, L and Martin, J and Lipzen, A and Dochy, N and Phillips, J and Barry, K and Geuten, K and Budak, H and Juenger, TE and Amasino, R and Caicedo, AL and Goodstein, D and Davidson, P and Mur, LAJ and Figueroa, M and Freeling, M and Catalan, P and Vogel, JP}, title = {Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {2184}, doi = {10.1038/s41467-017-02292-8}, pmid = {29259172}, issn = {2041-1723}, mesh = {Biological Variation, Population/*genetics ; Brachypodium/*genetics ; Chromosomes, Plant/genetics ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Genetic Variation/genetics ; Genome, Plant/*genetics ; Phylogeny ; Synteny/genetics ; }, abstract = {While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.}, }
@article {pmid29247056, year = {2018}, author = {Timms, VJ and Rockett, R and Bachmann, NL and Martinez, E and Wang, Q and Chen, SC and Jeoffreys, N and Howard, PJ and Smith, A and Adamson, S and Gilmour, R and Sheppeard, V and Sintchenko, V}, title = {Genome Sequencing Links Persistent Outbreak of Legionellosis in Sydney (New South Wales, Australia) to an Emerging Clone of Legionella pneumophila Sequence Type 211.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {5}, pages = {}, doi = {10.1128/AEM.02020-17}, pmid = {29247056}, issn = {1098-5336}, abstract = {The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions, the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using single-nucleotide polymorphism (SNP)-based core-genome multilocus sequencing typing (MLST) and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and those in suburb 1. These isolates were designated the &quot;main cluster&quot; and consisted of isolates from two patients from the CBD March outbreak, one patient and one tower isolate from suburb 1, and isolates from two cooling towers and three patients from the CBD May outbreak. All main cluster isolates were sequence type 211 (ST211), which previously has only been reported in Canada. Significantly, pangenome analysis identified mobile genetic elements containing a unique type IV A F-type secretion system (T4ASS), which was specific to the main cluster, and cocirculating clinical strains, suggesting a potential mechanism for increased fitness and persistence of the outbreak clone. Genome sequencing enabled linking of the geographically dispersed environmental sources of infection among the spatially and temporally coinciding cases of legionellosis in a highly populated urban setting. The discovery of a unique T4ASS emphasizes the role of genome recombination in the emergence of successful Lp1 clones.IMPORTANCE A new emerging clone has been responsible for a prolonged legionellosis outbreak in Sydney, Australia. The use of whole-genome sequencing linked two outbreaks thought to be unrelated and confirmed the outliers. These findings led to the resampling and subsequent identification of the source, guiding public health actions and bringing the outbreak to a close. Significantly, the outbreak clone was identified as sequence type 211 (ST211). Our study reports this ST in the Southern Hemisphere and presents a description of ST211 genomes from both clinical and environmental isolates. A unique mobile genetic element containing a type IV secretion system was identified in Lp1 ST211 isolates linked to the main cluster and Lp1 ST42 isolates that were cocirculating at the time of the outbreak.}, }
@article {pmid29247013, year = {2018}, author = {Kwong, JC and Chow, EPF and Stevens, K and Stinear, TP and Seemann, T and Fairley, CK and Chen, MY and Howden, BP}, title = {Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study.}, journal = {Sexually transmitted infections}, volume = {94}, number = {2}, pages = {151-157}, doi = {10.1136/sextrans-2017-053287}, pmid = {29247013}, issn = {1472-3263}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/pharmacology ; Cohort Studies ; DNA, Bacterial ; *Drug Resistance, Microbial ; Gonorrhea/epidemiology/*transmission ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Multilocus Sequence Typing ; Neisseria gonorrhoeae/drug effects/*genetics/isolation &amp; purification ; Prospective Studies ; Sexual Partners ; Sexual and Gender Minorities/*statistics &amp; numerical data ; *Whole Genome Sequencing ; Young Adult ; }, abstract = {OBJECTIVES: Drug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence (NG-MAST). We therefore aimed to systematically investigate the transmission of N. gonorrhoeae between men in sexual partnerships using WGS to compare isolates and their resistance to antibiotics at a genome level.<br><br>METHODS: 458 couples from a large prospective cohort of men who have sex with men (MSM) tested for gonorrhoea together between 2005 and 2014 were included, and WGS was conducted on all isolates from couples where both men were culture-positive for N. gonorrhoeae. Resistance-determining sequences were identified from genome assemblies, and comparison of isolates between and within individuals was performed by pairwise single nucleotide polymorphism and pangenome comparisons, and in silico predictions of NG-MAST and MLST.<br><br>RESULTS: For 33 of 34 (97%; 95% CI 85% to 100%) couples where both partners were positive for gonorrhoea, the resistance-determining genes and mutations were identical in isolates from each partner (94 isolates in total). Resistance determinants in isolates from 23 of 23 (100%; 95% CI 86% to 100%) men with multisite infections were also identical within an individual. These partner and within-host isolates were indistinguishable by NG-MAST, MLST and whole genomic comparisons.<br><br>CONCLUSIONS: These data support the transmission of antibiotic-resistant strains between sexual partners as a key driver of resistance rates in gonorrhoea among MSM. This improved understanding of the transmission dynamics of N. gonorrhoeae between sexual partners will inform treatment and prevention guidelines.}, }
@article {pmid29240874, year = {2018}, author = {Rasheed, A and Mujeeb-Kazi, A and Ogbonnaya, FC and He, Z and Rajaram, S}, title = {Wheat genetic resources in the post-genomics era: promise and challenges.}, journal = {Annals of botany}, volume = {121}, number = {4}, pages = {603-616}, doi = {10.1093/aob/mcx148}, pmid = {29240874}, issn = {1095-8290}, abstract = {Background: Wheat genetic resources have been used for genetic improvement since 1876, when Stephen Wilson (Transactions and Proceedings of the Botanical Society of Edinburgh 12: 286) consciously made the first wide hybrid involving wheat and rye in Scotland. Wide crossing continued with sporadic attempts in the first half of 19th century and became a sophisticated scientific discipline during the last few decades with considerable impact in farmers' fields. However, a large diversity of untapped genetic resources could contribute in meeting future wheat production challenges.<br><br>Perspectives and Conclusion: Recently the complete reference genome of hexaploid (Chinese Spring) and tetraploid (Triticum turgidum ssp. dicoccoides) wheat became publicly available coupled with on-going international efforts on wheat pan-genome sequencing. We anticipate that an objective appraisal is required in the post-genomics era to prioritize genetic resources for use in the improvement of wheat production if the goal of doubling yield by 2050 is to be met. Advances in genomics have resulted in the development of high-throughput genotyping arrays, improved and efficient methods of gene discovery, genomics-assisted selection and gene editing using endonucleases. Likewise, ongoing advances in rapid generation turnover, improved phenotyping, envirotyping and analytical methods will significantly accelerate exploitation of exotic genes and increase the rate of genetic gain in breeding. We argue that the integration of these advances will significantly improve the precision and targeted identification of potentially useful variation in the wild relatives of wheat, providing new opportunities to contribute to yield and quality improvement, tolerance to abiotic stresses, resistance to emerging biotic stresses and resilience to weather extremes.}, }
@article {pmid29238330, year = {2017}, author = {Henri, C and Leekitcharoenphon, P and Carleton, HA and Radomski, N and Kaas, RS and Mariet, JF and Felten, A and Aarestrup, FM and Gerner Smidt, P and Roussel, S and Guillier, L and Mistou, MY and Hendriksen, RS}, title = {An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2351}, doi = {10.3389/fmicb.2017.02351}, pmid = {29238330}, issn = {1664-302X}, abstract = {Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST). Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of L. monocytogenes. Methods: The clustering methods were evaluated on a collection of 207 L. monocytogenes genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses. Results: The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering. Conclusion: Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of L. monocytogenes. The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories.}, }
@article {pmid29237792, year = {2018}, author = {Knetsch, CW and Kumar, N and Forster, SC and Connor, TR and Browne, HP and Harmanus, C and Sanders, IM and Harris, SR and Turner, L and Morris, T and Perry, M and Miyajima, F and Roberts, P and Pirmohamed, M and Songer, JG and Weese, JS and Indra, A and Corver, J and Rupnik, M and Wren, BW and Riley, TV and Kuijper, EJ and Lawley, TD}, title = {Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans.}, journal = {Journal of clinical microbiology}, volume = {56}, number = {3}, pages = {}, doi = {10.1128/JCM.01384-17}, pmid = {29237792}, issn = {1098-660X}, support = {G0902453//Medical Research Council/United Kingdom ; MR/K000551/1//Medical Research Council/United Kingdom ; MR/L015080/1//Medical Research Council/United Kingdom ; }, abstract = {The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associated C. difficile RT027 lineage, the community-associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248 C. difficile RT078 strains from 22 countries. Our results demonstrate limited geographical clustering for C. difficile RT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome of C. difficile RT078. Thus, bidirectional spread of C. difficile RT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the &quot;One Health&quot; concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.}, }
@article {pmid29216329, year = {2017}, author = {Sekizuka, T and Ogasawara, Y and Ohkusa, T and Kuroda, M}, title = {Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189319}, doi = {10.1371/journal.pone.0189319}, pmid = {29216329}, issn = {1932-6203}, mesh = {Bacterial Proteins/genetics/metabolism ; Colitis, Ulcerative/*microbiology ; Fusobacterium/genetics/*isolation &amp; purification ; *Genome, Bacterial ; Humans ; *Transcriptome ; }, abstract = {Fusobacterium spp. present in the oral and gut flora is carcinogenic and is associated with the risk of pancreatic and colorectal cancers. Fusobacterium spp. is also implicated in a broad spectrum of human pathologies, including Crohn's disease and ulcerative colitis (UC). Here we report the complete genome sequence of Fusobacterium varium Fv113-g1 (genome size, 3.96 Mb) isolated from a patient with UC. Comparative genome analyses totally suggested that Fv113-g1 is basically assigned as F. varium, in particular, it could be reclassified as notable F. varium subsp. similar to F. ulcerans because of partial shared orthologs. Compared with the genome sequences of F. varium ATCC 27725 (genome size, 3.30 Mb) and other strains of Fusobacterium spp., Fv113-g1 possesses many accessary pan-genome sequences with noteworthy multiple virulence factors, including 44 autotransporters (type V secretion system, T5SS) and 13 Fusobacterium adhesion (FadA) paralogs involved in potential mucosal inflammation. Indeed, transcriptome analysis demonstrated that Fv113-g1-specific accessary genes, such as multiple T5SS and fadA paralogs, showed notably increased expression with D-MEM cultivation than with brain heart infusion broth. This implied that growth condition may enhance the expression of such potential virulence factors, leading to remarkable survival against other gut microorganisms and to the pathogenicity to human intestinal epithelium.}, }
@article {pmid29208130, year = {2017}, author = {Husain, F and Tang, K and Veeranagouda, Y and Boente, R and Patrick, S and Blakely, G and Wexler, HM}, title = {Novel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation.}, journal = {Microbial genomics}, volume = {3}, number = {11}, pages = {}, doi = {10.1099/mgen.0.000136}, pmid = {29208130}, issn = {2057-5858}, support = {R21 AI109545/AI/NIAID NIH HHS/United States ; }, abstract = {Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B. fragilis 638R. In one example, the transfer of a segment of ~435 Kb/356 genes replaced ~413 Kb/326 genes of the B. fragilis 638R chromosome. In addition to transfer of antibiotic resistance genes, these transfers (1) replaced complete divergent polysaccharide biosynthesis loci; (2) replaced DNA inversion-controlled intergenic shufflons (that control expression of genes encoding starch utilization system outer membrane proteins) with more complex, divergent shufflons; and (3) introduced additional intergenic shufflons encoding divergent Type 1 restriction/modification systems. Conjugative transposon-like genes within a transferred segment and within a putative integrative conjugative element (ICE5) ~45 kb downstream from the transferred segment both encode proteins that may be involved in the observed transfer. These data indicate that chromosomal transfer is a driver of antigenic diversity and nutrient adaptation in Bacteroides that (1) contributes to the dissemination of the extensive B. fragilis pan-genome, (2) allows rapid adaptation to a changing environment and (3) can confer pathogenic characteristics to host symbionts.}, }
@article {pmid29205771, year = {2018}, author = {Hurgobin, B and Golicz, AA and Bayer, PE and Chan, CK and Tirnaz, S and Dolatabadian, A and Schiessl, SV and Samans, B and Montenegro, JD and Parkin, IAP and Pires, JC and Chalhoub, B and King, GJ and Snowdon, R and Batley, J and Edwards, D}, title = {Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus.}, journal = {Plant biotechnology journal}, volume = {16}, number = {7}, pages = {1265-1274}, doi = {10.1111/pbi.12867}, pmid = {29205771}, issn = {1467-7652}, abstract = {Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.}, }
@article {pmid29204317, year = {2017}, author = {Cheng, G and Lu, Q and Ma, L and Zhang, G and Xu, L and Zhou, Z}, title = {BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3948}, doi = {10.7717/peerj.3948}, pmid = {29204317}, issn = {2167-8359}, abstract = {Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.}, }
@article {pmid29198880, year = {2018}, author = {Fuchs, S and Mehlan, H and Bernhardt, J and Hennig, A and Michalik, S and Surmann, K and Pané-Farré, J and Giese, A and Weiss, S and Backert, L and Herbig, A and Nieselt, K and Hecker, M and Völker, U and Mäder, U}, title = {AureoWiki ̵ The repository of the Staphylococcus aureus research and annotation community.}, journal = {International journal of medical microbiology : IJMM}, volume = {308}, number = {6}, pages = {558-568}, doi = {10.1016/j.ijmm.2017.11.011}, pmid = {29198880}, issn = {1618-0607}, abstract = {In light of continuously accumulating data and knowledge on major human pathogens, comprehensive and up-to-date sources of easily accessible information are urgently required. The AureoWiki database (http://aureowiki.med.uni-greifswald.de) provides detailed information on the genes and proteins of clinically and experimentally relevant S. aureus strains, currently covering NCTC 8325, COL, Newman, USA300_FPR3757, and N315. By implementing a pan-genome approach, AureoWiki facilitates the transfer of knowledge gained in studies with different S. aureus strains, thus supporting functional annotation and better understanding of this organism. All data related to a given gene or gene product is compiled on a strain-specific gene page. The gene pages contain sequence-based information complemented by data on, for example, protein function and localization, transcriptional regulation, and gene expression. The information provided is connected via links to other databases and published literature. Importantly, orthologous genes of the individual strains, which are linked by a pan-genome gene identifier and a unified gene name, are presented side by side using strain-specific tabs. The respective pan-genome gene page contains an orthologue table for 32 S. aureus strains, a multiple-strain genome viewer, a protein sequence alignment as well as other comparative information. The data collected in AureoWiki is also accessible through various download options in order to support bioinformatics applications. In addition, based on two large-scale gene expression data sets, AureoWiki provides graphical representations of condition-dependent mRNA levels and protein profiles under various laboratory and infection-related conditions.}, }
@article {pmid29187731, year = {2017}, author = {Yang, N and Xu, XW and Wang, RR and Peng, WL and Cai, L and Song, JM and Li, W and Luo, X and Niu, L and Wang, Y and Jin, M and Chen, L and Luo, J and Deng, M and Wang, L and Pan, Q and Liu, F and Jackson, D and Yang, X and Chen, LL and Yan, J}, title = {Contributions of Zea mays subspecies mexicana haplotypes to modern maize.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1874}, doi = {10.1038/s41467-017-02063-5}, pmid = {29187731}, issn = {2041-1723}, mesh = {*Evolution, Molecular ; Genome, Plant/*genetics ; Haplotypes ; Zea mays/*genetics ; }, abstract = {Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10-8 ~3.87 × 10-8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.}, }
@article {pmid29183332, year = {2017}, author = {Hall, AB and Yassour, M and Sauk, J and Garner, A and Jiang, X and Arthur, T and Lagoudas, GK and Vatanen, T and Fornelos, N and Wilson, R and Bertha, M and Cohen, M and Garber, J and Khalili, H and Gevers, D and Ananthakrishnan, AN and Kugathasan, S and Lander, ES and Blainey, P and Vlamakis, H and Xavier, RJ and Huttenhower, C}, title = {A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.}, journal = {Genome medicine}, volume = {9}, number = {1}, pages = {103}, doi = {10.1186/s13073-017-0490-5}, pmid = {29183332}, issn = {1756-994X}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; U54DE023798//National Institutes of Health (US)/ ; P30 DK043351/DK/NIDDK NIH HHS/United States ; P30DK43351//National Institute of Diabetes and Digestive and Kidney Diseases/ ; R01 DK092405/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; K99 DK113224/DK/NIDDK NIH HHS/United States ; R01DK92405//National Institute of Diabetes and Digestive and Kidney Diseases/ ; MCB-1453942//National Science Foundation (US)/ ; }, mesh = {Adult ; Aged ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Middle Aged ; Oxidative Stress ; Phylogeny ; Ruminococcus/genetics/*isolation &amp; purification ; Species Specificity ; Young Adult ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.<br><br>METHODS: We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn.<br><br>RESULTS: We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut.<br><br>CONCLUSIONS: This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.}, }
@article {pmid29170656, year = {2017}, author = {Lira, F and Berg, G and Martínez, JL}, title = {Double-Face Meets the Bacterial World: The Opportunistic Pathogen Stenotrophomonas maltophilia.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2190}, doi = {10.3389/fmicb.2017.02190}, pmid = {29170656}, issn = {1664-302X}, abstract = {Most studies on bacterial virulence focus on the pathogen itself. However, it is important to recall that the in-host behavior and the virulence of bacterial pathogens constitute a complex situation that depends on both the microorganisms and the infected host. While healthy people (the community) is infected by classical pathogenic microorganisms, able to cope with the anti-infection defenses of the host, in the case of people with basal diseases, debilitated or immunodepressed, the range of pathogens able to cause infection is wider and includes the so-named opportunistic pathogens, which lack the inherent ability to cause disease in healthy hosts and rarely produce infections in the community. Some of the most relevant opportunistic pathogens, as Stenotrophomonas maltophilia, have an environmental origin and, in occasions, present interesting biotechnological properties. Consequently, it is important knowing whether S. maltophilia isolates recovered from infections constitute a specific phylogenetic branch that has evolved toward acquiring a virulent phenotype as it happens in the case of classical pathogens or rather, any member of this bacterial species is capable of producing infection and its pathogenic behavior is mainly a consequence of the host situation. To address this question, we analyzed a set of environmental and clinical S. maltophilia strains. Our results indicate that this opportunistic pathogen presents a large core genome and that the distribution of genes in general, and of known virulence determinants in particular, is similar among environmental and clinical isolates. The majority of genes not belonging to the S. maltophilia core genome are present in just one or two of the analyzed strains. This indicates that, more than speciation into different lineages (virulent and environmental), the evolution of S. maltophilia is based in the strain-specific acquisition of genes, likely involved in the adaptation of this bacterial species to different microniches. In addition, both environmental and clinical isolates present low susceptibility to several antimicrobials. Altogether our results support that S. maltophilia does not present a specific evolutionary branch toward virulence and most likely infection is mainly the consequence of the impaired anti-infective response of the infected patients.}, }
@article {pmid29164068, year = {2017}, author = {Nourdin-Galindo, G and Sánchez, P and Molina, CF and Espinoza-Rojas, DA and Oliver, C and Ruiz, P and Vargas-Chacoff, L and Cárcamo, JG and Figueroa, JE and Mancilla, M and Maracaja-Coutinho, V and Yañez, AJ}, title = {Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {459}, doi = {10.3389/fcimb.2017.00459}, pmid = {29164068}, issn = {2235-2988}, mesh = {Animals ; Bacterial Proteins/genetics ; Fish Diseases/microbiology ; Fishes/microbiology ; Gene Ontology ; Genes, Bacterial/*genetics ; Genome Size ; Genome, Bacterial/*genetics ; *Genotype ; Host-Pathogen Interactions ; Kinetics ; Metabolic Networks and Pathways/genetics ; Operon ; Phylogeny ; Piscirickettsia/*genetics/growth &amp; development/isolation &amp; purification/pathogenicity ; Piscirickettsiaceae Infections/microbiology/veterinary ; Virulence Factors/genetics ; Whole Genome Sequencing ; }, abstract = {Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these genes could be directly associated with inter-genogroup differences in pathogenesis and host-pathogen interactions, information that could be useful in designing novel strategies for diagnosing and controlling P. salmonis infection.}, }
@article {pmid29154929, year = {2017}, author = {Sankarasubramanian, J and Vishnu, US and Gunasekaran, P and Rajendhran, J}, title = {Identification of genetic variants of Brucella spp. through genome-wide association studies.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {56}, number = {}, pages = {92-98}, doi = {10.1016/j.meegid.2017.11.016}, pmid = {29154929}, issn = {1567-7257}, mesh = {Animals ; Brucella/*classification/*genetics ; Brucellosis/microbiology ; Computational Biology/methods ; Genetic Association Studies ; *Genetic Variation ; *Genome, Bacterial ; *Genome-Wide Association Study ; Genomics/methods ; Phylogeny ; Polymorphism, Single Nucleotide ; Zoonoses/microbiology ; }, abstract = {Brucellosis is an important zoonotic disease caused by Brucella spp. We present a phylogeny of 552 strains based on genome-wide single nucleotide polymorphisms (SNPs) determined by an alignment-free k-mer approach. A total of 138,029 SNPs were identified from 552 Brucella genomes. Of these, 31,152 and 106,877 were core and non-core SNPs, respectively. Based on pan-genome analysis 11,937 and 972 genes were identified as pan and core genome, respectively. The pan-genome-wide analysis studies (Pan-GWAS) could not identify the group-specific variants in Brucella spp. Therefore, we focused on SNP based genome-wide association studies (SNP-GWAS) to identify the species-specific genetic determinants in Brucella spp. Phylogenetic tree representing eleven recognized Brucella spp. showed 16 major lineages. We identified 143 species-specific SNPs in Brucella abortus that are conserved in 311 B. abortus genomes. Of these, 141 species-specific SNPs were confined in the positively significant SNPs of B. abortus using SNP-GWAS. Since conserved in all the B. abortus genomes studied, these SNPs might have originated very early during the evolution of B. abortus and might be responsible for the evolution of B. abortus with cattle as the preferred host. Similarly, we identified 383 species-specific SNPs conserved in 132 Brucella melitensis genomes. Of these 379 species-specific SNPs were identified as positively associated using GWAS. Interestingly, >98% of the SNPs that are significantly, positively associated with the traits showed 100% sensitivity and 100% specificity. These identified species-specific core-SNPs identified in Brucella genomes could be responsible for the speciation and their respective host adaptation.}, }
@article {pmid29142289, year = {2017}, author = {Shariati J, V and Malboobi, MA and Tabrizi, Z and Tavakol, E and Owilia, P and Safari, M}, title = {Comprehensive genomic analysis of a plant growth-promoting rhizobacterium Pantoea agglomerans strain P5.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15610}, doi = {10.1038/s41598-017-15820-9}, pmid = {29142289}, issn = {2045-2322}, abstract = {In this study, we provide a comparative genomic analysis of Pantoea agglomerans strain P5 and 10 closely related strains based on phylogenetic analyses. A next-generation shotgun strategy was implemented using the Illumina HiSeq 2500 technology followed by core- and pan-genome analysis. The genome of P. agglomerans strain P5 contains an assembly size of 5082485 bp with 55.4% G + C content. P. agglomerans consists of 2981 core and 3159 accessory genes for Coding DNA Sequences (CDSs) based on the pan-genome analysis. Strain P5 can be grouped closely with strains PG734 and 299 R using pan and core genes, respectively. All the predicted and annotated gene sequences were allocated to KEGG pathways. Accordingly, genes involved in plant growth-promoting (PGP) ability, including phosphate solubilization, IAA and siderophore production, acetoin and 2,3-butanediol synthesis and bacterial secretion, were assigned. This study provides an in-depth view of the PGP characteristics of strain P5, highlighting its potential use in agriculture as a biofertilizer.}, }
@article {pmid29126241, year = {2018}, author = {Kajala, I and Bergsveinson, J and Friesen, V and Redekop, A and Juvonen, R and Storgårds, E and Ziola, B}, title = {Lactobacillus backii and Pediococcus damnosus isolated from 170-year-old beer recovered from a shipwreck lack the metabolic activities required to grow in modern lager beer.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {1}, pages = {}, doi = {10.1093/femsec/fix152}, pmid = {29126241}, issn = {1574-6941}, abstract = {In 2010, bottles of beer containing viable bacteria of the common beer-spoilage species Lactobacillus backii and Pediococcus damnosus were recovered from a shipwreck near the Åland Islands, Finland. The 170-year quiescent state maintained by the shipwreck bacteria presented a unique opportunity to study lactic acid bacteria (LAB) evolution vis-a-vis growth and survival in the beer environment. Three shipwreck bacteria (one L. backii strain and two P. damnosus strains) and modern-day beer-spoilage isolates of the same two species were genome sequenced, characterized for hop iso-α-acid tolerance, and growth in degassed lager and wheat beer. In addition, plasmid variants of the modern-day P. damnosus strain were analyzed for the effect of plasmid-encoded genes on growth in lager beer. Coding content on two plasmids was identified as essential for LAB growth in modern lager beer. Three chromosomal regions containing genes related to sugar transport and cell wall polysaccharides were shared by pediococci able to grow in beer. Our results show that the three shipwreck bacteria lack the necessary plasmid-located genetic content to grow in modern lager beer, but carry additional genes related to acid tolerance and biofilm formation compared to their modern counterparts.}, }
@article {pmid29100523, year = {2017}, author = {Yu, J and Song, Y and Ren, Y and Qing, Y and Liu, W and Sun, Z}, title = {Genome-level comparisons provide insight into the phylogeny and metabolic diversity of species within the genus Lactococcus.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {213}, doi = {10.1186/s12866-017-1120-5}, pmid = {29100523}, issn = {1471-2180}, mesh = {Base Composition ; *Carbohydrate Metabolism ; DNA, Bacterial/genetics ; *Genetic Variation ; Genome Size ; Genome, Bacterial/*genetics ; Lactococcus/*classification/enzymology/*genetics ; *Phylogeny ; Species Specificity ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: The genomic diversity of different species within the genus Lactococcus and the relationships between genomic differentiation and environmental factors remain unclear. In this study, type isolates of ten Lactococcus species/subspecies were sequenced to assess their genomic characteristics, metabolic diversity, and phylogenetic relationships.<br><br>RESULTS: The total genome sizes varied between 1.99 (Lactococcus plantarum) and 2.46 megabases (Mb; L. lactis subsp. lactis), and the G + C content ranged from 34.81 (L. lactis subsp. hordniae) to 39.67% (L. raffinolactis) with an average value of 37.02%. Analysis of genome dynamics indicated that the genus Lactococcus has an open pan-genome, while the core genome size decreased with sequential addition at the genus and species group levels. A phylogenetic dendrogram based on the concatenated amino acid sequences of 643 core genes was largely consistent with the phylogenetic tree obtained by 16S ribosomal RNA (rRNA) genes, but it provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis.<br><br>CONCLUSIONS: Comparative genomics indicated that species in the genus Lactococcus had high degrees of diversity in genome size, gene content, and carbohydrate metabolism. This may be important for the specific adaptations that allow different Lactococcus species to survive in different environments. These results provide a quantitative basis for understanding the genomic and metabolic diversity within the genus Lactococcus, laying the foundation for future studies on taxonomy and functional genomics.}, }
@article {pmid29079617, year = {2017}, author = {Pantůček, R and Sedláček, I and Indráková, A and Vrbovská, V and Mašlaňová, I and Kovařovic, V and Švec, P and Králová, S and Krištofová, L and Kekláková, J and Petráš, P and Doškař, J}, title = {Staphylococcus edaphicus sp. nov., isolated in Antarctica, harbours mecC gene and genomic islands with suspected role in adaptation to extreme environment.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01746-17}, pmid = {29079617}, issn = {1098-5336}, abstract = {Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources, stone fragments and sandy soil in James Ross Island, Antarctica. Here we describe properties of novel species of the genus Staphylococcus that has near identical 16S rRNA gene sequence to Staphylococcus saprophyticus However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at whole genome level, average nucleotide identity <85 %, and inferred DNA-DNA hybridization <30%. It forms a separate branch in S. saprophyticus phylogenetic clade confirmed by multilocus sequence analysis of six housekeeping genes rpoB, hsp60, tuf, dnaJ, gap, and sod MALDI-TOF MS and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbours. In contrast to S. saprophyticus subsp. saprophyticus, strains were pyrrolidonyl arylamidase- and β-glucuronidase-positive, β -galactosidase-negative, nitrate was reduced and acid produced aerobically from d-mannose. Whole genome sequencing of 2.75 Mb large chromosome revealed the presence of a number of mobile genetic elements including the 27-kb-long pseudo staphylococcus cassette chromosome mec (ψSCCmecP5085) harboring mecC gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environment, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidin, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactams producers, which are common in a polar environment. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus edaphicus sp. nov. The type strain is P5085T (=CCM 8730T = DSM 104441T).IMPORTANCE The description of Staphylococcus edaphicus sp. nov. enables the comparison of multidrug-resistant staphylococci from human and veterinary sources evolved in the globalized world to their geographically distant relative from the extreme Antarctic environment. Although this new species was not exposed to the pressure of antibiotic treatment in human or veterinary practice, mobile genetic elements carrying antimicrobial resistance genes were found in the genome. The presented genomic characteristics elucidate the evolutionary relationships in the Staphylococcus genus with a special focus on antimicrobial resistance, pathogenicity and survival traits. Genes encoded on mobile genetic elements were arranged in unique combinations but retained conserved locations for the integration of mobile genetic elements. These findings point to enormous plasticity of the staphylococcal pangenome shaped by horizontal gene transfer. Thus S. edaphicus can act not only as a reservoir of antibiotic resistance in a natural environment, but also as a mediator for the spread and evolution of resistance genes.}, }
@article {pmid29077859, year = {2018}, author = {Ding, W and Baumdicker, F and Neher, RA}, title = {panX: pan-genome analysis and exploration.}, journal = {Nucleic acids research}, volume = {46}, number = {1}, pages = {e5}, doi = {10.1093/nar/gkx977}, pmid = {29077859}, issn = {1362-4962}, abstract = {Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.}, }
@article {pmid29067021, year = {2017}, author = {Chen, X and Hitchings, MD and Mendoza, JE and Balanza, V and Facey, PD and Dyson, PJ and Bielza, P and Del Sol, R}, title = {Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1969}, doi = {10.3389/fmicb.2017.01969}, pmid = {29067021}, issn = {1664-302X}, abstract = {Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis) from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector-immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.}, }
@article {pmid29061896, year = {2017}, author = {Hall, JPJ and Brockhurst, MA and Harrison, E}, title = {Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1735}, pages = {}, doi = {10.1098/rstb.2016.0424}, pmid = {29061896}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; }, abstract = {In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also 'horizontally' between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.}, }
@article {pmid29058585, year = {2017}, author = {Zhang, DF and Zhi, XY and Zhang, J and Paoli, GC and Cui, Y and Shi, C and Shi, X}, title = {Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {808}, doi = {10.1186/s12864-017-4149-9}, pmid = {29058585}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; *Genome, Bacterial ; Genomics/*methods ; Humans ; International Agencies ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Homology ; Staphylococcal Infections/genetics/*microbiology ; Staphylococcus/classification/genetics/isolation &amp; purification/*pathogenicity ; Virulence ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Staphylococcus argenteus and S. schweitzeri, were recently proposed as novel species within S. aureus complex (SAC). S. argenteus has been reported in many countries and can threaten human health. S. schweitzeri has not been associated with human infections, but has been isolated from non-human primates. Questions regarding the evolution of pathogenicity of these two species will remain elusive until an exploratory evolutionary framework is established.<br><br>RESULTS: We present genomic comparison analysis among members of SAC based on a pan-genome definition, which included 15 S. argenteus genomes (five newly sequenced), six S. schweitzeri genomes and 30 divergent S. aureus genomes. The three species had divergent core genomes and rare interspecific recombination was observed among the core genes. However, some subtypes of staphylococcal cassette chromosome mec (SCCmec) elements and prophages were present in different species. Of 111 tested virulence genes of S. aureus, 85 and 86 homologous genes were found in S. argenteus and S. schweitzeri, respectively. There was no difference in virulence gene content among the three species, but the sequence of most core virulence genes was divergent. Analysis of the agr locus and the genes in the capsular polysaccharides biosynthetic operon revealed that they both diverged before the speciation of SAC members. Furthermore, the widespread geographic distribution of S. argenteus, sequence type 2250, showed ambiguous biogeographical structure among geographically isolated populations, demonstrating an international spread of this pathogen.<br><br>CONCLUSIONS: S. argenteus has spread among several countries, and invasive infections and persistent carriage may be not limited to currently reported regions. S. argenteus probably had undergone a recent host adaption and can cause human infections with a similar pathogenic potential.}, }
@article {pmid29047329, year = {2017}, author = {Guo, X and Li, S and Zhang, J and Wu, F and Li, X and Wu, D and Zhang, M and Ou, Z and Jie, Z and Yan, Q and Li, P and Yi, J and Peng, Y}, title = {Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {800}, doi = {10.1186/s12864-017-4195-3}, pmid = {29047329}, issn = {1471-2164}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Humans ; Mammals/*microbiology ; Mice ; Molecular Sequence Annotation ; Verrucomicrobia/drug effects/*genetics/*physiology ; *Whole Genome Sequencing ; }, abstract = {BACKGROUND: Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content.<br><br>RESULTS: Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins. Phylogenetic analysis identified three species-level A. muciniphila phylogroups exhibiting distinct metabolic and functional features. Based on the comprehensive genome catalogue, we reconstructed 106 newly A. muciniphila metagenome assembled genomes (MAGs) from available metagenomic datasets of human, mouse and pig gut microbiomes, revealing a transcontinental distribution of A. muciniphila phylogroups across mammalian gut microbiotas. Accurate quantitative analysis of A. muciniphila phylogroups in human subjects further demonstrated its strong correlation with body mass index and anti-diabetic drug usage. Furthermore, we found that, during their mammalian gut evolution history, A. muciniphila acquired extra genes, especially antibiotic resistance genes, from symbiotic microbes via recent lateral gene transfer.<br><br>CONCLUSIONS: The genome repertoire of A. muciniphila provided insights into population structure, evolutionary and functional specificity of this significant bacterium.}, }
@article {pmid29020009, year = {2017}, author = {Meyer, KA and Davis, TW and Watson, SB and Denef, VJ and Berry, MA and Dick, GJ}, title = {Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0183859}, doi = {10.1371/journal.pone.0183859}, pmid = {29020009}, issn = {1932-6203}, mesh = {Base Sequence ; CRISPR-Cas Systems/genetics ; *Eutrophication ; *Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Great Lakes Region ; Metagenome ; Microcystis/*genetics/isolation &amp; purification ; Phylogeny ; Species Specificity ; }, abstract = {Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of &quot;omics&quot; data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M. wesenbergii LE013-01) and one from upstream Lake St. Clair (M. cf aeruginosa LSC13-02), and compared these data to the genomes of seventeen Microcystis spp. from across the globe as well as one metagenome and seven metatranscriptomes from a 2014 Lake Erie Microcystis bloom. For the publically available strains analyzed, the core genome is ~1900 genes, representing ~11% of total genes in the pan-genome and ~45% of each strain's genome. The flexible genome content was related to Microcystis subclades defined by phylogenetic analysis of both housekeeping genes and total core genes. To our knowledge this is the first evidence that the flexible genome is linked to the core genome of the Microcystis species complex. The majority of strain-specific genes were present and expressed in bloom communities in Lake Erie. Roughly 8% of these genes from the lower Great Lakes are involved in genome plasticity (rapid gain, loss, or rearrangement of genes) and resistance to foreign genetic elements (such as CRISPR-Cas systems). Intriguingly, strain-specific genes from Microcystis cultured from around the world were also present and expressed in the Lake Erie blooms, suggesting that the Microcystis pangenome is truly global. The presence and expression of flexible genes, including strain-specific genes, suggests that strain-level genomic diversity may be important in maintaining Microcystis abundance during bloom events.}, }
@article {pmid29017450, year = {2017}, author = {Zhou, G and Peng, H and Wang, YS and Huang, XM and Xie, XB and Shi, QS}, title = {Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {765}, doi = {10.1186/s12864-017-4157-9}, pmid = {29017450}, issn = {1471-2164}, mesh = {Biofilms ; Citrobacter/*genetics/physiology ; Genome, Bacterial/genetics ; *Genomics ; *Industry ; }, abstract = {BACKGROUND: In our previous study, Citrobacter werkmanii BF-6 was isolated from an industrial spoilage sample and demonstrated an excellent ability to form biofilms, which could be affected by various environmental factors. However, the genome sequence of this organism has not been reported so far.<br><br>RESULTS: We report the complete genome sequence of C. werkmanii BF-6 together with the description of the genome features and its annotation. The size of the complete chromosome is 4,929,789 bp with an average coverage of 137×. The chromosome exhibits an average G + C content of 52.0%, and encodes 4570 protein coding genes, 84 tRNA genes, 25 rRNA operons, 3 microsatellite sequences and 34 minisatellite sequences. A previously unknown circular plasmid designated as pCW001 was also found with a length of 212,549 bp and a G + C content of 48.2%. 73.5%, 75.6% and 92.6% of the protein coding genes could be assigned to GO Ontology, KEGG Pathway, and COG (Clusters of Orthologous Groups) categories respectively. C. werkmanii BF-6 and C. werkmanii NRBC 105721 exhibited the closest evolutionary relationships based on 16S ribosomal RNA and core-pan genome assay. Furthermore, C. werkmanii BF-6 exhibits typical bacterial biofilm formation and development. In the RT-PCR experiments, we found that a great number of biofilm related genes, such as bsmA, bssR, bssS, hmsP, tabA, csgA, csgB, csgC, csgD, csgE, and csgG, were involved in C. werkmanii BF-6 biofilm formation.<br><br>CONCLUSIONS: This is the first complete genome of C. werkmanii. Our work highlights the potential genetic mechanisms involved in biofilm formation and paves a way for further application of C. werkmanii in biofilms research.}, }
@article {pmid28977764, year = {2017}, author = {Bergsveinson, J and Ziola, B}, title = {Comparative genomic and plasmid analysis of beer-spoiling and non-beer-spoiling Lactobacillus brevis isolates.}, journal = {Canadian journal of microbiology}, volume = {63}, number = {12}, pages = {970-983}, doi = {10.1139/cjm-2017-0405}, pmid = {28977764}, issn = {1480-3275}, mesh = {Beer/microbiology ; *Food Microbiology ; Genetic Variation ; Genome, Bacterial/*genetics ; Lactobacillus brevis/*genetics/isolation &amp; purification ; Plasmids/*genetics ; }, abstract = {Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.}, }
@article {pmid28970823, year = {2017}, author = {Benevides, L and Burman, S and Martin, R and Robert, V and Thomas, M and Miquel, S and Chain, F and Sokol, H and Bermudez-Humaran, LG and Morrison, M and Langella, P and Azevedo, VA and Chatel, JM and Soares, S}, title = {New Insights into the Diversity of the Genus Faecalibacterium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1790}, doi = {10.3389/fmicb.2017.01790}, pmid = {28970823}, issn = {1664-302X}, abstract = {Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of Faecalibacterium. For this, we used 12 newly sequenced, assembled, and curated genomes of F. prausnitzii, which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of Faecalibacterium strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters-A, B, and C-composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains. Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach, together with ANI, in the in silico classification of new species. Altogether, our results provide evidence not only for the reconsideration of the phylogenetic and genomic relatedness among strains currently assigned to F. prausnitzii, but also the need for lineage (strain-based) differentiation of this taxon to better define how specific members might be associated with positive or negative host interactions.}, }
@article {pmid28968784, year = {2017}, author = {Médigue, C and Calteau, A and Cruveiller, S and Gachet, M and Gautreau, G and Josso, A and Lajus, A and Langlois, J and Pereira, H and Planel, R and Roche, D and Rollin, J and Rouy, Z and Vallenet, D}, title = {MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbx113}, pmid = {28968784}, issn = {1477-4054}, abstract = {The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources.}, }
@article {pmid28959245, year = {2017}, author = {De Maayer, P and Aliyu, H and Vikram, S and Blom, J and Duffy, B and Cowan, DA and Smits, THM and Venter, SN and Coutinho, TA}, title = {Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1755}, doi = {10.3389/fmicb.2017.01755}, pmid = {28959245}, issn = {1664-302X}, abstract = {Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.}, }
@article {pmid28957508, year = {2017}, author = {Déraspe, M and Raymond, F and Boisvert, S and Culley, A and Roy, PH and Laviolette, F and Corbeil, J}, title = {Phenetic Comparison of Prokaryotic Genomes Using k-mers.}, journal = {Molecular biology and evolution}, volume = {34}, number = {10}, pages = {2716-2729}, doi = {10.1093/molbev/msx200}, pmid = {28957508}, issn = {1537-1719}, mesh = {Bacteria/genetics ; Biological Evolution ; Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; Evolution, Molecular ; Genome, Bacterial/*genetics ; Genomics/methods ; Metagenomics ; Phylogeny ; Prokaryotic Cells ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets.}, }
@article {pmid28957464, year = {2017}, author = {Yano, H and Iwamoto, T and Nishiuchi, Y and Nakajima, C and Starkova, DA and Mokrousov, I and Narvskaya, O and Yoshida, S and Arikawa, K and Nakanishi, N and Osaki, K and Nakagawa, I and Ato, M and Suzuki, Y and Maruyama, F}, title = {Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis.}, journal = {Genome biology and evolution}, volume = {9}, number = {9}, pages = {2403-2417}, doi = {10.1093/gbe/evx183}, pmid = {28957464}, issn = {1759-6653}, mesh = {*Adaptation, Physiological ; Alleles ; Animals ; *Evolution, Molecular ; Homologous Recombination ; Humans ; Lung/microbiology ; Mycobacterium Infections/microbiology ; Mycobacterium avium/*genetics/isolation &amp; purification ; Operon ; Polymorphism, Genetic ; Swine ; Trehalose/genetics/metabolism ; }, abstract = {Mycobacterium avium subsp. hominissuis (MAH) is one of the most common nontuberculous mycobacterial species responsible for chronic lung disease in humans. Despite increasing worldwide incidence, little is known about the genetic mechanisms behind the population evolution of MAH. To elucidate the local adaptation mechanisms of MAH, we assessed genetic population structure, the mutual homologous recombination, and gene content for 36 global MAH isolates, including 12 Japanese isolates sequenced in the present study. We identified five major MAH lineages and found that extensive mutual homologous recombination occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant in the Japanese isolates. We identified alleles unique to these two East Asian lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in one mammalian cell entry operon, which presumably originated from as yet undiscovered mycobacterial lineages. Several genes and alleles unique to East Asian strains were located in the fragments introduced via recombination between East Asian lineages, suggesting implication of recombination in local adaptation. These patterns of MAH genomes are consistent with the signature of distribution conjugative transfer, a mode of sexual reproduction reported for other mycobacterial species.}, }
@article {pmid28945251, year = {2017}, author = {Eggertsson, HP and Jonsson, H and Kristmundsdottir, S and Hjartarson, E and Kehr, B and Masson, G and Zink, F and Hjorleifsson, KE and Jonasdottir, A and Jonasdottir, A and Jonsdottir, I and Gudbjartsson, DF and Melsted, P and Stefansson, K and Halldorsson, BV}, title = {Graphtyper enables population-scale genotyping using pangenome graphs.}, journal = {Nature genetics}, volume = {49}, number = {11}, pages = {1654-1660}, doi = {10.1038/ng.3964}, pmid = {28945251}, issn = {1546-1718}, mesh = {*Algorithms ; Alleles ; Base Sequence ; Computer Graphics ; *Genome, Human ; Genotyping Techniques/*instrumentation ; HLA Antigens/genetics ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; *Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA/methods/*statistics &amp; numerical data ; Software ; }, abstract = {A fundamental requirement for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to use this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in the whole genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in both small and population-scale sequencing studies.}, }
@article {pmid28942844, year = {2017}, author = {Lee, JY and Han, GG and Kim, EB and Choi, YJ}, title = {Comparative genomics of Lactobacillus salivarius strains focusing on their host adaptation.}, journal = {Microbiological research}, volume = {205}, number = {}, pages = {48-58}, doi = {10.1016/j.micres.2017.08.008}, pmid = {28942844}, issn = {1618-0623}, mesh = {Acclimatization/*genetics ; Animals ; Bacterial Outer Membrane Proteins/genetics ; Base Sequence ; Carbohydrate Metabolism ; Cell Wall/chemistry/genetics ; Chickens ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics/physiology ; Genetic Structures ; *Genome, Bacterial ; Genomics ; Humans ; Lactobacillus salivarius/classification/*genetics/isolation &amp; purification/*physiology ; Phylogeny ; Probiotics ; Species Specificity ; Swine ; Symbiosis/genetics/physiology ; }, abstract = {Lactobacillus salivarius is an important member of the animal gut microflora and is a promising probiotic bacterium. However, there is a lack of research on the genomic diversity of L. salivarius species. In this study, we generated 21 L. salivarius draft genomes, and investigated the pan-genome of L. salivarius strains isolated from humans, pigs and chickens using all available genomes, focusing on host adaptation. Phylogenetic clustering showed a distinct categorization of L. salivarius strains depending on their hosts. In the pan-genome, 15 host-specific genes and 16 dual-host-shared genes that only one host isolate did not possess were identified. Comparison of 56 extracellular protein encoding genes and 124 orthologs related to exopolysaccharide production in the pan-genome revealed that extracellular components of the assayed bacteria have been globally acquired and mutated under the selection pressure for host adaptation. We also found the three host-specific genes that are responsible for energy production in L. salivarius. These results showed that L. salivarius has evolved to adapt to host habitats in two ways, by gaining the abilities for niche adhesion and efficient utilization of nutrients. Our study offers a deeper understanding of the probiotic species L. salivarius, and provides a basis for future studies on L. salivarius and other mutualistic bacteria.}, }
@article {pmid28922838, year = {2017}, author = {Jeukens, J and Kukavica-Ibrulj, I and Emond-Rheault, JG and Freschi, L and Levesque, RC}, title = {Comparative genomics of a drug-resistant Pseudomonas aeruginosa panel and the challenges of antimicrobial resistance prediction from genomes.}, journal = {FEMS microbiology letters}, volume = {364}, number = {18}, pages = {}, doi = {10.1093/femsle/fnx161}, pmid = {28922838}, issn = {1574-6968}, mesh = {Drug Resistance, Multiple, Bacterial/*genetics ; Genes, MDR ; Genomics/*methods ; Genotype ; Humans ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/*genetics ; Whole Genome Sequencing/methods ; }, abstract = {Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa. This study focuses on a commercially available panel of seven MDR P. aeruginosa strains. The main goals were to sequence and compare these strains' genomes, attempt to predict AMR from whole genomes using two different methods and determine whether this panel could be an informative complement to the international P. aeruginosa reference panel. As expected, the results highlight the complexity of associating genotype and AMR phenotype in P. aeruginosa, mainly due to the intricate regulation of resistance mechanisms. Our results also urge caution in the interpretation of predicted resistomes regarding the occurrence of gene identity discrepancies between strains. We envision that, in addition to accounting for the genomic diversity of P. aeruginosa, future development of predictive tools will need to incorporate a transcriptomic, proteomic and/or metabolomic component.}, }
@article {pmid28912444, year = {2017}, author = {Chun, BH and Kim, KH and Jeon, HH and Lee, SH and Jeon, CO}, title = {Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11504}, doi = {10.1038/s41598-017-12016-z}, pmid = {28912444}, issn = {2045-2322}, abstract = {The genomic and metabolic features of Leuconostoc (Leu) mesenteroides were investigated through pan-genomic and transcriptomic analyses. Relatedness analysis of 17 Leu. mesenteroides strains available in GenBank based on 16S rRNA gene sequence, average nucleotide identity, in silico DNA-DNA hybridization, molecular phenotype, and core-genome indicated that Leu. mesenteroides has been separated into different phylogenetic lineages. Pan-genome of Leu. mesenteroides strains, consisting of 999 genes in core-genome, 1,432 genes in accessory-genome, and 754 genes in unique genome, and their COG and KEGG analyses showed that Leu. mesenteroides harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The reconstruction of fermentative metabolic pathways for Leu. mesenteroides strains showed that Leu. mesenteroides produces various metabolites such as lactate, ethanol, acetate, CO2, mannitol, diacetyl, acetoin, and 2,3-butanediol through an obligate heterolactic fermentation from various carbohydrates. Fermentative metabolic features of Leu. mesenteroides during kimchi fermentation were investigated through transcriptional analyses for the KEGG pathways and reconstructed metabolic pathways of Leu. mesenteroides using kimchi metatranscriptomic data. This was the first study to investigate the genomic and metabolic features of Leu. mesenteroides through pan-genomic and metatranscriptomic analyses, and may provide insights into its genomic and metabolic features and a better understanding of kimchi fermentations by Leu. mesenteroides.}, }
@article {pmid28911112, year = {2017}, author = {Cury, J and Touchon, M and Rocha, EPC}, title = {Integrative and conjugative elements and their hosts: composition, distribution and organization.}, journal = {Nucleic acids research}, volume = {45}, number = {15}, pages = {8943-8956}, doi = {10.1093/nar/gkx607}, pmid = {28911112}, issn = {1362-4962}, support = {281605//European Research Council/International ; }, mesh = {Actinobacteria/classification/genetics/metabolism ; Archaea/classification/genetics/metabolism ; *Conjugation, Genetic ; DNA Replication ; *DNA Transposable Elements ; DNA, Bacterial/*genetics/metabolism ; Evolution, Molecular ; Firmicutes/classification/genetics/metabolism ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Integrases/genetics/metabolism ; Lysogeny ; *Phylogeny ; Plasmids/*chemistry/metabolism ; Proteobacteria/classification/genetics/metabolism ; Recombinases/genetics/metabolism ; }, abstract = {Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species' pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses revealed that ICEs are structured in functional modules. Integrases and conjugation systems have different evolutionary histories, even if the gene repertoires of ICEs can be grouped in function of conjugation types. Our characterization of the composition and organization of ICEs paves the way for future functional and evolutionary analyses of their cargo genes, composed of a majority of unknown function genes.}, }
@article {pmid28894437, year = {2017}, author = {Esposito, A and Pompilio, A and Bettua, C and Crocetta, V and Giacobazzi, E and Fiscarelli, E and Jousson, O and Di Bonaventura, G}, title = {Evolution of Stenotrophomonas maltophilia in Cystic Fibrosis Lung over Chronic Infection: A Genomic and Phenotypic Population Study.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1590}, doi = {10.3389/fmicb.2017.01590}, pmid = {28894437}, issn = {1664-302X}, abstract = {Stenotrophomonas maltophilia has been recognized as an emerging multi-drug resistant opportunistic pathogen in cystic fibrosis (CF) patients. We report a comparative genomic and phenotypic analysis of 91 S. maltophilia strains from 10 CF patients over a 12-year period. Draft genome analyses included in silico Multi-Locus Sequence Typing (MLST), Single-Nucleotide Polymorphisms (SNPs), and pangenome characterization. Growth rate, biofilm formation, motility, mutation frequency, in vivo virulence, and in vitro antibiotic susceptibility were determined and compared with population structure over time. The population consisted of 20 different sequence types (STs), 11 of which are new ones. Pangenome and SNPs data showed that this population is composed of three major phylogenetic lineages. All patients were colonized by multiple STs, although most of them were found in a single patient and showed persistence over years. Only few phenotypes showed some correlation with population phylogenetic structure. Our results show that S. maltophilia adaptation to CF lung is associated with consistent genotypic and phenotypic heterogeneity. Stenotrophomonas maltophilia infecting multiple hosts likely experiences different selection pressures depending on the host environment. The poor genotype-phenotype correlation suggests the existence of complex regulatory mechanisms that need to be explored in order to better design therapeutic strategies.}, }
@article {pmid28890711, year = {2017}, author = {Bolotin, E and Hershberg, R}, title = {Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1536}, doi = {10.3389/fmicb.2017.01536}, pmid = {28890711}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) serves as an important source of innovation for bacterial species. We used a pangenome-based approach to identify genes that were horizontally acquired by four closely related bacterial species, belonging to the Enterobacteriaceae family. This enabled us to examine the extent to which such closely related species tend to share horizontally acquired genes. We find that a high percent of horizontally acquired genes are shared among these closely related species. Furthermore, we demonstrate that the extent of sharing of horizontally acquired genes among these four closely related species is predictive of the extent to which these genes will be found in additional bacterial species. Finally, we show that acquired genes shared by more species tend to be better optimized for expression within the genomes of their new hosts. Combined, our results demonstrate the existence of a large pool of frequently horizontally acquired genes that have distinct characteristics from horizontally acquired genes that are less frequently shared between species.}, }
@article {pmid28887527, year = {2017}, author = {Kim, Y and Koh, I and Young Lim, M and Chung, WH and Rho, M}, title = {Pan-genome analysis of Bacillus for microbiome profiling.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10984}, doi = {10.1038/s41598-017-11385-9}, pmid = {28887527}, issn = {2045-2322}, abstract = {Recent advances in high-throughput sequencing technology allow for in-depth studies on microbial genomes and their communities. While multiple strains of the same species could display genomic variations with different gene contents in diverse habitats and hosts, the essential functions for a specific species are conserved as core genes that are shared among strains. We have comprehensively analyzed 238 strains of five different Bacillus species to identify the properties of core and strain-specific genes. Core and strain-specific genes in each Bacillus species show significant differences in their functions and genomic signatures. Using the core genes defined in this study, we have precisely identified the Bacillus species that exist in food microbiomes. Without resorting to culture-based whole genome sequencing, an unexpectedly large portion of the core genes, 98.22% of core genes in B. amyloliquefaciens and 97.77% of B. subtilis, were reconstructed from the microbiome. We have performed a pan-genome analysis on the core gene data of multiple Bacillus species to investigate the Bacillus species in food microbiome. Our findings provide a comprehensive genetic landscape of the Bacillus species, which is also consistent with previous studies on a limited number of strains and species. Analysis based on comprehensive core genes should thus serve as a powerful profiling tool to better understand major constituents in fermented food microbiomes.}, }
@article {pmid28887423, year = {2017}, author = {Schmedes, SE and Woerner, AE and Budowle, B}, title = {Forensic human identification using skin microbiomes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01672-17}, pmid = {28887423}, issn = {1098-5336}, abstract = {The human microbiome contributes significantly to the genetic content of the human body. Genetic and environmental factors help shape the microbiome, and as such, the microbiome can be unique to an individual. Previous studies have demonstrated the potential to use microbiome profiling for forensic applications, however a method has yet to identify stable features of skin microbiomes that produce high classification accuracies for samples collected over reasonably long time intervals. A novel approach is described to classify skin microbiomes to their donors by comparing two features types, Propionibacterium acnes pangenome presence/absence features and nucleotide diversities of stable clade-specific markers. Supervised learning was used to attribute skin microbiomes from 14 skin body sites from 12 healthy individuals sampled at three time points over a >2.5 year period with accuracies up to 100% for three body sites. Feature selection identified a reduced subset of markers from each body site that are highly individualizing, identifying 187 markers from 12 clades. Classification accuracies were compared in a formal model testing framework, and the results of this indicate that learners trained on nucleotide diversity perform significantly better than those trained on presence/absence encodings. This study used supervised learning to identify individuals with high accuracy and associated stable features from skin microbiomes over a period of up to almost 3 years. These selected features provide a preliminary marker panel for future development of a robust and reproducible method for skin microbiome profiling for forensic human identification.Importance A novel approach is described to attribute skin microbiomes, collected over a period of >2.5 years, to their individual hosts with a high degree of accuracy. Nucleotide diversities of stable clade-specific markers with supervised learning was used to classify skin microbiomes from a particular individual with up to 100% classification accuracy for three body sites. Attribute selection was used to identify 187 genetic markers from 12 clades which provide the greatest differentiation of individual skin microbiomes from 14 skin sites. This study performs skin microbiome profiling from a supervised learning approach and obtains high classification accuracy for samples collected from individuals over a relatively long time period for potential application to forensic human identification.}, }
@article {pmid28878862, year = {2017}, author = {Ktari, A and Nouioui, I and Furnholm, T and Swanson, E and Ghodhbane-Gtari, F and Tisa, LS and Gtari, M}, title = {Permanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence of canonical nod genes, which are highly homologous to those detected in Candidatus Frankia Dg1 genome.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {51}, doi = {10.1186/s40793-017-0261-3}, pmid = {28878862}, issn = {1944-3277}, abstract = {Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to &quot;Frankia discariae&quot; with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited. Since the first three Frankia genomes were sequenced, additional genome sequences covering more diverse strains have helped provide insight into the depth of the pangenome and attempts to identify bacterial signaling molecules like the rhizobial canonical nod genes. The genome sequence of Frankia sp. strain NRRL B-16219 was generated and assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content. Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes, 1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL B-16219 draft genome contained genes homologous to the rhizobial common nodulation genes clustered in two areas. The first cluster contains nodACIJH genes whereas the second has nodAB and nodH genes in the upstream region. Phylogenetic analysis shows that Frankia nod genes are more deeply rooted than their sister groups from rhizobia. PCR-sequencing suggested the widespread occurrence of highly homologous nodA and nodB genes in microsymbionts of field collected Ceanothus americanus.}, }
@article {pmid28861061, year = {2017}, author = {Lean, SS and Yeo, CC}, title = {Small, Enigmatic Plasmids of the Nosocomial Pathogen, Acinetobacter baumannii: Good, Bad, Who Knows?.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1547}, doi = {10.3389/fmicb.2017.01547}, pmid = {28861061}, issn = {1664-302X}, abstract = {Acinetobacter baumannii is a Gram-negative nosocomial pathogen that has become a serious healthcare concern within a span of two decades due to its ability to rapidly acquire resistance to all classes of antimicrobial compounds. One of the key features of the A. baumannii genome is an open pan genome with a plethora of plasmids, transposons, integrons, and genomic islands, all of which play important roles in the evolution and success of this clinical pathogen, particularly in the acquisition of multidrug resistance determinants. An interesting genetic feature seen in majority of A. baumannii genomes analyzed is the presence of small plasmids that usually ranged from 2 to 10 kb in size, some of which harbor antibiotic resistance genes and homologs of plasmid mobilization genes. These plasmids are often overlooked when compared to their larger, conjugative counterparts that harbor multiple antibiotic resistance genes and transposable elements. In this mini-review, we will examine our current knowledge of these small A. baumannii plasmids and look into their genetic diversity and phylogenetic relationships. Some of these plasmids, such as the Rep-3 superfamily group and the pRAY-type, which has no recognizable replicase genes, are quite widespread among diverse A. baumannii clinical isolates worldwide, hinting at their usefulness to the lifestyle of this pathogen. Other small plasmids especially those from the Rep-1 superfamily are truly enigmatic, encoding only hypothetical proteins of unknown function, leading to the question of whether these small plasmids are &quot;good&quot; or &quot;bad&quot; to their host A. baumannii.}, }
@article {pmid28855980, year = {2017}, author = {Lesho, E and Snesrud, E and Kwak, Y and Ong, A and Maybank, R and Laguio-Vila, M and Falsey, AR and Hinkle, M}, title = {Pseudomonas Endocarditis with an unstable phenotype: the challenges of isolate characterization and Carbapenem stewardship with a partial review of the literature.}, journal = {Antimicrobial resistance and infection control}, volume = {6}, number = {}, pages = {87}, doi = {10.1186/s13756-017-0245-5}, pmid = {28855980}, issn = {2047-2994}, abstract = {BACKGROUND: Pseudomonas endocarditis is exceedingly rare, especially in patients without predisposing risks. We present such a case that included unexpected switches in antibacterial resistance profiles in two Pseudomonas aeruginosa (PA) strains with the same whole-genome sequence. The case also involved diagnostic and treatment challenges, such as issues with automated testing platforms, choosing the optimal aminoglycoside, minimizing unnecessary carbapenem exposure, and the need for faster, more informative laboratory tests.<br><br>CASE PRESENTATION: On hospital day one (HD-1) a cefepime and piperacillin-tazobactam (FEP-TZP)-susceptible P. aeruginosa was isolated from the bloodstream of a 62-year-old man admitted for evaluation of possible endocarditis and treated with gentamicin and cefepime. On HD-2, his antibiotic regimen was changed to tobramycin and cefepime. On HD-11, he underwent aortic valve replacement, and P. aeruginosa was isolated from the explanted valve. Unexpectedly, it was FEP-TZP-resistant, so cefepime was switched to meropenem. On HD-14, in preparation for whole-genome sequencing (WGS), valve and blood isolates were removed from cryo-storage, re-cultured, and simultaneously tested with the same platforms, reagents, and inoculations previously used. Curiously, the valve isolate was now FEP-TZP-susceptible. WGS revealed that both isolates were phylogenetically identical, differing by a single nucleotide in a chemotaxis-encoding gene. They also contained the same resistance genes (blaADC35, aph(3')-II, blaOXA-50, catB7, fosA).<br><br>CONCLUSION: Repeated testing on alternate platforms and WGS did not definitively determine the resistance mechanism(s), which in this case, is most likely unstable de-repression of a chromosomal AmpC β-lactamase, porin alterations, or efflux upregulation, with reversion to baseline (non-efflux) transcription. Although sub-culture on specialized media to select for less fit (more resistant) colonies, followed by transcriptome analysis, and multiple sequence alignment, might have revealed the mechanism and better informed the optimal choice of β-lactam, such approaches are neither rapid, nor feasible for hospital laboratories. In this era of escalating drug resistance and dwindling antibiotics, use of the most potent anti-pseudomonals must be balanced with stewardship. Clinicians need access to validated genomic correlates of resistance, and faster, more informative diagnostics. Therefore, we placed these isolates and their sequences in the public domain for inclusion in the Pseudomonas pan-genome and database projects for further countermeasure development.}, }
@article {pmid28852435, year = {2017}, author = {Hollensteiner, J and Poehlein, A and Spröer, C and Bunk, B and Sheppard, AE and Rosentstiel, P and Schulenburg, H and Liesegang, H}, title = {Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {48}, doi = {10.1186/s40793-017-0259-x}, pmid = {28852435}, issn = {1944-3277}, abstract = {10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis of the genome revealed a large number of mobile elements involved in genome plasticity including 11 plasmids and 16 chromosomal prophages. Three different nematicidal toxin genes were identified and classified according to the Cry toxin naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are located on the chromosome in close proximity to three separate prophages. Moreover, four putative toxin genes of different toxin classes were identified on the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with three closely related 10.1601/nm.5000 strains enabled determination of the pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons, mostly represented by phage genes, morons and cryptic genes.}, }
@article {pmid28846694, year = {2017}, author = {Skov, L and ,  and Schierup, MH}, title = {Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion.}, journal = {PLoS genetics}, volume = {13}, number = {8}, pages = {e1006834}, doi = {10.1371/journal.pgen.1006834}, pmid = {28846694}, issn = {1553-7404}, mesh = {Chromosomes, Human, Y/*genetics ; Denmark ; *Evolution, Molecular ; Fathers ; Gene Conversion/genetics ; Heterochromatin/*genetics ; Humans ; INDEL Mutation/*genetics ; Infertility, Male/genetics/pathology ; Inverted Repeat Sequences/genetics ; Male ; Nuclear Family ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations. It also plays an important role in male fertility. However, its evolution is difficult to fully understand because of repetitive sequences, inverted repeats and the potentially large role of gene conversion. Here we perform an evolutionary analysis of 62 Y-chromosomes of Danish descent sequenced using a wide range of library insert sizes and high coverage, thus allowing large regions of these chromosomes to be well assembled. These include 17 father-son pairs, which we use to validate variation calling. Using a recent method that can integrate variants based on both mapping and de novo assembly, we genotype 10898 SNVs and 2903 indels (max length of 27241 bp) in our sample and show by father-son concordance and experimental validation that the non-recurrent SNP and indel variation on the Y chromosome tree is called very accurately. This includes variation called in a 0.9 Mb centromeric heterochromatic region, which is by far the most variable in the Y chromosome. Among the variation is also longer sequence-stretches not present in the reference genome but shared with the chimpanzee Y chromosome. We analyzed 2.7 Mb of large inverted repeats (palindromes) for variation patterns among the two palindrome arms and identified 603 mutation and 416 gene conversions events. We find clear evidence for GC-biased gene conversion in the palindromes (and a balancing AT mutation bias), but irrespective of this, also a strong bias towards gene conversion towards the ancestral state, suggesting that palindromic gene conversion may alleviate Muller's ratchet. Finally, we also find a large number of large-scale gene duplications and deletions in the palindromic regions (at least 24) and find that such events can consist of complex combinations of simultaneous insertions and deletions of long stretches of the Y chromosome.}, }
@article {pmid28824598, year = {2017}, author = {Tsai, MH and Liu, YY and Soo, VW}, title = {PathoBacTyper: A Web Server for Pathogenic Bacteria Identification and Molecular Genotyping.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1474}, doi = {10.3389/fmicb.2017.01474}, pmid = {28824598}, issn = {1664-302X}, abstract = {With the decline in the cost of whole-genome sequencing because of the introduction of next-generation sequencing (NGS) techniques, many public health and clinical laboratories have started to use bacterial whole genomes for epidemiological surveillance and clinical investigation. For epidemiological and clinical purposes in this &quot;NGS era,&quot; whole-genome-scale single nucleotide polymorphism (wgSNP) analysis for genotyping is considered suitable. In this paper, we present an online service, PathoBacTyper (http://halst.nhri.org.tw/PathoBacTyper/), for pathogenic bacteria identification and genotyping based on wgSNP analysis. More than 400 pathogenic bacteria can be identified and genotyped through this service. Four data sets containing 59 Salmonella Heidelberg isolates from three outbreaks with the same pulsed-field gel electrophoresis pattern, 34 Salmonella Typhimurium isolates from six outbreaks, 103 isolates of hospital-associated vancomycin-resistant Enterococcus faecium and 15 Legionella pneumophila isolates from clinical and environmental samples in Israel were used for demonstrating the operation and testing the performance of the PathoBacTyper service. The test results reveal the applicability of this service for epidemiological typing and clinical investigation.}, }
@article {pmid28824571, year = {2017}, author = {Belbahri, L and Chenari Bouket, A and Rekik, I and Alenezi, FN and Vallat, A and Luptakova, L and Petrovova, E and Oszako, T and Cherrad, S and Vacher, S and Rateb, ME}, title = {Comparative Genomics of Bacillus amyloliquefaciens Strains Reveals a Core Genome with Traits for Habitat Adaptation and a Secondary Metabolites Rich Accessory Genome.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1438}, doi = {10.3389/fmicb.2017.01438}, pmid = {28824571}, issn = {1664-302X}, abstract = {The Gram positive, non-pathogenic endospore-forming soil inhabiting prokaryote Bacillus amyloliquefaciens is a plant growth-promoting rhizobacterium. Bacillus amyloliquefaciens processes wide biocontrol abilities and numerous strains have been reported to suppress diverse bacterial, fungal and fungal-like pathogens. Knowledge about strain level biocontrol abilities is warranted to translate this knowledge into developing more efficient biocontrol agents and bio-fertilizers. Ever-expanding genome studies of B. amyloliquefaciens are showing tremendous increase in strain-specific new secondary metabolite clusters which play key roles in the suppression of pathogens and plant growth promotion. In this report, we have used genome mining of all sequenced B. amyloliquefaciens genomes to highlight species boundaries, the diverse strategies used by different strains to promote plant growth and the diversity of their secondary metabolites. Genome composition of the targeted strains suggest regions of genomic plasticity that shape the structure and function of these genomes and govern strain adaptation to different niches. Our results indicated that B. amyloliquefaciens: (i) suffer taxonomic imprecision that blurs the debate over inter-strain genome diversity and dynamics, (ii) have diverse strategies to promote plant growth and development, (iii) have an unlocked, yet to be delimited impressive arsenal of secondary metabolites and products, (iv) have large number of so-called orphan gene clusters, i.e., biosynthetic clusters for which the corresponding metabolites are yet unknown, and (v) have a dynamic pan genome with a secondary metabolite rich accessory genome.}, }
@article {pmid28824552, year = {2017}, author = {Laing, CR and Whiteside, MD and Gannon, VPJ}, title = {Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1345}, doi = {10.3389/fmicb.2017.01345}, pmid = {28824552}, issn = {1664-302X}, abstract = {Food safety is a global concern, with upward of 2.2 million deaths due to enteric disease every year. Current whole-genome sequencing platforms allow routine sequencing of enteric pathogens for surveillance, and during outbreaks; however, a remaining challenge is the identification of genomic markers that are predictive of strain groups that pose the most significant health threats to humans, or that can persist in specific environments. We have previously developed the software program Panseq, which identifies the pan-genome among a group of sequences, and the SuperPhy platform, which utilizes this pan-genome information to identify biomarkers that are predictive of groups of bacterial strains. In this study, we examined the pan-genome of 4893 genomes of Salmonella enterica, an enteric pathogen responsible for the loss of more disability adjusted life years than any other enteric pathogen. We identified a pan-genome of 25.3 Mbp, a strict core of 1.5 Mbp present in all genomes, and a conserved core of 3.2 Mbp found in at least 96% of these genomes. We also identified 404 genomic regions of 1000 bp that were specific to the species S. enterica. These species-specific regions were found to encode mostly hypothetical proteins, effectors, and other proteins related to virulence. For each of the six S. enterica subspecies, markers unique to each were identified. No serovar had pan-genome regions that were present in all of its genomes and absent in all other serovars; however, each serovar did have genomic regions that were universally present among all constituent members, and statistically predictive of the serovar. The phylogeny based on SNPs within the conserved core genome was found to be highly concordant to that produced by a phylogeny using the presence/absence of 1000 bp regions of the entire pan-genome. Future studies could use these predictive regions as components of a vaccine to prevent salmonellosis, as well as in simple and rapid diagnostic tests for both in silico and wet-lab applications, with uses ranging from food safety to public health. Lastly, the tools and methods described in this study could be applied as a pan-genomics framework to other population genomic studies seeking to identify markers for other bacterial species and their sub-groups.}, }
@article {pmid28821232, year = {2017}, author = {Oshone, R and Ngom, M and Chu, F and Mansour, S and Sy, MO and Champion, A and Tisa, LS}, title = {Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {633}, doi = {10.1186/s12864-017-4056-0}, pmid = {28821232}, issn = {1471-2164}, mesh = {Cell Membrane/metabolism ; Fagales/*microbiology ; Frankia/cytology/*genetics/metabolism/*physiology ; *Gene Expression Profiling ; Nitrogen/pharmacology ; Nucleotides/metabolism ; Osmotic Pressure ; Phenotype ; *Proteomics ; Salt-Tolerance/*genetics ; Trees/*microbiology ; Up-Regulation ; }, abstract = {BACKGROUND: Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the Casuarina. The salt tolerance of Casuarina is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium Frankia. Identification and molecular characterization of salt-tolerant Casuarina species and associated Frankia is imperative for the successful utilization of Casuarina trees in saline soil reclamation efforts. In this study, salt-tolerant and salt-sensitive Casuarina associated Frankia strains were identified and comparative genomics, transcriptome profiling, and proteomics were employed to elucidate the molecular mechanisms of salt and osmotic stress tolerance.<br><br>RESULTS: Salt-tolerant Frankia strains (CcI6 and Allo2) that could withstand up to 1000 mM NaCl and a salt-sensitive Frankia strain (CcI3) which could withstand only up to 475 mM NaCl were identified. The remaining isolates had intermediate levels of salt tolerance with MIC values ranging from 650 mM to 750 mM. Comparative genomic analysis showed that all of the Frankia isolates from Casuarina belonged to the same species (Frankia casuarinae). Pangenome analysis revealed a high abundance of singletons among all Casuarina isolates. The two salt-tolerant strains contained 153 shared single copy genes (most of which code for hypothetical proteins) that were not found in the salt-sensitive(CcI3) and moderately salt-tolerant (CeD) strains. RNA-seq analysis of one of the two salt-tolerant strains (Frankia sp. strain CcI6) revealed hundreds of genes differentially expressed under salt and/or osmotic stress. Among the 153 genes, 7 and 7 were responsive to salt and osmotic stress, respectively. Proteomic profiling confirmed the transcriptome results and identified 19 and 8 salt and/or osmotic stress-responsive proteins in the salt-tolerant (CcI6) and the salt-sensitive (CcI3) strains, respectively.<br><br>CONCLUSION: Genetic differences between salt-tolerant and salt-sensitive Frankia strains isolated from Casuarina were identified. Transcriptome and proteome profiling of a salt-tolerant strain was used to determine molecular differences correlated with differential salt-tolerance and several candidate genes were identified. Mechanisms involving transcriptional and translational regulation, cell envelop remodeling, and previously uncharacterized proteins appear to be important for salt tolerance. Physiological and mutational analyses will further shed light on the molecular mechanism of salt tolerance in Casuarina associated Frankia isolates.}, }
@article {pmid28818331, year = {2017}, author = {Hick, PM and Subramaniam, K and Thompson, PM and Waltzek, TB and Becker, JA and Whittington, RJ}, title = {Molecular epidemiology of Epizootic haematopoietic necrosis virus (EHNV).}, journal = {Virology}, volume = {511}, number = {}, pages = {320-329}, doi = {10.1016/j.virol.2017.07.029}, pmid = {28818331}, issn = {1096-0341}, mesh = {Animals ; DNA Virus Infections/veterinary/virology ; *Disease Outbreaks ; Endemic Diseases ; Fish Diseases/*epidemiology/*virology ; Fishes ; Genes, Viral ; *Genetic Variation ; Genome, Viral ; Iatrogenic Disease/epidemiology/veterinary ; *Molecular Epidemiology ; Ranavirus/*classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; }, abstract = {Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591-127,487 nucleotides with 97.47% pairwise identity and 106-109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3.43 × 10-4 substitutions per site. Evolutionary analysis of the core genome strongly supported historical epidemiological evidence of iatrogenic spread of EHNV to naïve hosts and establishment of endemic status in discrete ecological niches. There was no evidence of structural genome reorganization, however, the complement of non-core genes and variation in repeat elements enabled fine scale molecular epidemiological investigation of this unpredictable pathogen of fish.}, }
@article {pmid28798737, year = {2017}, author = {Tripathi, C and Mishra, H and Khurana, H and Dwivedi, V and Kamra, K and Negi, RK and Lal, R}, title = {Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1410}, doi = {10.3389/fmicb.2017.01410}, pmid = {28798737}, issn = {1664-302X}, abstract = {Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%). We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5) by recruiting raw metagenomic data (from the same niche) against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.}, }
@article {pmid28774965, year = {2017}, author = {Jensen, JM and Villesen, P and Friborg, RM and ,  and Mailund, T and Besenbacher, S and Schierup, MH}, title = {Assembly and analysis of 100 full MHC haplotypes from the Danish population.}, journal = {Genome research}, volume = {27}, number = {9}, pages = {1597-1607}, doi = {10.1101/gr.218891.116}, pmid = {28774965}, issn = {1549-5469}, mesh = {Alleles ; Chromosome Mapping ; Denmark ; Genetic Variation/*genetics ; *Genetics, Population ; Haplotypes/genetics ; Humans ; Linkage Disequilibrium/*genetics ; Major Histocompatibility Complex/*genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Genes in the major histocompatibility complex (MHC, also known as HLA) play a critical role in the immune response and variation within the extended 4-Mb region shows association with major risks of many diseases. Yet, deciphering the underlying causes of these associations is difficult because the MHC is the most polymorphic region of the genome with a complex linkage disequilibrium structure. Here, we reconstruct full MHC haplotypes from de novo assembled trios without relying on a reference genome and perform evolutionary analyses. We report 100 full MHC haplotypes and call a large set of structural variants in the regions for future use in imputation with GWAS data. We also present the first complete analysis of the recombination landscape in the entire region and show how balancing selection at classical genes have linked effects on the frequency of variants throughout the region.}, }
@article {pmid28768476, year = {2017}, author = {Bazinet, AL}, title = {Pan-genome and phylogeny of Bacillus cereus sensu lato.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {176}, doi = {10.1186/s12862-017-1020-1}, pmid = {28768476}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Bacillus cereus/*classification/*genetics ; Bayes Theorem ; Cluster Analysis ; Codon/genetics ; DNA Transposable Elements/genetics ; Genes, Bacterial ; Genetic Association Studies ; *Genome, Bacterial ; Likelihood Functions ; *Phylogeny ; Quantitative Trait, Heritable ; Recombination, Genetic/genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {BACKGROUND: Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., &quot;pan-GWAS&quot; analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered.<br><br>METHODS: A rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes.<br><br>RESULTS: The B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are &quot;core&quot; (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering.<br><br>CONCLUSIONS: All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.}, }
@article {pmid28764658, year = {2017}, author = {Lugli, GA and Milani, C and Turroni, F and Duranti, S and Mancabelli, L and Mangifesta, M and Ferrario, C and Modesto, M and Mattarelli, P and Jiří, K and van Sinderen, D and Ventura, M}, title = {Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {568}, doi = {10.1186/s12864-017-3955-4}, pmid = {28764658}, issn = {1471-2164}, mesh = {Bifidobacterium/*genetics ; Evolution, Molecular ; *Genomics ; *Phylogeny ; }, abstract = {BACKGROUND: Members of the Bifidobacteriaceae family represent both dominant microbial groups that colonize the gut of various animals, especially during the suckling stage of their life, while they also occur as pathogenic bacteria of the urogenital tract. The pan-genome of the genus Bifidobacterium has been explored in detail in recent years, though genomics of the Bifidobacteriaceae family has not yet received much attention. Here, a comparative genomic analyses of 67 Bifidobacteriaceae (sub) species including all currently recognized genera of this family, i.e., Aeriscardovia, Alloscardovia, Bifidobacterium, Bombiscardovia, Gardnerella, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia, was performed. Furthermore, in order to include a representative of each of the 67 (currently recognized) (sub) species belonging to the Bifidobacteriaceae family, we sequenced the genomes of an additional 11 species from this family, accomplishing the most extensive comparative genomic analysis performed within this family so far.<br><br>RESULTS: Phylogenomics-based analyses revealed the deduced evolutionary pathway followed by each member of the Bifidobacteriaceae family, highlighting Aeriscardovia aeriphila LMG 21773 as the deepest branch in the evolutionary tree of this family. Furthermore, functional analyses based on genome content unveil connections between a given member of the family, its carbohydrate utilization abilities and its corresponding host. In this context, bifidobacterial (sub) species isolated from humans and monkeys possess the highest relative number of acquired glycosyl hydrolase-encoding genes, probably in order to enhance their metabolic ability to utilize different carbon sources consumed by the host.<br><br>CONCLUSIONS: Within the Bifidobacteriaceae family, genomics of the genus Bifidobacterium has been extensively investigated. In contrast, very little is known about the genomics of members of the other eight genera of this family. In this study, we decoded the genome sequences of each member of the Bifidobacteriaceae family. Thanks to subsequent comparative genomic and phylogenetic analyses, the deduced pan-genome of this family, as well as the predicted evolutionary development of each taxon belonging to this family was assessed.}, }
@article {pmid28744269, year = {2017}, author = {Yu, Z and Ma, Y and Zhong, W and Qiu, J and Li, J}, title = {Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1278}, doi = {10.3389/fmicb.2017.01278}, pmid = {28744269}, issn = {1664-302X}, abstract = {Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.}, }
@article {pmid28742023, year = {2017}, author = {Lees, JA and Croucher, NJ and Goldblatt, D and Nosten, F and Parkhill, J and Turner, C and Turner, P and Bentley, SD}, title = {Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, doi = {10.7554/eLife.26255}, pmid = {28742023}, issn = {2050-084X}, support = {//Wellcome Trust/United Kingdom ; 098051//Wellcome Trust/United Kingdom ; 1365620//Medical Research Council/United Kingdom ; 104169/Z/14/Z//Wellcome Trust/United Kingdom ; 083735/Z/07/Z//Wellcome Trust/United Kingdom ; }, mesh = {Age Factors ; Anti-Bacterial Agents/pharmacology ; Carrier State ; Child, Preschool ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; *Genetic Variation ; *Genome, Bacterial ; Genome-Wide Association Study ; Genotype ; *Host-Pathogen Interactions ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Markov Chains ; Models, Genetic ; Nasopharynx/immunology/*microbiology ; Phylogeny ; Serogroup ; Streptococcus pneumoniae/classification/drug effects/*genetics/isolation &amp; purification ; Time Factors ; }, abstract = {Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.}, }
@article {pmid28736702, year = {2017}, author = {Solorzano Zambrano, L and Usai, G and Vangelisti, A and Mascagni, F and Giordani, T and Bernardi, R and Cavallini, A and Gucci, R and Caruso, G and D'Onofrio, C and Quartacci, MF and Picciarelli, P and Conti, B and Lucchi, A and Natali, L}, title = {Cultivar-specific transcriptome prediction and annotation in Ficus carica L.}, journal = {Genomics data}, volume = {13}, number = {}, pages = {64-66}, doi = {10.1016/j.gdata.2017.07.005}, pmid = {28736702}, issn = {2213-5960}, abstract = {The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv. Dottato. Then, putative gene sequences were predicted and annotated. Finally, a comparison was performed between cvs. Dottato and Horaishi predicted transcriptomes. Our data provide a resource (available at the Sequence Read Archive database under SRP109082) to be used for functional genomics of fig, in order to fill the gap of knowledge still existing in this species concerning plant development, defense and adaptation to the environment.}, }
@article {pmid28720902, year = {2017}, author = {Xu, H and Qin, S and Lan, Y and Liu, M and Cao, X and Qiao, D and Cao, Y and Cao, Y}, title = {Comparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5720}, doi = {10.1038/s41598-017-06160-9}, pmid = {28720902}, issn = {2045-2322}, abstract = {The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus. Furthermore, a large number of genes gained are associated with carbohydrate transport and metabolism. It indicates that the evolution of glycometabolism is a key factor for the environmental adaptability of Paenibacillus species. Interestingly, through horizontal gene transfer, Paenibacillus sp. SSG-1 acquired an approximately 150 kb DNA fragment and shows an agar-degrading characteristic distinct from most other non-marine bacteria. This region may be transported in bacteria as a complete unit responsible for agar degradation. Taken together, these results provide insights into the evolutionary pattern of Paenibacillus and have implications for studies on the taxonomy and functional genomics of this genus.}, }
@article {pmid28717847, year = {2017}, author = {Meng, P and Lu, C and Zhang, Q and Lin, J and Chen, F}, title = {Exploring the Genomic Diversity and Cariogenic Differences of Streptococcus mutans Strains Through Pan-Genome and Comparative Genome Analysis.}, journal = {Current microbiology}, volume = {74}, number = {10}, pages = {1200-1209}, doi = {10.1007/s00284-017-1305-z}, pmid = {28717847}, issn = {1432-0991}, support = {PKUSS20130210//Peking University School of Stomatology/ ; }, mesh = {Bacterial Typing Techniques ; Computational Biology/methods ; Databases, Genetic ; *Genetic Variation ; *Genome, Bacterial ; *Genomics/methods ; Molecular Sequence Annotation ; Streptococcus mutans/*classification/*genetics ; Virulence Factors/genetics ; }, abstract = {Pan-genome refers to the sum of genes that can be found in a given bacterial species, including the core-genome and the dispensable genome. In this study, the genomes from 183 Streptococcus mutans (S. mutans) isolates were analyzed from the pan-genome perspective. This analysis revealed that S. mutans has an &quot;open&quot; pan-genome, implying that there are plenty of new genes to be found as more genomes are sequenced. Additionally, S. mutans has a limited core-genome, which is composed of genes related to vital activities within the bacterium, such as metabolism and hereditary information storage or processing, occupying 35.6 and 26.6% of the core genes, respectively. We estimate the theoretical core-genome size to be about 1083 genes, which are fewer than other Streptococcus species. In addition, core genes suffer larger selection pressures in comparison to those that are less widely distributed. Not surprisingly, the distribution of putative virulence genes in S. mutans strains does not correlate with caries status, indicating that other factors are also responsible for cariogenesis. These results contribute to a more understanding of the evolutionary characteristics and dynamic changes within the genome components of the species. This also helps to form a new theoretical foundation for preventing dental caries. Furthermore, this study sets an example for analyzing large genomic datasets of pathogens from the pan-genome perspective.}, }
@article {pmid28710456, year = {2017}, author = {Jeong, DW and Heo, S and Ryu, S and Blom, J and Lee, JH}, title = {Genomic insights into the virulence and salt tolerance of Staphylococcus equorum.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5383}, doi = {10.1038/s41598-017-05918-5}, pmid = {28710456}, issn = {2045-2322}, abstract = {To shed light on the genetic background behind the virulence and salt tolerance of Staphylococcus equorum, we performed comparative genome analysis of six S. equorum strains. Data on four previously published genome sequences were obtained from the NCBI database, while those on strain KM1031 displaying resistance to multiple antibiotics and strain C2014 causing haemolysis were determined in this study. Examination of the pan-genome of five of the six S. equorum strains showed that the conserved core genome retained the genes for general physiological processes and survival of the species. In this comparative genomic analysis, the factors that distinguish the strains from each other, including acquired genomic factors in mobile elements, were identified. Additionally, the high salt tolerance of strains enabling growth at a NaCl concentration of 25% (w/v) was attributed to the genes encoding potassium voltage-gated channels. Among the six strains, KS1039 does not possess any of the functional virulence determinants expressed in the other strains.}, }
@article {pmid28706512, year = {2017}, author = {Machado, H and Gram, L}, title = {Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1204}, doi = {10.3389/fmicb.2017.01204}, pmid = {28706512}, issn = {1664-302X}, abstract = {Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.}, }
@article {pmid28705964, year = {2017}, author = {Rothen, J and Schindler, T and Pothier, JF and Younan, M and Certa, U and Daubenberger, C and Pflüger, V and Jores, J}, title = {Draft Genome Sequences of Seven Streptococcus agalactiae Strains Isolated from Camelus dromedarius at the Horn of Africa.}, journal = {Genome announcements}, volume = {5}, number = {28}, pages = {}, doi = {10.1128/genomeA.00525-17}, pmid = {28705964}, issn = {2169-8287}, abstract = {We present draft whole-genome sequences of seven Streptococcus agalactiae strains isolated from Camelus dromedarius in Kenya and Somalia. These data are an extension to the group B Streptococcus (GBS) pangenome and might provide more insight into the underlying mechanisms of pathogenicity and antibiotic resistance of camel GBS.}, }
@article {pmid28674418, year = {2017}, author = {Proença, JT and Barral, DC and Gordo, I}, title = {Commensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli -macrophage interaction.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4504}, doi = {10.1038/s41598-017-04081-1}, pmid = {28674418}, issn = {2045-2322}, abstract = {Escherichia coli is both a harmless commensal in the intestines of many mammals, as well as a dangerous pathogen. The evolutionary paths taken by strains of this species in the commensal-to-pathogen transition are complex and can involve changes both in the core genome, as well in the pan-genome. One way to understand the likely paths that a commensal strain of E. coli takes when evolving pathogenicity is through experimentally evolving the strain under the selective pressures that it will have to withstand as a pathogen. Here, we report that a commensal strain, under continuous pressure from macrophages, recurrently acquired a transposable element insertion, which resulted in two key phenotypic changes: increased intracellular survival, through the delay of phagosome maturation and increased ability to escape macrophages. We further show that the acquisition of the pathoadaptive traits was accompanied by small but significant changes in the transcriptome of macrophages upon infection. These results show that under constant pressures from a key component of the host immune system, namely macrophage phagocytosis, commensal E. coli rapidly acquires pathoadaptive mutations that cause transcriptome changes associated to the host-microbe duet.}, }
@article {pmid28664513, year = {2017}, author = {Yang, JA and Yang, SH and Kim, J and Kwon, KK and Oh, HM}, title = {Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {55}, number = {7}, pages = {583-591}, doi = {10.1007/s12275-017-7172-2}, pmid = {28664513}, issn = {1976-3794}, mesh = {Animals ; Base Composition ; Biotin/metabolism ; Brachyura/*microbiology ; Flavobacteriaceae/*genetics/isolation &amp; purification ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Intestines/microbiology ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Annotation ; Nitrogen/metabolism ; Pentose Phosphate Pathway/genetics ; Phylogeny ; Republic of Korea ; Sequence Analysis, DNA ; Shellfish/*microbiology ; Thiamine/metabolism ; }, abstract = {Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden-Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.}, }
@article {pmid28645159, year = {2017}, author = {Jimenez-Infante, F and Ngugi, DK and Vinu, M and Blom, J and Alam, I and Bajic, VB and Stingl, U}, title = {Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {7}, pages = {}, doi = {10.1093/femsec/fix083}, pmid = {28645159}, issn = {1574-6941}, mesh = {*Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Aquatic Organisms/*classification/*genetics ; Bacterial Adhesion/physiology ; Genome, Bacterial/*genetics ; Indian Ocean ; Phylogeny ; Seawater/microbiology ; }, abstract = {The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea: one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter.}, }
@article {pmid28642379, year = {2017}, author = {Veseli, IA and Tang, C and Pombert, JF}, title = {Complete Genome Sequence of Staphylococcus lutrae ATCC 700373, a Potential Pathogen Isolated from Deceased Otters.}, journal = {Genome announcements}, volume = {5}, number = {25}, pages = {}, doi = {10.1128/genomeA.00572-17}, pmid = {28642379}, issn = {2169-8287}, abstract = {Despite their relevance to human health, not all staphylococcal species have been characterized. As such, the potential zoonotic threats posed by uninvestigated species and their contribution to the staphylococcal pangenome are unclear. Here, we report the complete genome sequence of Staphylococcus lutrae ATCC 700373, a coagulase-positive species isolated from deceased otters.}, }
@article {pmid28637301, year = {2017}, author = {Münch, PC and Stecher, B and McHardy, AC}, title = {EDEN: evolutionary dynamics within environments.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {20}, pages = {3292-3295}, doi = {10.1093/bioinformatics/btx394}, pmid = {28637301}, issn = {1367-4811}, mesh = {Bacteria/genetics ; *Biological Evolution ; Metagenomics/*methods ; Phenotype ; *Phylogeny ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses.<br><br>EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden.<br><br>Contact: alice.mchardy@helmholtz-hzi.de.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28633403, year = {2017}, author = {Anderson, RE and Kouris, A and Seward, CH and Campbell, KM and Whitaker, RJ}, title = {Structured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1699-1710}, doi = {10.1093/gbe/evx104}, pmid = {28633403}, issn = {1759-6653}, mesh = {*DNA Transposable Elements ; Evolution, Molecular ; Gene Deletion ; Genome, Archaeal ; Hot Springs/chemistry/microbiology ; Phylogeny ; Plasmids/genetics ; Sulfolobus acidocaldarius/classification/*genetics/isolation &amp; purification ; }, abstract = {The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring &quot;islands&quot; in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldarius genomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobus species result in the relatively low diversity of the S. acidocaldarius genome.}, }
@article {pmid28629190, year = {2017}, author = {Borchert, E and Knobloch, S and Dwyer, E and Flynn, S and Jackson, SA and Jóhannsson, R and Marteinsson, VT and O'Gara, F and Dobson, ADW}, title = {Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from 'Deep Sea' Sponges.}, journal = {Marine drugs}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/md15060184}, pmid = {28629190}, issn = {1660-3397}, mesh = {Animals ; *Biotechnology ; Cold Temperature ; Genome, Bacterial ; Porifera/*microbiology ; Pseudoalteromonas/enzymology/*genetics ; Recombinant Proteins/biosynthesis ; beta-Galactosidase/genetics ; beta-Glucosidase/genetics ; }, abstract = {The marine genus Pseudoalteromonas is known for its versatile biotechnological potential with respect to the production of antimicrobials and enzymes of industrial interest. We have sequenced the genomes of three Pseudoalteromonas sp. strains isolated from different deep sea sponges on the Illumina MiSeq platform. The isolates have been screened for various industrially important enzymes and comparative genomics has been applied to investigate potential relationships between the isolates and their host organisms, while comparing them to free-living Pseudoalteromonas spp. from shallow and deep sea environments. The genomes of the sponge associated Pseudoalteromonas strains contained much lower levels of potential eukaryotic-like proteins which are known to be enriched in symbiotic sponge associated microorganisms, than might be expected for true sponge symbionts. While all the Pseudoalteromonas shared a large distinct subset of genes, nonetheless the number of unique and accessory genes is quite large and defines the pan-genome as open. Enzymatic screens indicate that a vast array of enzyme activities is expressed by the isolates, including β-galactosidase, β-glucosidase, and protease activities. A β-glucosidase gene from one of the Pseudoalteromonas isolates, strain EB27 was heterologously expressed in Escherichia coli and, following biochemical characterization, the recombinant enzyme was found to be cold-adapted, thermolabile, halotolerant, and alkaline active.}, }
@article {pmid28625995, year = {2017}, author = {Lau, CH and van Engelen, K and Gordon, S and Renaud, J and Topp, E}, title = {NOVEL ANTIBIOTIC RESISTANCE DETERMINANTS FROM AGRICULTURAL SOIL EXPOSED TO ANTIBIOTICS WIDELY USED IN HUMAN MEDICINE AND ANIMAL FARMING.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00989-17}, pmid = {28625995}, issn = {1098-5336}, abstract = {Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized for accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are &quot;hotspots&quot; for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria. Using functional metagenomics, we interrogated the &quot;resistome&quot; of bacterial communities found in a collection of Canadian agricultural soil, some of which had been receiving antibiotics widely used in human medicine (macrolides) or food animal production (sulfamethazine, chlortetracycline and tylosin) for up to 16 years. Of the 34 new antibiotic resistance genes (ARGs) recovered, the majority were predicted to encode for (multi)drug efflux systems, while a few share little to no homology with established resistance determinants. We characterized several novel gene products, including putative enzymes that can confer high-level resistance against aminoglycosides, sulfonamides, and broad range of beta-lactams, with respect to their resistance mechanisms and clinical significance. By coupling high-resolution proteomics analysis with functional metagenomics, we discovered an unusual peptide, PPPAZI 4, encoded within an alternative open-reading frame not predicted by bioinformatics tools. Expression of the proline-rich PPPAZI 4 can promote resistance against different macrolides but not other ribosomal-targeting antibiotics, implicating a new macrolide-specific resistance mechanism that could be fundamentally linked to the evolutionary design of this peptide.IMPORTANCE Antibiotic resistance is a clinical phenomenon with an evolutionary link to the microbial pangenome. Genes and protogenes encoding for specialized and potential resistance mechanisms are abundant in natural environments, but understanding of their identity and genomic context remain limited. Our discovery of several previously-unknown antibiotic resistance genes from uncultured soil microorganisms indicates that soil is a significant reservoir of resistance determinants, which, once acquired and &quot;re-purposed&quot; by pathogenic bacteria, can have serious impacts on therapeutic outcomes. This study provides valuable insights into the diversity and identity of resistance within the soil microbiome. The finding of a novel peptide-mediated resistance mechanism involving an unpredicted gene product also highlights the usefulness of integrating proteomics analysis into metagenomics-driven gene discovery.}, }
@article {pmid28624550, year = {2017}, author = {Kayansamruaj, P and Dong, HT and Hirono, I and Kondo, H and Senapin, S and Rodkhum, C}, title = {Comparative genome analysis of fish pathogen Flavobacterium columnare reveals extensive sequence diversity within the species.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {54}, number = {}, pages = {7-17}, doi = {10.1016/j.meegid.2017.06.012}, pmid = {28624550}, issn = {1567-7257}, mesh = {Animals ; Fish Diseases/*microbiology ; Fishes/microbiology ; Flavobacteriaceae Infections/*microbiology/*veterinary ; Flavobacterium/classification/*genetics ; Genome, Bacterial/*genetics ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA ; }, abstract = {Flavobacterium columnare is one of the deadliest fish pathogens causing devastating mortality in various freshwater fish species globally. To gain an insight into bacterial genomic contents and structures, comparative genome analyses were performed using the reference and newly sequenced genomes of F. columnare including genomovar I, II and I/II strains isolated from Thailand, Europe and the USA. Bacterial genomes varied in size from 3.09 to 3.39Mb (2714 to 3101 CDSs). The pan-genome analysis revealed open pan-genome nature of F. columnare strains, which possessed at least 4953 genes and tended to increase progressively with the addition of a new genome. Genomic islands (GIs) present in bacterial genomes were diverse, in which 65% (39 out of 60) of possible GIs were strain-specific. A CRISPR/cas investigation indicated at least two different CRISPR systems with varied spacer profiles. On the other hand, putative virulence genes, including those related to gliding motility, type IX secretion system (T9SS), outer membrane proteins (Omp), were equally distributed among F. columnare strains. The MLSA scheme categorized bacterial strains into nine different sequence types (ST 9-17). Phylogenetic analyses based on either 16S rRNA, MLSA and concatenated SNPs of core genome revealed the diversity of F. columnare strains. DNA homology analysis indicated that the estimated digital DNA-DNA hybridization (dDDH) between strains of genomovar I and II can be as low as 42.6%, while the three uniquely tilapia-originated strains from Thailand (1214, NK01 and 1215) were clearly dissimilar to other F. columnare strains as the dDDH values were only 27.7-30.4%. Collectively, this extensive diversity among bacterial strains suggested that species designation of F. columnare would potentially require re-emendation.}, }
@article {pmid28620358, year = {2017}, author = {Soberón-Chávez, G and Alcaraz, LD and Morales, E and Ponce-Soto, GY and Servín-González, L}, title = {The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {959}, doi = {10.3389/fmicb.2017.00959}, pmid = {28620358}, issn = {1664-302X}, abstract = {One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3'-5'-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the position of its interaction with respect to RNA polymerase binding site. The aim of this work is to review the biological role and phylogenetic relations that some members of the CRP family of transcriptional regulators (also known as cAMP receptor protein family) have in different bacterial species. This work is not intended to give an exhaustive revision of bacterial CRP-orthologs, but to provide examples of the role that these proteins play in the expression of genes that are fundamental for the life style of some bacterial species. We highlight the conservation of their structural characteristics and of their binding to conserved-DNA sequences, in contrast to their very diverse repertoire of gene activation. CRP activates a wide variety of fundamental genes for the biological characteristic of each bacterial species, which in several instances form part of their core-genome (defined as the gene sequences present in all members of a bacterial species). We present evidence that support the fact that some of the transcriptional regulators that belong to the CRP family in different bacterial species, and some of the genes that are regulated by them, can be inherited by horizontal gene transfer. These data are discussed in the framework of bacterial evolution models.}, }
@article {pmid28615683, year = {2017}, author = {Collins, FWJ and O'Connor, PM and O'Sullivan, O and Gómez-Sala, B and Rea, MC and Hill, C and Ross, RP}, title = {Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3481}, doi = {10.1038/s41598-017-03339-y}, pmid = {28615683}, issn = {2045-2322}, abstract = {Lactobacilli constitute a large genus of Gram-positive lactic acid bacteria which have widespread roles ranging from gut commensals to starters in fermented foods. A combination of in silico and laboratory-based screening allowed us to determine the overall bacteriocin producing potential of representative strains of each species of the genus. The genomes of 175 lactobacilli and 38 associated species were screened for the presence of antimicrobial producing genes and combined with screening for antimicrobial activity against a range of indicators. There also appears to be a link between the strains' environment and bacteriocin production, with those from the animal and human microbiota encoding over twice as many bacteriocins as those from other sources. Five novel bacteriocins were identified belonging to differing bacteriocin classes, including two-peptide bacteriocins (muricidin and acidocin X) and circular bacteriocins (paracyclicin). In addition, there was a clear clustering of helveticin type bacteriolysins in the Lactobacillus acidophilus group of species. This combined in silico and in vitro approach to screening has demonstrated the true diversity and complexity of bacteriocins across the genus. It also highlights their biological importance in terms of communication and competition between closely related strains in diverse complex microbial environments.}, }
@article {pmid28615466, year = {2017}, author = {Howell, KJ and Weinert, LA and Peters, SE and Wang, J and Hernandez-Garcia, J and Chaudhuri, RR and Luan, SL and Angen, Ø and Aragon, V and Williamson, SM and Langford, PR and Rycroft, AN and Wren, BW and Maskell, DJ and Tucker, AW}, title = {&quot;Pathotyping&quot; Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence.}, journal = {Journal of clinical microbiology}, volume = {55}, number = {9}, pages = {2617-2628}, doi = {10.1128/JCM.02464-16}, pmid = {28615466}, issn = {1098-660X}, support = {BB/G019177/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G020744/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G019274/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; BB/G018553/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 109385/Z/15/Z//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Genome/genetics ; Haemophilus Infections/*diagnosis/microbiology/*veterinary ; Haemophilus parasuis/*genetics/isolation &amp; purification/*pathogenicity ; Molecular Diagnostic Techniques/*methods ; Multiplex Polymerase Chain Reaction ; Swine ; Swine Diseases/*diagnosis/microbiology ; Virulence/genetics ; }, abstract = {Haemophilus parasuis is a diverse bacterial species that is found in the upper respiratory tracts of pigs and can also cause Glässer's disease and pneumonia. A previous pangenome study of H. parasuis identified 48 genes that were associated with clinical disease. Here, we describe the development of a generalized linear model (termed a pathotyping model) to predict the potential virulence of isolates of H. parasuis based on a subset of 10 genes from the pangenome. A multiplex PCR (mPCR) was constructed based on these genes, the results of which were entered into the pathotyping model to yield a prediction of virulence. This new diagnostic mPCR was tested on 143 field isolates of H. parasuis that had previously been whole-genome sequenced and a further 84 isolates from the United Kingdom from cases of H. parasuis-related disease in pigs collected between 2013 and 2014. The combination of the mPCR and the pathotyping model predicted the virulence of an isolate with 78% accuracy for the original isolate collection and 90% for the additional isolate collection, providing an overall accuracy of 83% (81% sensitivity and 93% specificity) compared with that of the &quot;current standard&quot; of detailed clinical metadata. This new pathotyping assay has the potential to aid surveillance and disease control in addition to serotyping data.}, }
@article {pmid28611758, year = {2017}, author = {Cao, P and Guo, D and Liu, J and Jiang, Q and Xu, Z and Qu, L}, title = {Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {961}, doi = {10.3389/fmicb.2017.00961}, pmid = {28611758}, issn = {1664-302X}, abstract = {Pasteurella multocida, a Gram-negative opportunistic pathogen, has led to a broad range of diseases in mammals and birds, including fowl cholera in poultry, pneumonia and atrophic rhinitis in swine and rabbit, hemorrhagic septicemia in cattle, and bite infections in humans. In order to better interpret the genetic diversity and adaptation evolution of this pathogen, seven genomes of P. multocida strains isolated from fowls, rabbit and pigs were determined by using high-throughput sequencing approach. Together with publicly available P. multocida genomes, evolutionary features were systematically analyzed in this study. Clustering of 70,565 protein-coding genes showed that the pangenome of 33 P. multocida strains was composed of 1,602 core genes, 1,364 dispensable genes, and 1,070 strain-specific genes. Of these, we identified a full spectrum of genes related to virulence factors and revealed genetic diversity of these potential virulence markers across P. multocida strains, e.g., bcbAB, fcbC, lipA, bexDCA, ctrCD, lgtA, lgtC, lic2A involved in biogenesis of surface polysaccharides, hsf encoding autotransporter adhesin, and fhaB encoding filamentous haemagglutinin. Furthermore, based on genome-wide positive selection scanning, a total of 35 genes were subject to strong selection pressure. Extensive analyses of protein subcellular location indicated that membrane-associated genes were highly abundant among all positively selected genes. The detected amino acid sites undergoing adaptive selection were preferably located in extracellular space, perhaps associated with bacterial evasion of host immune responses. Our findings shed more light on conservation and distribution of virulence-associated genes across P. multocida strains. Meanwhile, this study provides a genetic context for future researches on the mechanism of adaptive evolution in P. multocida.}, }
@article {pmid28599670, year = {2017}, author = {Kong, LC and Guo, X and Wang, Z and Gao, YH and Jia, BY and Liu, SM and Ma, HX}, title = {Whole genome sequencing of an ExPEC that caused fatal pneumonia at a pig farm in Changchun, China.}, journal = {BMC veterinary research}, volume = {13}, number = {1}, pages = {169}, doi = {10.1186/s12917-017-1093-5}, pmid = {28599670}, issn = {1746-6148}, mesh = {Animals ; Bacterial Capsules/metabolism ; China ; DNA, Bacterial ; Escherichia coli Infections/microbiology/pathology/*veterinary ; Extraintestinal Pathogenic Escherichia coli/classification/drug effects/*genetics/isolation &amp; purification ; Farms ; *Genome, Bacterial ; Lung/microbiology/pathology ; Mice ; Microbial Sensitivity Tests ; Multigene Family ; Phylogeny ; Pneumonia, Bacterial/microbiology/*veterinary ; Polysaccharides, Bacterial/biosynthesis ; Sequence Analysis, DNA/veterinary ; Serotyping ; Swine ; Swine Diseases/*microbiology/pathology ; Virulence/genetics ; }, abstract = {BACKGROUND: In recent years, highly frequent swine respiratory diseases have been caused by extraintestinal pathogenic Escherichia coli (ExPEC) in China. Due to this increase in ExPECs, this bacterial pathogen has become a threat to the development of the Chinese swine industry. To investigate ExPEC pathogenesis, we isolated a strain (named SLPE) from lesioned porcine lungs from Changchun in China, reported the draft genome and performed comparative genomic analyses.<br><br>RESULTS: Based on the gross post-mortem examination, bacterial isolation, animal regression test and 16S rRNA gene sequence analysis, the pathogenic bacteria was identified as an ExPEC. The SLPE draft genome was 4.9 Mb with a G + C content of 51.7%. The phylogenomic comparison indicated that the SLPE strain belongs to the B1 monophyletic phylogroups and that its closest relative is Avian Pathogenic Escherichia coli (APEC) O78. However, the distribution diagram of the pan-genome virulence genes demonstrated significant differences between SLPE and APEC078. We also identified a capsular polysaccharide synthesis gene cluster (CPS) in the SLPE strain genomes using blastp.<br><br>CONCLUSIONS: We isolated the ExPEC (SLPE) from swine lungs in China, performed the whole genome sequencing and compared the sequence with other Escherichia coli (E. coli). The comparative genomic analysis revealed several genes including several virulence factors that are ExPEC strain-specific, such as fimbrial adhesins (papG II), ireA, pgtP, hlyF, the pix gene cluster and fecR for their further study. We found a CPS in the SLPE strain genomes for the first time, and this CPS is closely related to the CPS from Klebsiella pneumoniae.}, }
@article {pmid28593194, year = {2017}, author = {Gordon, DM and Geyik, S and Clermont, O and O'Brien, CL and Huang, S and Abayasekara, C and Rajesh, A and Kennedy, K and Collignon, P and Pavli, P and Rodriguez, C and Johnston, BD and Johnson, JR and Decousser, JW and Denamur, E}, title = {Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection.}, journal = {mSphere}, volume = {2}, number = {3}, pages = {}, doi = {10.1128/mSphere.00168-17}, pmid = {28593194}, issn = {2379-5042}, abstract = {The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. IMPORTANCEEscherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages.}, }
@article {pmid28567447, year = {2017}, author = {Kumar, R and Verma, H and Haider, S and Bajaj, A and Sood, U and Ponnusamy, K and Nagar, S and Shakarad, MN and Negi, RK and Singh, Y and Khurana, JP and Gilbert, JA and Lal, R}, title = {Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.}, journal = {mSystems}, volume = {2}, number = {3}, pages = {}, doi = {10.1128/mSystems.00020-17}, pmid = {28567447}, issn = {2379-5077}, abstract = {Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups-rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed β-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats-freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism's genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe's respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.}, }
@article {pmid28567052, year = {2017}, author = {Minio, A and Lin, J and Gaut, BS and Cantu, D}, title = {How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {826}, doi = {10.3389/fpls.2017.00826}, pmid = {28567052}, issn = {1664-462X}, }
@article {pmid28542514, year = {2017}, author = {Pantoja, Y and Pinheiro, K and Veras, A and Araújo, F and Lopes de Sousa, A and Guimarães, LC and Silva, A and Ramos, RTJ}, title = {PanWeb: A web interface for pan-genomic analysis.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0178154}, doi = {10.1371/journal.pone.0178154}, pmid = {28542514}, issn = {1932-6203}, mesh = {Algorithms ; Computational Biology ; Computer Graphics ; Databases, Genetic ; Escherichia coli/classification/genetics ; Genome, Bacterial ; *Genomics ; High-Throughput Nucleotide Sequencing ; Internet ; Phylogeny ; Programming Languages ; *Software ; *User-Computer Interface ; }, abstract = {With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species. Thus, a new approach to comparative genomics, termed pan-genomics, was developed. In pan-genomics, various organisms of the same species or genus are compared. Currently, there are many tools that can perform pan-genomic analyses, such as PGAP (Pan-Genome Analysis Pipeline), Panseq (Pan-Genome Sequence Analysis Program) and PGAT (Prokaryotic Genome Analysis Tool). Among these software tools, PGAP was developed in the Perl scripting language and its reliance on UNIX platform terminals and its requirement for an extensive parameterized command line can become a problem for users without previous computational knowledge. Thus, the aim of this study was to develop a web application, known as PanWeb, that serves as a graphical interface for PGAP. In addition, using the output files of the PGAP pipeline, the application generates graphics using custom-developed scripts in the R programming language. PanWeb is freely available at http://www.computationalbiology.ufpa.br/panweb.}, }
@article {pmid28534829, year = {2017}, author = {Finke, JF and Winget, DM and Chan, AM and Suttle, CA}, title = {Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution.}, journal = {Viruses}, volume = {9}, number = {5}, pages = {}, doi = {10.3390/v9050116}, pmid = {28534829}, issn = {1999-4915}, mesh = {Base Sequence ; Chlorophyta/classification/*genetics/*virology ; DNA Viruses/*genetics ; DNA-Directed DNA Polymerase/genetics ; Environment ; Gene Transfer, Horizontal/*genetics ; Genes, Viral ; Genetic Variation ; Genome, Viral/*genetics ; Marine Biology ; Phycodnaviridae/classification/*genetics/isolation &amp; purification/pathogenicity ; Phylogeny ; Phytoplankton/virology ; }, abstract = {Prasinophytes, a group of eukaryotic phytoplankton, has a global distribution and is infected by large double-stranded DNA viruses (prasinoviruses) in the family Phycodnaviridae. This study examines the genetic repertoire, phylogeny, and environmental distribution of phycodnaviruses infecting Micromonas pusilla, other prasinophytes and chlorophytes. Based on comparisons among the genomes of viruses infecting M. pusilla and other phycodnaviruses, as well as the genome from a host isolate of M. pusilla, viruses infecting M. pusilla (MpVs) share a limited set of core genes, but vary strongly in their flexible pan-genome that includes numerous metabolic genes, such as those associated with amino acid synthesis and sugar manipulation. Surprisingly, few of these presumably host-derived genes are shared with M. pusilla, but rather have their closest non-viral homologue in bacteria and other eukaryotes, indicating horizontal gene transfer. A comparative analysis of full-length DNA polymerase (DNApol) genes from prasinoviruses with their overall gene content, demonstrated that the phylogeny of DNApol gene fragments reflects the gene content of the viruses; hence, environmental DNApol gene sequences from prasinoviruses can be used to infer their overall genetic repertoire. Thus, the distribution of virus ecotypes across environmental samples based on DNApol sequences implies substantial underlying differences in gene content that reflect local environmental conditions. Moreover, the high diversity observed in the genetic repertoire of prasinoviruses has been driven by horizontal gene transfer throughout their evolutionary history, resulting in a broad suite of functional capabilities and a high diversity of prasinovirus ecotypes.}, }
@article {pmid28521770, year = {2017}, author = {Rand, KD and Grytten, I and Nederbragt, AJ and Storvik, GO and Glad, IK and Sandve, GK}, title = {Coordinates and intervals in graph-based reference genomes.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {263}, doi = {10.1186/s12859-017-1678-9}, pmid = {28521770}, issn = {1471-2105}, mesh = {Algorithms ; *Computer Graphics ; Genetic Loci ; *Genome, Human ; Genomics/*methods ; Humans ; Internet ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes.<br><br>RESULTS: We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable.<br><br>CONCLUSION: More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created from GRCh38 is available at https://github.com/uio-cels/genomicgraphcoords .}, }
@article {pmid28490487, year = {2017}, author = {Esaiassen, E and Hjerde, E and Cavanagh, JP and Simonsen, GS and Klingenberg, C and , }, title = {Bifidobacterium Bacteremia: Clinical Characteristics and a Genomic Approach To Assess Pathogenicity.}, journal = {Journal of clinical microbiology}, volume = {55}, number = {7}, pages = {2234-2248}, doi = {10.1128/JCM.00150-17}, pmid = {28490487}, issn = {1098-660X}, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Bacteremia/*microbiology ; Bifidobacterium/classification/*genetics/isolation &amp; purification/*pathogenicity ; Female ; Genomics ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Infant ; Infant, Newborn ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Norway ; Retrospective Studies ; Virulence Factors/genetics ; *Whole Genome Sequencing ; }, abstract = {Bifidobacteria are commensals that colonize the orogastrointestinal tract and rarely cause invasive human infections. However, an increasing number of bifidobacterial blood culture isolates has lately been observed in Norway. In order to investigate the pathogenicity of the Bifidobacterium species responsible for bacteremia, we studied Bifidobacterium isolates from 15 patients for whom cultures of blood obtained from 2013 to 2015 were positive. We collected clinical data and analyzed phenotypic and genotypic antibiotic susceptibility. All isolates (11 Bifidobacterium longum, 2 B. breve, and 2 B. animalis isolates) were subjected to whole-genome sequencing. The 15 patients were predominantly in the extreme lower or upper age spectrum, many were severely immunocompromised, and 11 of 15 had gastrointestinal tract-related conditions. In two elderly patients, the Bifidobacterium bacteremia caused a sepsis-like picture, interpreted as the cause of death. Most bifidobacterial isolates had low MICs (≤0.5 mg/liter) to beta-lactam antibiotics, vancomycin, and clindamycin and relatively high MICs to ciprofloxacin and metronidazole. We performed a pangenomic comparison of invasive and noninvasive B. longum isolates based on 65 sequences available from GenBank and the sequences of 11 blood culture isolates from this study. Functional annotation identified unique genes among both invasive and noninvasive isolates of Bifidobacterium Phylogenetic clusters of invasive isolates were identified for a subset of the B. longum subsp. longum isolates. However, there was no difference in the number of putative virulence genes between invasive and noninvasive isolates. In conclusion, Bifidobacterium has an invasive potential in the immunocompromised host and may cause a sepsis-like picture. Using comparative genomics, we could not delineate specific pathogenicity traits characterizing invasive isolates.}, }
@article {pmid28450142, year = {2017}, author = {Bhardwaj, T and Somvanshi, P}, title = {Pan-genome analysis of Clostridium botulinum reveals unique targets for drug development.}, journal = {Gene}, volume = {623}, number = {}, pages = {48-62}, doi = {10.1016/j.gene.2017.04.019}, pmid = {28450142}, issn = {1879-0038}, mesh = {Clostridium botulinum/classification/drug effects/*genetics/pathogenicity ; Drug Resistance, Bacterial/*genetics ; *Genome, Bacterial ; Phylogeny ; Virulence/genetics ; }, abstract = {Clostridium botulinum, a formidable pathogen is responsible for the emerging cause of food poisoning cases on the global canvas. The endemicity of bacterium Clostridium botulinum is reflected by the sudden hospital outbreaks and increased resistance towards multiple drugs. Therefore, a combined approach of in-silico comparative genomic analysis with statistical analysis was applied to overcome the limitation of bench-top technologies. Owing to the paucity of genomic data available by the advent of third generation sequencing technologies, several 'omics' technologies were applied to understand the underlying evolutionary pattern and lifestyle of the bacterial pathogen using phylogenomics. The calculation of pan-genome, core genome and singletons provides view of genetic repertoire of the bacterial pathogen lineage at the successive level, orthology shared and specific gene subsets. In addition, assessment of pathogenomic potential, resistome, toxin/antitoxin family in successive pathogenic strains of Clostridium botulinum aids in revealing more specific targets for drug design and development.}, }
@article {pmid28447607, year = {2017}, author = {Shivaraj, SM and Deshmukh, RK and Rai, R and Bélanger, R and Agrawal, PK and Dash, PK}, title = {Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum).}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {46137}, doi = {10.1038/srep46137}, pmid = {28447607}, issn = {2045-2322}, abstract = {Membrane intrinsic proteins (MIPs) form transmembrane channels and facilitate transport of myriad substrates across the cell membrane in many organisms. Majority of plant MIPs have water transporting ability and are commonly referred as aquaporins (AQPs). In the present study, we identified aquaporin coding genes in flax by genome-wide analysis, their structure, function and expression pattern by pan-genome exploration. Cross-genera phylogenetic analysis with known aquaporins from rice, arabidopsis, and poplar showed five subgroups of flax aquaporins representing 16 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), 2 small basic intrinsic proteins (SIPs), and 3 uncharacterized intrinsic proteins (XIPs). Amongst aquaporins, PIPs contained hydrophilic aromatic arginine (ar/R) selective filter but TIP, NIP, SIP and XIP subfamilies mostly contained hydrophobic ar/R selective filter. Analysis of RNA-seq and microarray data revealed high expression of PIPs in multiple tissues, low expression of NIPs, and seed specific expression of TIP3 in flax. Exploration of aquaporin homologs in three closely related Linum species bienne, grandiflorum and leonii revealed presence of 49, 39 and 19 AQPs, respectively. The genome-wide identification of aquaporins, first in flax, provides insight to elucidate their physiological and developmental roles in flax.}, }
@article {pmid28439658, year = {2017}, author = {Lee, JY and Han, GG and Choi, J and Jin, GD and Kang, SK and Chae, BJ and Kim, EB and Choi, YJ}, title = {Pan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {709-721}, doi = {10.1007/s00248-017-0977-z}, pmid = {28439658}, issn = {1432-184X}, support = {914005-04//Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture, Food and Rural Affairs, Republic of Korea/ ; 520160476//2016 Research Grant from Kangwon National University/ ; }, mesh = {Animals ; Feces/microbiology ; *Genome, Bacterial ; Genomics/methods ; Lactobacillus reuteri/chemistry/*genetics ; Probiotics/*analysis/metabolism ; *Sus scrofa/genetics/metabolism/microbiology ; }, abstract = {After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of L. reuteri associated with host specificity and antipathogenic effect. We isolated 104 L. reuteri strains from porcine feces, and 16 strains, composed of eight strains exhibiting the higher antipathogenic effect (group HS) and eight strains exhibiting the lower effect (group LS), were selected for genomic comparison. We generated draft genomes of the 16 isolates and investigated their pan-genome together with the 26 National Center for Biotechnology Information-registered genomes. L. reuteri genomes organized six clades with multi-locus sequence analysis, and the clade IV includes the 16 isolates. First, we identified six L. reuteri clade IV-specific genes including three hypothetical protein-coding genes. The three annotated genes encode transposases and cell surface proteins, indicating that these genes are the result of adaptation to the host gastrointestinal epithelia and that these host-specific traits were acquired by horizontal gene transfer. We also identified differences between groups HS and LS in the pdu-cbi-cob-hem gene cluster, which is essential for reuterin and cobalamin synthesis, and six genes specific to group HS are revealed. While the strains of group HS possessed all genes of this cluster, LS strains have lost many genes of the cluster. This study provides a deeper understanding of the relationship between probiotic properties and genomic features of L. reuteri.}, }
@article {pmid28427330, year = {2017}, author = {Karlsen, C and Hjerde, E and Klemetsen, T and Willassen, NP}, title = {Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {313}, doi = {10.1186/s12864-017-3693-7}, pmid = {28427330}, issn = {1471-2164}, mesh = {Animals ; CRISPR-Cas Systems/*genetics ; Evolution, Molecular ; Fishes/*microbiology ; *Genomics ; Moritella/*genetics/physiology/virology ; Plasmids/genetics ; Prophages/physiology ; }, abstract = {BACKGROUND: Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M. viscosa strains. Matches between M. viscosa clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) were analysed to correlate CRISPR-Cas with adaptive immunity against MGEs.<br><br>RESULTS: The comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follow the phylogenetic lineages. A subset of the spacer content match prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid-like element distribution were reflected in the content of the CRISPR-spacer profiles.<br><br>CONCLUSIONS: Our data suggests that CRISPR-Cas mediated interactions with MGEs impact genome properties among M. viscosa, and that patterns in spacer and MGE distributions are linked to strain relationships.}, }
@article {pmid28414633, year = {2017}, author = {Giampetruzzi, A and Saponari, M and Loconsole, G and Boscia, D and Savino, VN and Almeida, RPP and Zicca, S and Landa, BB and Chacón-Diaz, C and Saldarelli, P}, title = {Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America.}, journal = {Phytopathology}, volume = {107}, number = {7}, pages = {816-827}, doi = {10.1094/PHYTO-12-16-0420-R}, pmid = {28414633}, issn = {0031-949X}, mesh = {Costa Rica ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; *Genome-Wide Association Study ; *Genotype ; Italy ; Phylogeny ; Polymorphism, Single Nucleotide ; Xylella/*genetics ; }, abstract = {Xylella fastidiosa is a plant-pathogenic bacterium recently introduced in Europe that is causing decline in olive trees in the South of Italy. Genetic studies have consistently shown that the bacterial genotype recovered from infected olive trees belongs to the sequence type ST53 within subspecies pauca. This genotype, ST53, has also been reported to occur in Costa Rica. The ancestry of ST53 was recently clarified, showing it contains alleles that are monophyletic with those of subsp. pauca in South America. To more robustly determine the phylogenetic placement of ST53 within X. fastidiosa, we performed a comparative analysis based on single nucleotide polymorphisms (SNPs) and the study of the pan-genome of the 27 currently public available whole genome sequences of X. fastidiosa. The resulting maximum-parsimony and maximum likelihood trees constructed using the SNPs and the pan-genome analysis are consistent with previously described X. fastidiosa taxonomy, distinguishing the subsp. fastidiosa, multiplex, pauca, sandyi, and morus. Within the subsp. pauca, the Italian and three Costa Rican isolates, all belonging to ST53, formed a compact phylotype in a clade divergent from the South American pauca isolates, also distinct from the recently described coffee isolate CFBP8072 imported into Europe from Ecuador. These findings were also supported by the gene characterization of a conjugative plasmid shared by all the four ST53 isolates. Furthermore, isolates of the ST53 clade possess an exclusive locus encoding a putative ATP-binding protein belonging to the family of histidine kinase-like ATPase gene, which is not present in isolates from the subspecies multiplex, sandyi, and pauca, but was detected in ST21 isolates of the subspecies fastidiosa from Costa Rica. The clustering and distinctiveness of the ST53 isolates supports the hypothesis of their common origin, and the limited genetic diversity among these isolates suggests this is an emerging clade within subsp. pauca.}, }
@article {pmid28403535, year = {2017}, author = {Bayer, PE and Hurgobin, B and Golicz, AA and Chan, CK and Yuan, Y and Lee, H and Renton, M and Meng, J and Li, R and Long, Y and Zou, J and Bancroft, I and Chalhoub, B and King, GJ and Batley, J and Edwards, D}, title = {Assembly and comparison of two closely related Brassica napus genomes.}, journal = {Plant biotechnology journal}, volume = {15}, number = {12}, pages = {1602-1610}, doi = {10.1111/pbi.12742}, pmid = {28403535}, issn = {1467-7652}, support = {BB/E017363/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Brassica napus/genetics ; Expressed Sequence Tags ; Genes, Plant ; *Genome, Plant ; Molecular Sequence Annotation ; Repetitive Sequences, Nucleic Acid ; }, abstract = {As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome.}, }
@article {pmid28383665, year = {2017}, author = {Jeukens, J and Freschi, L and Vincent, AT and Emond-Rheault, JG and Kukavica-Ibrulj, I and Charette, SJ and Levesque, RC}, title = {A pan-genomic approach to understand the basis of host adaptation in Achromobacter.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evx061}, pmid = {28383665}, issn = {1759-6653}, abstract = {Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis (CF) lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the CF lung, not to mention other host environments. The goals of this first genus-wide comparative genomics study were to clarify the taxonomy of this genus and identify genomic features associated with pathogenicity and host adaptation. This was done with a widely applicable approach based on pan-genome analysis. First, using all publicly available genomes, a combination of phylogenetic analysis based on 1,780 conserved genes with average nucleotide identity and accessory genome composition allowed the identification of a largely clinical lineage composed of A. xylosoxidans A insuavis A. dolens and A. ruhlandii. Within this lineage, we identified 35 positively selected genes involved in metabolism, regulation and efflux-mediated antibiotic resistance. Second, resistome analysis showed that this clinical lineage carried additional antibiotic resistance genes compared to other isolates. Finally, we identified putative mobile elements that contribute 53% of the genus's resistome and support horizontal gene transfer between Achromobacter and other ecologically similar genera. This study provides strong phylogenetic and pan-genomic bases to motivate further research on Achromobacter, and contributes to the understanding of opportunistic pathogen evolution.}, }
@article {pmid28379509, year = {2017}, author = {Okura, M and Nozawa, T and Watanabe, T and Murase, K and Nakagawa, I and Takamatsu, D and Osaki, M and Sekizaki, T and Gottschalk, M and Hamada, S and Maruyama, F}, title = {A locus encoding variable defence systems against invading DNA identified in Streptococcus suis.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evx062}, pmid = {28379509}, issn = {1759-6653}, abstract = {Streptococcus suis, an important zoonotic pathogen, is known to have an open pan-genome and to develop a competent state. In S. suis, limited genetic lineages are suggested to be associated with zoonosis. However, little is known about the evolution of diversified lineages and their respective phenotypic or ecological characteristics. In this study, we performed comparative genome analyses of S. suis, with a focus on the competence genes, mobile genetic elements (MGEs), and genetic elements related to various defence systems against exogenous DNAs (defence elements) that are associated with gene gain/loss/exchange mediated by horizontal DNA movements and their restrictions. Our genome analyses revealed a conserved competence-inducing peptide type (pherotype) of the competence system and large-scale genome rearrangements in certain clusters based on the genome phylogeny of 58 S. suis strains. Moreover, the profiles of the defence elements were similar or identical to each other among the strains belonging to the same genomic clusters. Our findings suggest that these genetic characteristics of each cluster might exert specific effects on the phenotypic or ecological differences between the clusters. We also found certain loci that shift several types of defence elements in S. suis. Of note, one of these loci is a previously unrecognised variable region in bacteria, at which strains of distinct clusters code for different and various defence elements. This locus might represent a novel defence mechanism that has evolved via an arms race between bacteria and invading DNAs, mediated by MGEs and genetic competence.}, }
@article {pmid28377746, year = {2017}, author = {Bhattacharyya, C and Bakshi, U and Mallick, I and Mukherji, S and Bera, B and Ghosh, A}, title = {Genome-Guided Insights into the Plant Growth Promotion Capabilities of the Physiologically Versatile Bacillus aryabhattai Strain AB211.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {411}, doi = {10.3389/fmicb.2017.00411}, pmid = {28377746}, issn = {1664-302X}, abstract = {Bacillus aryabhattai AB211 is a plant growth promoting, Gram-positive firmicute, isolated from the rhizosphere of tea (Camellia sinensis), one of the oldest perennial crops and a major non-alcoholic beverage widely consumed all over the world. The whole genome of B. aryabhattai AB211 was sequenced, annotated and evaluated with special focus on genomic elements related to plant microbe interaction. It's genome sequence reveals the presence of a 5,403,026 bp chromosome. A total of 5226 putative protein-coding sequences, 16 rRNA, 120 tRNA, 8 ncRNAs, 58 non-protein coding genes, and 11 prophage regions were identified. Genome sequence comparisons between strain AB211 and other related environmental strains of B. aryabhattai, identified about 3558 genes conserved among all B. aryabhattai genomes analyzed. Most of the common genes involved in plant growth promotion activities were found to be present within core genes of all the genomes used for comparison, illustrating possible common plant growth promoting traits shared among all the strains of B. aryabhattai. Besides the core genes, some genes were exclusively identified in the genome of strain AB211. Functional annotation of the genes predicted in the strain AB211 revealed the presence of genes responsible for mineral phosphate solubilization, siderophores, acetoin, butanediol, exopolysaccharides, flagella biosynthesis, surface attachment/biofilm formation, and indole acetic acid production, most of which were experimentally verified in the present study. Genome analysis and experimental evidence suggested that AB211 has robust central carbohydrate metabolism implying that this bacterium can efficiently utilize the root exudates and other organic materials as an energy source. Genes for the production of peroxidases, catalases, and superoxide dismutases, that confer resistance to oxidative stresses in plants were identified in AB211 genome. Besides these, genes for heat shock tolerance, cold shock tolerance, glycine-betaine production, and antibiotic/heavy metal resistance that enable bacteria to survive biotic/abiotic stress were also identified. Based on the genome sequence information and experimental evidence as presented in this study, strain AB211 appears to be metabolically diverse and exhibits tremendous potential as a plant growth promoting bacterium.}, }
@article {pmid28369371, year = {2017}, author = {Hu, Z and Sun, C and Lu, KC and Chu, X and Zhao, Y and Lu, J and Shi, J and Wei, C}, title = {EUPAN enables pan-genome studies of a large number of eukaryotic genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {15}, pages = {2408-2409}, doi = {10.1093/bioinformatics/btx170}, pmid = {28369371}, issn = {1367-4811}, mesh = {Eukaryota/*genetics ; Genetics, Population/*methods ; *Genome ; Genomics/methods ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Summary: Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms.<br><br>EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html .<br><br>Contact: ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28369330, year = {2017}, author = {MacArthur, I and Anastasi, E and Alvarez, S and Scortti, M and Vázquez-Boland, JA}, title = {Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island.}, journal = {Genome biology and evolution}, volume = {9}, number = {5}, pages = {1241-1247}, doi = {10.1093/gbe/evx057}, pmid = {28369330}, issn = {1759-6653}, support = {BB/J004227/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actinomycetales Infections/microbiology/veterinary ; Animals ; Cattle ; *Evolution, Molecular ; *Genomic Islands ; Host-Pathogen Interactions ; Phylogeny ; Plasmids ; Rhodococcus equi/*genetics/isolation &amp; purification/pathogenicity ; }, abstract = {The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes. Plasmids within each host-associated type were highly similar despite their diverse origins. Variation was accounted for by scattered single nucleotide polymorphisms and short nucleotide indels, while larger indels-mostly in the plasticity region near the vap pathogencity island (PAI)-defined plasmid genomic subtypes. Only one of the plasmids analyzed, of pVAPN type, was exceptionally divergent due to accumulation of indels in the housekeeping backbone. Each host-associated plasmid type carried a unique PAI differing in vap gene complement, suggesting animal host-specific evolution of the vap multigene family. Complete conservation of the vap PAI was observed within each host-associated plasmid type. Both diversity of host-associated plasmid types and clonality of specific chromosomal-plasmid genomic type combinations were observed within the same R. equi phylogenomic subclade. Our data indicate that the overall strong conservation of the R. equi host-associated virulence plasmids is the combined result of host-driven selection, lateral transfer between strains, and geographical spread due to international livestock exchanges.}, }
@article {pmid28356072, year = {2017}, author = {Kelleher, P and Bottacini, F and Mahony, J and Kilcawley, KN and van Sinderen, D}, title = {Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {267}, doi = {10.1186/s12864-017-3650-5}, pmid = {28356072}, issn = {1471-2164}, mesh = {Amino Acid Transport Systems/genetics ; Carbohydrate Metabolism/genetics ; Carrier Proteins/genetics ; Cluster Analysis ; Comparative Genomic Hybridization ; *Evolution, Molecular ; *Genome, Bacterial ; Lactococcus lactis/classification/*genetics ; Lipid Metabolism/genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/classification/metabolism ; }, abstract = {BACKGROUND: Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production.<br><br>RESULTS: In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon.<br><br>CONCLUSIONS: Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.}, }
@article {pmid28356070, year = {2017}, author = {Wang, D and Li, S and Guo, F and Ning, K and Wang, L}, title = {Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {268}, doi = {10.1186/s12864-017-3655-0}, pmid = {28356070}, issn = {1471-2164}, mesh = {Comparative Genomic Hybridization ; Escherichia coli/*genetics ; Gene Rearrangement ; *Genome, Bacterial ; Pseudomonas aeruginosa/*genetics ; Sequence Inversion/*genetics ; }, abstract = {BACKGROUND: Genome rearrangement describes gross changes of chromosomal regions, plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. With more and more complete genomes accomplished, lots of genomic comparisons have been conducted in order to find genome rearrangements and the mechanisms which underlie the rearrangement events. In our opinion, genomic comparison of different individuals/strains within the same species (pan-genome) is more helpful to reveal the mechanisms for genome rearrangements since genomes of the same species are much closer to each other.<br><br>RESULTS: We study the mechanism for inversion events via core-genome scaffold comparison of different strains within the same species. We focus on two kinds of bacteria, Pseudomonas aeruginosa and Escherichia coli, and investigate the inversion events among different strains of the same species. We find an interesting phenomenon that long (larger than 10,000 bp) inversion regions are flanked by a pair of Inverted Repeats (IRs). This mechanism can also explain why the breakpoint reuses for inversion events happen. We study the prevalence of the phenomenon and find that it is a major mechanism for inversions. The other observation is that for different rearrangement events such as transposition and inverted block interchange, the two ends of the swapped regions are also associated with repeats so that after the rearrangement operations the two ends of the swapped regions remain unchanged. To our knowledge, this is the first time such a phenomenon is reported for transposition event.<br><br>CONCLUSIONS: In both Pseudomonas aeruginosa and Escherichia coli strains, IRs were found at the two ends of long sequence inversions. The two ends of the inversion remained unchanged before and after the inversion event. The existence of IRs can explain the breakpoint reuse phenomenon. We also observed that other rearrangement operations such as transposition, inverted transposition, and inverted block interchange, had repeats (not necessarily inverted) at the ends of each segment, where the ends remained unchanged before and after the rearrangement operations. This suggests that the conservation of ends could possibly be a popular phenomenon in many types of chromosome rearrangement events.}, }
@article {pmid28352257, year = {2017}, author = {Zeng, L and Wang, D and Hu, N and Zhu, Q and Chen, K and Dong, K and Zhang, Y and Yao, Y and Guo, X and Chang, YF and Zhu, Y}, title = {A Novel Pan-Genome Reverse Vaccinology Approach Employing a Negative-Selection Strategy for Screening Surface-Exposed Antigens against leptospirosis.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {396}, doi = {10.3389/fmicb.2017.00396}, pmid = {28352257}, issn = {1664-302X}, abstract = {Reverse vaccinology (RV) has been widely used for screening of surface-exposed proteins (PSEs) of important pathogens, including outer membrane proteins (OMPs), and extracellular proteins (ECPs) as potential vaccine candidates. In this study, we applied a novel RV negative strategy and a pan-genome analysis for screening of PSEs from 17 L. interrogans strains covering 11 predominately epidemic serovars and 17 multilocus typing (MLST) sequence types (STs) worldwide. Our results showed, for instance, out of a total of 633 predicted PSEs in strain 56601, 92.8% were OMPs or ECPs (588/633). Among the 17 strains, 190 core PSEs, 913 dispensable PSEs and 861 unique PSEs were identified. Of the 190 PSEs, 121 were further predicted to be highly antigenic and thus may serve as potential vaccine candidates against leptospirosis. With the exception of LipL45, OmpL1, and LigB, the majority of the 121 PSEs were newly identified antigens. For example, hypothetical proteins BatC, LipL71, and the OmpA family proteins sharing many common features, such as surface-exposed localization, universal conservation, and eliciting strong antibody responses in patients, are regarded as the most promising vaccine antigens. Additionally, a wide array of potential virulence factors among the predicted PSEs including TonB-dependent receptor, sphingomyelinase 2, leucine-rich repeat protein, and 4 neighboring hypothetical proteins were identified as potential antigenicity, and deserve further investigation. Our results can contribute to the prediction of suitable antigens as potential vaccine candidates against leptospirosis and also provide further insights into mechanisms of leptospiral pathogenicity. In addition, our novel negative-screening strategy combined with pan-genome analysis can be a routine RV method applied to numerous other pathogens.}, }
@article {pmid28348877, year = {2017}, author = {Lees, JA and Kremer, PH and Manso, AS and Croucher, NJ and Ferwerda, B and Serón, MV and Oggioni, MR and Parkhill, J and Brouwer, MC and van der Ende, A and van de Beek, D and Bentley, SD}, title = {Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis.}, journal = {Microbial genomics}, volume = {3}, number = {1}, pages = {e000103}, doi = {10.1099/mgen.0.000103}, pmid = {28348877}, issn = {2057-5858}, support = {281156//European Research Council/International ; 098051//Wellcome Trust/United Kingdom ; 1365620//Medical Research Council/United Kingdom ; 104169/Z/14/Z//Wellcome Trust/United Kingdom ; MR/M003078/1//Medical Research Council/United Kingdom ; }, abstract = {Recent studies have provided evidence for rapid pathogen genome diversification, some of which could potentially affect the course of disease. We have previously described such variation seen between isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis. Here, we performed whole-genome sequencing of paired isolates from the blood and CSF of 869 meningitis patients to determine whether such variation frequently occurs between these two niches in cases of bacterial meningitis. Using a combination of reference-free variant calling approaches, we show that no genetic adaptation occurs in either invaded niche during bacterial meningitis for two major pathogen species, Streptococcus pneumoniae and Neisseria meningitidis. This study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood-brain barrier. Our findings place the focus back on bacterial evolution between nasopharyngeal carriage and invasion, or diversity of the host, as likely mechanisms for determining invasiveness.}, }
@article {pmid28348852, year = {2016}, author = {Jamrozy, DM and Harris, SR and Mohamed, N and Peacock, SJ and Tan, CY and Parkhill, J and Anderson, AS and Holden, MT}, title = {Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic.}, journal = {Microbial genomics}, volume = {2}, number = {5}, pages = {e000058}, doi = {10.1099/mgen.0.000058}, pmid = {28348852}, issn = {2057-5858}, support = {098051//Wellcome Trust/United Kingdom ; }, abstract = {Staphylococcus aureus USA300 represents the dominant community-associated methicillin-resistant S. aureus lineage in the USA, where it is a major cause of skin and soft tissue infections. Previous comparative genomic studies have described the population structure and evolution of USA300 based on geographically restricted isolate collections. Here, we investigated the USA300 population by sequencing genomes of a geographically distributed panel of 191 clinical S. aureus isolates belonging to clonal complex 8 (CC8), derived from the Tigecycline Evaluation and Surveillance Trial program. Isolates were collected at 12 healthcare centres across nine USA states in 2004, 2009 or 2010. Reconstruction of evolutionary relationships revealed that CC8 was dominated by USA300 isolates (154/191, 81 %), which were heterogeneous and demonstrated limited phylogeographic clustering. Analysis of the USA300 core genomes revealed an increase in median pairwise SNP distance from 62 to 98 between 2004 and 2010, with a stable pattern of above average dN/dS ratios. The phylogeny of the USA300 population indicated that early diversification events led to the formation of nested clades, which arose through cumulative acquisition of predominantly non-synonymous SNPs in various coding sequences. The accessory genome of USA300 was largely homogenous and consisted of elements previously associated with this lineage. We observed an emergence of SCCmec negative and ACME negative USA300 isolates amongst more recent samples, and an increase in the prevalence of ϕSa5 prophage. Together, the analysed S. aureus USA300 collection revealed an evolving pan-genome through increased core genome heterogeneity and temporal variation in the frequency of certain accessory elements.}, }
@article {pmid28348841, year = {2016}, author = {Sheridan, PO and Martin, JC and Lawley, TD and Browne, HP and Harris, HM and Bernalier-Donadille, A and Duncan, SH and O'Toole, PW and Scott, KP and Flint, HJ}, title = {Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes.}, journal = {Microbial genomics}, volume = {2}, number = {2}, pages = {e000043}, doi = {10.1099/mgen.0.000043}, pmid = {28348841}, issn = {2057-5858}, abstract = {Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.}, }
@article {pmid28347275, year = {2017}, author = {Zhou, P and Silverstein, KA and Ramaraj, T and Guhlin, J and Denny, R and Liu, J and Farmer, AD and Steele, KP and Stupar, RM and Miller, JR and Tiffin, P and Mudge, J and Young, ND}, title = {Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {261}, doi = {10.1186/s12864-017-3654-1}, pmid = {28347275}, issn = {1471-2164}, mesh = {Comparative Genomic Hybridization ; DNA Copy Number Variations/*genetics ; *Genome, Plant ; Heat-Shock Proteins/genetics ; High-Throughput Nucleotide Sequencing ; Medicago truncatula/*genetics ; Plant Proteins/genetics ; Proteins/genetics ; RNA, Plant/chemistry/isolation &amp; purification/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome.<br><br>RESULTS: Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable - estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation.<br><br>CONCLUSIONS: Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation.}, }
@article {pmid28333270, year = {2017}, author = {Hughes, D and Andersson, DI}, title = {Environmental and genetic modulation of the phenotypic expression of antibiotic resistance.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {3}, pages = {374-391}, doi = {10.1093/femsre/fux004}, pmid = {28333270}, issn = {1574-6976}, mesh = {Adaptation, Physiological/*physiology ; Anti-Bacterial Agents/*pharmacology ; *Bacteria/drug effects/genetics/growth &amp; development ; Biofilms/*drug effects/growth &amp; development ; Drug Resistance, Multiple, Bacterial/*genetics ; Environment ; Gene Transfer, Horizontal/genetics ; Genotype ; Humans ; Mutation ; Phenotype ; }, abstract = {Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic 'dark matter') that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.}, }
@article {pmid28325850, year = {2017}, author = {Lee, AH and Flibotte, S and Sinha, S and Paiero, A and Ehrlich, RL and Balashov, S and Ehrlich, GD and Zlosnik, JE and Mell, JC and Nislow, C}, title = {Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs.}, journal = {Genome research}, volume = {27}, number = {4}, pages = {650-662}, doi = {10.1101/gr.213363.116}, pmid = {28325850}, issn = {1549-5469}, support = {R01 DC002148/DC/NIDCD NIH HHS/United States ; }, mesh = {Adolescent ; Animals ; Biofilms ; Burkholderia Infections/complications/*microbiology ; Burkholderia cenocepacia/*genetics/isolation &amp; purification/pathogenicity/physiology ; Child ; Child, Preschool ; Cystic Fibrosis/complications/*microbiology ; Genotype ; Humans ; Lung/microbiology ; Moths/microbiology ; *Phenotype ; *Polymorphism, Genetic ; Virulence ; Young Adult ; }, abstract = {Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures-including immune responses and therapeutic interventions-shape bacterial genomes. We carried out genomic and phenotypic analyses of 215 serially collected Burkholderia cenocepacia isolates from 16 cystic fibrosis patients, spanning a period of 2-20 yr and a broad range of epidemic lineages. Systematic phenotypic tests identified longitudinal bacterial series that manifested progressive changes in liquid media growth, motility, biofilm formation, and acute insect virulence, but not in mucoidy. The results suggest that distinct lineages follow distinct evolutionary trajectories during lung infection. Pan-genome analysis identified 10,110 homologous gene clusters present only in a subset of strains, including genes restricted to different molecular types. Our phylogenetic analysis based on 2148 orthologous gene clusters from all isolates is consistent with patient-specific clades. This suggests that initial colonization of patients was likely by individual strains, followed by subsequent diversification. Evidence of clonal lineages shared by some patients was observed, suggesting inter-patient transmission. We observed recurrent gene losses in multiple independent longitudinal series, including complete loss of Chromosome III and deletions on other chromosomes. Recurrently observed loss-of-function mutations were associated with decreases in motility and biofilm formation. Together, our study provides the first comprehensive genome-phenome analyses of B. cenocepacia infection in cystic fibrosis lungs and serves as a valuable resource for understanding the genomic and phenotypic underpinnings of bacterial evolution.}, }
@article {pmid28321969, year = {2017}, author = {Udaondo, Z and Duque, E and Ramos, JL}, title = {The pangenome of the genus Clostridium.}, journal = {Environmental microbiology}, volume = {19}, number = {7}, pages = {2588-2603}, doi = {10.1111/1462-2920.13732}, pmid = {28321969}, issn = {1462-2920}, mesh = {Bacterial Proteins/genetics/metabolism ; Clostridium/classification/*genetics/metabolism ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Multilocus Sequence Typing ; Phylogeny ; Protein-Serine-Threonine Kinases/genetics/metabolism ; S-Adenosylmethionine/metabolism ; }, abstract = {The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS-GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non-random and scale-free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S-adenosylmethionine and the ribonuclease P-protein, suggesting pivotal roles for them in Clostridium.}, }
@article {pmid28293680, year = {2017}, author = {Castillo, D and Alvise, PD and Xu, R and Zhang, F and Middelboe, M and Gram, L}, title = {Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits.}, journal = {mSystems}, volume = {2}, number = {1}, pages = {}, doi = {10.1128/mSystems.00001-17}, pmid = {28293680}, issn = {2379-5077}, abstract = {Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.}, }
@article {pmid28288685, year = {2017}, author = {Hur, J and Özgür, A and He, Y}, title = {Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.}, journal = {Journal of biomedical semantics}, volume = {8}, number = {1}, pages = {12}, doi = {10.1186/s13326-017-0122-4}, pmid = {28288685}, issn = {2041-1480}, mesh = {Bacterial Vaccines/*immunology ; *Biological Ontologies ; Data Mining/*methods ; Escherichia coli/*genetics/*immunology ; *Gene Regulatory Networks ; Genomics ; }, abstract = {BACKGROUND: Pathogenic Escherichia coli infections cause various diseases in humans and many animal species. However, with extensive E. coli vaccine research, we are still unable to fully protect ourselves against E. coli infections. To more rational development of effective and safe E. coli vaccine, it is important to better understand E. coli vaccine-associated gene interaction networks.<br><br>METHODS: In this study, we first extended the Vaccine Ontology (VO) to semantically represent various E. coli vaccines and genes used in the vaccine development. We also normalized E. coli gene names compiled from the annotations of various E. coli strains using a pan-genome-based annotation strategy. The Interaction Network Ontology (INO) includes a hierarchy of various interaction-related keywords useful for literature mining. Using VO, INO, and normalized E. coli gene names, we applied an ontology-based SciMiner literature mining strategy to mine all PubMed abstracts and retrieve E. coli vaccine-associated E. coli gene interactions. Four centrality metrics (i.e., degree, eigenvector, closeness, and betweenness) were calculated for identifying highly ranked genes and interaction types.<br><br>RESULTS: Using vaccine-related PubMed abstracts, our study identified 11,350 sentences that contain 88 unique INO interactions types and 1,781 unique E. coli genes. Each sentence contained at least one interaction type and two unique E. coli genes. An E. coli gene interaction network of genes and INO interaction types was created. From this big network, a sub-network consisting of 5 E. coli vaccine genes, including carA, carB, fimH, fepA, and vat, and 62 other E. coli genes, and 25 INO interaction types was identified. While many interaction types represent direct interactions between two indicated genes, our study has also shown that many of these retrieved interaction types are indirect in that the two genes participated in the specified interaction process in a required but indirect process. Our centrality analysis of these gene interaction networks identified top ranked E. coli genes and 6 INO interaction types (e.g., regulation and gene expression).<br><br>CONCLUSIONS: Vaccine-related E. coli gene-gene interaction network was constructed using ontology-based literature mining strategy, which identified important E. coli vaccine genes and their interactions with other genes through specific interaction types.}, }
@article {pmid28287462, year = {2017}, author = {Hurgobin, B and Edwards, D}, title = {SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?.}, journal = {Biology}, volume = {6}, number = {1}, pages = {}, doi = {10.3390/biology6010021}, pmid = {28287462}, issn = {2079-7737}, abstract = {Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species; it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation. The advent of next-generation sequencing (NGS) coupled with the heritability of SNPs make them ideal markers for genetic analysis of human, animal, and microbial data. SNPs have also been extensively used in crop genetics for association mapping, quantitative trait loci (QTL) analysis, analysis of genetic diversity, and phylogenetic analysis. This review focuses on the use of pangenomes for SNP discovery. It highlights the advantages of using a pangenome rather than a single reference for this purpose. This review also demonstrates how extra information not captured in a single reference alone can be used to provide additional support for linking genotypic data to phenotypic data.}, }
@article {pmid28283403, year = {2017}, author = {Choudoir, MJ and Panke-Buisse, K and Andam, CP and Buckley, DH}, title = {Genome Surfing As Driver of Microbial Genomic Diversity.}, journal = {Trends in microbiology}, volume = {25}, number = {8}, pages = {624-636}, doi = {10.1016/j.tim.2017.02.006}, pmid = {28283403}, issn = {1878-4380}, mesh = {*Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Microbial ; Genomics ; Models, Genetic ; Phylogeny ; Streptomyces/genetics ; }, abstract = {Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms.}, }
@article {pmid28261241, year = {2017}, author = {Contreras-Moreira, B and Cantalapiedra, CP and García-Pereira, MJ and Gordon, SP and Vogel, JP and Igartua, E and Casas, AM and Vinuesa, P}, title = {Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {184}, doi = {10.3389/fpls.2017.00184}, pmid = {28261241}, issn = {1664-462X}, abstract = {The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of expressed sequences can recapitulate phylogeny and reproduce two properties observed in A. thaliana gene models: accessory loci show lower expression and higher non-synonymous substitution rates than core genes. Finally, accessory sequences were observed to preferentially encode transposon components in both species, plus disease resistance genes in cultivated barleys, and a variety of protein domains from other families that appear frequently associated with presence/absence variation in the literature. These results demonstrate that pan-genome analyses are useful to explore germplasm diversity.}, }
@article {pmid28258140, year = {2017}, author = {Bansal, K and Midha, S and Kumar, S and Patil, PB}, title = {Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {9}, pages = {}, doi = {10.1128/AEM.02993-16}, pmid = {28258140}, issn = {1098-5336}, mesh = {Citrus/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; *Genetic Variation ; Genome, Bacterial ; Genotype ; India ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; Sequence Homology ; Xanthomonas/*classification/*genetics/isolation &amp; purification ; }, abstract = {Citrus canker, caused by Xanthomonas citri pv. citri, is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed that X. citri pv. citri is related to many other pathovars, which can be collectively referred as Xanthomonas citri pathovars (XCPs). From the present study, we report the genome sequences of 18 XCPs and compared them with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster, suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, the majority of these XCPs were first noticed in India, corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role of interstrain genomic flux of these XCPs since their diversification from a common ancestor. Even though there are wide variations in type III gene effectomes, we identified three core effectors which can be valuable in resistance-breeding programs. Overall, genomic examination of ecological relatives allowed us to dissect the tremendous genomic potential of X. citri species to rapidly evolve into specialized strains infecting diverse crop plants.IMPORTANCE Host specialization is one of the characteristic features of highly evolved pathogens such as the Xanthomonas group of phytopathogenic bacteria. Since the hosts involve staple crops and economically important fruits such as citrus, detailed understanding of the diversity and evolution of such strains infecting diverse plants is important for quarantine purposes. In the present study, we carried out genomic investigation of members of a phylogenetically and ecologically defined group of Xanthomonas strains pathogenic to diverse plants, including citrus. This group includes the oldest Xanthomonas pathovars and also recently emerged pathovars in a particular country where they are endemic. Our high-throughput genomic study has provided novel insights into the evolution of a unique lineage consisting of serious pathogens and their ecological relatives, suggesting the nature, scope, and pattern of rapid and recent diversification. Further, from the level of species to that of clonal variants, the study revealed interesting genomic patterns in diversification of a Xanthomonas lineage and perhaps will inspire careful study of the host range of the included pathovars.}, }
@article {pmid28236274, year = {2017}, author = {Ibrahim, M and Subramanian, A and Anishetty, S}, title = {Comparative pan genome analysis of oral Prevotella species implicated in periodontitis.}, journal = {Functional &amp; integrative genomics}, volume = {17}, number = {5}, pages = {513-536}, doi = {10.1007/s10142-017-0550-3}, pmid = {28236274}, issn = {1438-7948}, mesh = {Bacterial Proteins/chemistry/genetics ; Bacterial Secretion Systems/*genetics ; Cysteine Proteases/chemistry/genetics ; *Genome, Bacterial ; Periodontitis/microbiology ; Phylogeny ; Prevotella/classification/*genetics/pathogenicity ; Protein Domains ; Sequence Alignment ; Sequence Homology ; }, abstract = {Prevotella is part of the oral bacterial community implicated in periodontitis. Pan genome analyses of eight oral Prevotella species, P. dentalis, P. enoeca, P. fusca, P. melaninogenica, P. denticola, P. intermedia 17, P. intermedia 17-2 and P. sp. oral taxon 299 are presented in this study. Analysis of the Prevotella pan genome revealed features such as secretion systems, resistance to oxidative stress and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems that enable the bacteria to adapt to the oral environment. We identified the presence of type VI secretion system (T6SS) in P. fusca and P. intermedia strains. For some VgrG and Hcp proteins which were not part of the core T6SS loci, we used gene neighborhood analysis and identified putative effector proteins and putative polyimmunity loci in P. fusca and polymorphic toxin systems in P. intermedia strains. Earlier studies have identified the presence of Por secretion system (PorSS) in P. gingivalis, P. melaninogenica and P. intermedia. We noted the presence of their homologs in six other oral Prevotella studied here. We suggest that in Prevotella, PorSS is used to secrete cysteine proteases such as interpain and C-terminal domain containing proteins with a &quot;Por_secre_tail&quot; domain. We identified subtype I-B CRISPR-Cas system in P. enoeca. Putative CRISPR-Cas system subtypes for 37 oral Prevotella and 30 non-oral Prevotella species were also predicted. Further, we performed a BLASTp search of the Prevotella proteins which are also conserved in the red-complex pathogens, against the human proteome to identify potential broad-spectrum drug targets. In summary, the use of a pan genome approach enabled identification of secretion systems and defense mechanisms in Prevotella that confer adaptation to the oral cavity.}, }
@article {pmid28231383, year = {2017}, author = {Montenegro, JD and Golicz, AA and Bayer, PE and Hurgobin, B and Lee, H and Chan, CK and Visendi, P and Lai, K and Doležel, J and Batley, J and Edwards, D}, title = {The pangenome of hexaploid bread wheat.}, journal = {The Plant journal : for cell and molecular biology}, volume = {90}, number = {5}, pages = {1007-1013}, doi = {10.1111/tpj.13515}, pmid = {28231383}, issn = {1365-313X}, mesh = {Chromosomes, Plant/genetics ; Genetic Variation/genetics ; Genome, Plant/*genetics ; Polymorphism, Single Nucleotide/genetics ; Triticum/*genetics ; }, abstract = {There is an increasing understanding that variation in gene presence-absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene presence-absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140 500 ± 102 genes, a core genome of 81 070 ± 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal single nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at http://appliedbioinformatics.com.au/cgi-bin/gb2/gbrowse/WheatPan/, and data are available to download from http://wheatgenome.info/wheat_genome_databases.php.}, }
@article {pmid28198668, year = {2017}, author = {Yang, J and Yang, S}, title = {Comparative analysis of Corynebacterium glutamicum genomes: a new perspective for the industrial production of amino acids.}, journal = {BMC genomics}, volume = {18}, number = {Suppl 1}, pages = {940}, doi = {10.1186/s12864-016-3255-4}, pmid = {28198668}, issn = {1471-2164}, mesh = {Alleles ; Amino Acids/*biosynthesis ; Corynebacterium glutamicum/classification/*genetics/metabolism ; *Genome, Bacterial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Corynebacterium glutamicum is a non-pathogenic bacterium widely used in industrial amino acid production and metabolic engineering research. Although the genome sequences of some C. glutamicum strains are available, comprehensive comparative genome analyses of these species have not been done. Six wild type C. glutamicum strains were sequenced using next-generation sequencing technology in our study. Together with 20 previously reported strains, we present a comprehensive comparative analysis of C. glutamicum genomes.<br><br>RESULTS: By average nucleotide identity (ANI) analysis, we show that 10 strains, which were previously classified either in the genus Brevibacterium, or as some other species within the genus Corynebacterium, should be reclassified as members of the species C. glutamicum. C. glutamicum has an open pan-genome with 2359 core genes. An additional NAD+/NADP+ specific glutamate dehydrogenase (GDH) gene (gdh) was identified in the glutamate synthesis pathway of some C. glutamicum strains. For analyzing variations related to amino acid production, we have developed an efficient pipeline that includes three major steps: multi locus sequence typing (MLST), phylogenomic analysis based on single nucleotide polymorphisms (SNPs), and a thorough comparison of all genomic variation amongst ancestral or closely related wild type strains. This combined approach can provide new perspectives on the industrial use of C. glutamicum.<br><br>CONCLUSIONS: This is the first comprehensive comparative analysis of C. glutamicum genomes at the pan-genomic level. Whole genome comparison provides definitive evidence for classifying the members of this species. Identifying an aditional gdh gene in some C. glutamicum strains may accelerate further research on glutamate synthesis. Our proposed pipeline can provide a clear perspective, including the presumed ancestor, the strain breeding trajectory, and the genomic variations necessary to increase amino acid production in C. glutamicum.}, }
@article {pmid28194158, year = {2017}, author = {Checcucci, A and Azzarello, E and Bazzicalupo, M and De Carlo, A and Emiliani, G and Mancuso, S and Spini, G and Viti, C and Mengoni, A}, title = {Role and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene?.}, journal = {Frontiers in genetics}, volume = {8}, number = {}, pages = {6}, doi = {10.3389/fgene.2017.00006}, pmid = {28194158}, issn = {1664-8021}, abstract = {Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR). acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior.}, }
@article {pmid28173009, year = {2017}, author = {Monat, C and Pera, B and Ndjiondjop, MN and Sow, M and Tranchant-Dubreuil, C and Bastianelli, L and Ghesquière, A and Sabot, F}, title = {De Novo Assemblies of Three Oryza glaberrima Accessions Provide First Insights about Pan-Genome of African Rices.}, journal = {Genome biology and evolution}, volume = {9}, number = {1}, pages = {1-6}, doi = {10.1093/gbe/evw253}, pmid = {28173009}, issn = {1759-6653}, mesh = {Africa ; Genetic Variation ; *Genome, Plant ; Molecular Sequence Annotation ; Oryza/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals. The three assemblies shown large common regions, but almost 25% of the genome present collinearity breakpoints or are even individual specific.}, }
@article {pmid28158295, year = {2017}, author = {Wang, J and Haapalainen, M and Schott, T and Thompson, SM and Smith, GR and Nissinen, AI and Pirhonen, M}, title = {Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0171531}, doi = {10.1371/journal.pone.0171531}, pmid = {28158295}, issn = {1932-6203}, mesh = {Animals ; DNA, Plant ; Daucus carota/microbiology/parasitology ; Genome, Bacterial ; *Haplotypes ; Hemiptera/microbiology ; Operon ; Phylogeny ; Prophages/genetics ; RNA, Plant ; RNA, Ribosomal ; Rhizobiaceae/classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso) are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp) and FIN111 (1.20 Mbp), were obtained from carrot psyllids (Trioza apicalis) harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species.}, }
@article {pmid28138100, year = {2017}, author = {Sansevere, EA and Luo, X and Park, JY and Yoon, S and Seo, KS and Robinson, DA}, title = {Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE6013 Elements in Staphylococcus aureus.}, journal = {Journal of bacteriology}, volume = {199}, number = {8}, pages = {}, doi = {10.1128/JB.00629-16}, pmid = {28138100}, issn = {1098-5530}, support = {P20 GM103646/GM/NIGMS NIH HHS/United States ; R01 GM080602/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Conjugation, Genetic/*physiology ; Gene Expression Regulation, Bacterial/physiology ; Genetic Variation ; Protein Domains ; Staphylococcus aureus/*enzymology/genetics/*physiology ; Transposases/*metabolism ; }, abstract = {ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013 A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.}, }
@article {pmid28130242, year = {2017}, author = {Pedersen, TL}, title = {Hierarchical sets: analyzing pangenome structure through scalable set visualizations.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {11}, pages = {1604-1612}, doi = {10.1093/bioinformatics/btx034}, pmid = {28130242}, issn = {1367-4811}, mesh = {Algorithms ; Bacteria/*genetics ; Cluster Analysis ; Escherichia/genetics ; *Genome, Bacterial ; Genomics/*methods ; Sequence Analysis, DNA/*methods ; Shigella/genetics ; *Software ; }, abstract = {Motivation: The increase in available microbial genome sequences has resulted in an increase in the size of the pangenomes being analyzed. Current pangenome visualizations are not intended for the pangenome sizes possible today and new approaches are necessary in order to convert the increase in available information to increase in knowledge. As the pangenome data structure is essentially a collection of sets we explore the potential for scalable set visualization as a tool for pangenome analysis.<br><br>Results: We present a new hierarchical clustering algorithm based on set arithmetics that optimizes the intersection sizes along the branches. The intersection and union sizes along the hierarchy are visualized using a composite dendrogram and icicle plot, which, in pangenome context, shows the evolution of pangenome and core size along the evolutionary hierarchy. Outlying elements, i.e. elements whose presence pattern do not correspond with the hierarchy, can be visualized using hierarchical edge bundles. When applied to pangenome data this plot shows putative horizontal gene transfers between the genomes and can highlight relationships between genomes that is not represented by the hierarchy. We illustrate the utility of hierarchical sets by applying it to a pangenome based on 113 Escherichia and Shigella genomes and find it provides a powerful addition to pangenome analysis.<br><br>The described clustering algorithm and visualizations are implemented in the hierarchicalSets R package available from CRAN (https://cran.r-project.org/web/packages/hierarchicalSets).<br><br>Contact: thomasp85@gmail.com.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28125655, year = {2017}, author = {Baraúna, RA and Ramos, RT and Veras, AA and Pinheiro, KC and Benevides, LJ and Viana, MV and Guimarães, LC and Edman, JM and Spier, SJ and Azevedo, V and Silva, A}, title = {Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0170676}, doi = {10.1371/journal.pone.0170676}, pmid = {28125655}, issn = {1932-6203}, mesh = {Animals ; Corynebacterium Infections/*genetics/microbiology ; Corynebacterium pseudotuberculosis/*genetics/pathogenicity ; Genome, Bacterial/*genetics ; Genotype ; High-Throughput Nucleotide Sequencing ; Horse Diseases/*genetics/microbiology ; Horses/microbiology ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Rhodococcus equi/*genetics/pathogenicity ; }, abstract = {Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as &quot;pigeon fever&quot; which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two distinct clades, one formed by nitrate non-reducing species (biovar ovis) and another formed by nitrate-reducing species (biovar equi). In the latter group, the strains isolated from California were more related to each other, while the strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A total of 1,355 core genes were identified, corresponding to 42.5% of the pangenome. This pangenome has one of the smallest core genomes described in the literature, suggesting a high genetic variability of biovar equi of C. pseudotuberculosis. The analysis of the similarity between the resistance islands identified a higher proximity between the strains that caused more severe infectious conditions (infection in the internal organs). Pathogenicity islands were largely conserved between strains. Several genes that modulate the pathogenicity of C. pseudotuberculosis were described including peptidases, recombination enzymes, micoside synthesis enzymes, bacteriocins with antimicrobial activity and several others. Finally, no genotypic differences were observed between the strains that caused the three different types of infection (external abscess formation, infection with abscess formation in the internal organs, and ulcerative lymphangitis). Instead, it was noted that there is a higher phenetic correlation between strains isolated at California compared to the other strains. Additionally, high variability of resistance islands suggests gene acquisition through several events of horizontal gene transfer.}, }
@article {pmid28123380, year = {2016}, author = {Knight, DR and Squire, MM and Collins, DA and Riley, TV}, title = {Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2138}, doi = {10.3389/fmicb.2016.02138}, pmid = {28123380}, issn = {1664-302X}, abstract = {Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42% of human strains showed a clonal relationship (separated by ≤2 SNVs in their core genome) with one or more porcine strains, consistent with recent inter-host transmission. Clones were spread over a vast geographic area with 50% of the human cases occurring without recent healthcare exposure. These findings suggest a persistent community reservoir with long-range dissemination, potentially due to agricultural recycling of piggery effluent. We also provide the first pan-genome analysis for this lineage, characterizing its resistome, prophage content, and in silico virulence potential. The RT014 is defined by a large &quot;open&quot; pan-genome (7587 genes) comprising a core genome of 2296 genes (30.3% of the total gene repertoire) and an accessory genome of 5291 genes. Antimicrobial resistance genotypes and phenotypes varied across host populations and ST lineages and were characterized by resistance to tetracycline [tetM, tetA(P), tetB(P) and tetW], clindamycin/erythromycin (ermB), and aminoglycosides (aph3-III-Sat4A-ant6-Ia). Resistance was mediated by clinically important mobile genetic elements, most notably Tn6194 (harboring ermB) and a novel variant of Tn5397 (harboring tetM). Numerous clinically important prophages (Siphoviridae and Myoviridae) were identified as well as an uncommon accessory gene regulator locus (agr3). Conservation in the pathogenicity locus and S-layer correlated with ST affiliation, further extending the concept of clonal C. difficile lineages. This study provides novel insights on the genetic variability and strain relatedness of C. difficile RT014, a lineage of emerging One Health importance. Ongoing molecular and genomic surveillance of strains in humans, animals, food, and the environment is imperative to identify opportunities to reduce the overall CDI burden.}, }
@article {pmid28117406, year = {2017}, author = {Pancrace, C and Barny, MA and Ueoka, R and Calteau, A and Scalvenzi, T and Pédron, J and Barbe, V and Piel, J and Humbert, JF and Gugger, M}, title = {Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41181}, doi = {10.1038/srep41181}, pmid = {28117406}, issn = {2045-2322}, abstract = {Planktothrix is a dominant cyanobacterial genus forming toxic blooms in temperate freshwater ecosystems. We sequenced the genome of planktic and non planktic Planktothrix strains to better represent this genus diversity and life style at the genomic level. Benthic and biphasic strains are rooting the Planktothrix phylogenetic tree and widely expand the pangenome of this genus. We further investigated in silico the genetic potential dedicated to gas vesicles production, nitrogen fixation as well as natural product synthesis and conducted complementary experimental tests by cell culture, microscopy and mass spectrometry. Significant differences for the investigated features could be evidenced between strains of different life styles. The benthic Planktothrix strains showed unexpected characteristics such as buoyancy, nitrogen fixation capacity and unique natural product features. In comparison with Microcystis, another dominant toxic bloom-forming genus in freshwater ecosystem, different evolutionary strategies were highlighted notably as Planktothrix exhibits an overall greater genetic diversity but a smaller genomic plasticity than Microcystis. Our results are shedding light on Planktothrix evolution, phylogeny and physiology in the frame of their diverse life styles.}, }
@article {pmid28115376, year = {2017}, author = {Thépault, A and Méric, G and Rivoal, K and Pascoe, B and Mageiros, L and Touzain, F and Rose, V and Béven, V and Chemaly, M and Sheppard, SK}, title = {Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {7}, pages = {}, doi = {10.1128/AEM.03085-16}, pmid = {28115376}, issn = {1098-5336}, support = {//Wellcome Trust/United Kingdom ; BB/I02464X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1//Medical Research Council/United Kingdom ; 088786/C/09/Z//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacterial Typing Techniques ; Campylobacter/isolation &amp; purification ; Campylobacter Infections/*epidemiology/*microbiology/transmission ; Campylobacter jejuni/classification/*genetics ; Chickens/microbiology ; Disease Reservoirs/microbiology ; *Food Microbiology ; France/epidemiology ; Genetic Markers ; *Genome, Bacterial ; Genomics ; Humans ; Multilocus Sequence Typing ; Ruminants/microbiology ; United Kingdom/epidemiology ; }, abstract = {Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multilocus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles at seven MLST loci among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1,810 genes identified by gene-by-gene comparison of 884 genomes of Campylobacter jejuni isolates from animal reservoirs, the environment, and clinical cases. Fifteen loci involved in metabolic activities, protein modification, signal transduction, and stress response or coding for hypothetical proteins were selected as host-segregating markers and used to attribute the source of 42 French and 281 United Kingdom clinical C. jejuni isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the United Kingdom. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs, suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modeling to account for differences in production, behavior, and food consumption.IMPORTANCE Accurately quantifying the relative contribution of different host reservoirs to human Campylobacter infection is an ongoing challenge. This study, based on the development of a novel source attribution approach, provides the first results of source attribution in Campylobacter jejuni in France. A systematic analysis using gene-by-gene comparison of 884 genomes of C. jejuni isolates, with a pan-genome list of genes, identified 15 novel epidemiological markers for source attribution. The different proportions of French and United Kingdom clinical isolates attributed to each host reservoir illustrate a potential role for local/national variations in C. jejuni transmission dynamics.}, }
@article {pmid28105943, year = {2016}, author = {Sultanov, RI and Arapidi, GP and Vinogradova, SV and Govorun, VM and Luster, DG and Ignatov, AN}, title = {Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants.}, journal = {BMC genomics}, volume = {17}, number = {Suppl 14}, pages = {1010}, doi = {10.1186/s12864-016-3358-y}, pmid = {28105943}, issn = {1471-2164}, mesh = {Bacterial Secretion Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology/methods ; DNA Transposable Elements ; Genes, Bacterial ; *Genome, Bacterial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Plant Diseases/*microbiology ; Pseudomonas syringae/classification/*genetics/pathogenicity ; Quorum Sensing/genetics ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: In recent years, the damage caused by bacterial pathogens to major crops has been increasing worldwide. Pseudomonas syringae is a widespread bacterial species that infects almost all major crops. Different P. syringae strains use a wide range of biochemical mechanisms, including phytotoxins and effectors of the type III and type IV secretion systems, which determine the specific nature of the pathogen virulence.<br><br>RESULTS: Strains 1845 (isolated from dicots) and 2507 (isolated from monocots) were selected for sequencing because they specialize on different groups of plants. We compared virulence factors in these and other available genomes of phylogroup 2 to find genes responsible for the specialization of bacteria. We showed that strain 1845 belongs to the clonal group that has been infecting monocots in Russia and USA for a long time (at least 50 years). Strain 1845 has relatively recently changed its host plant to dicots.<br><br>CONCLUSIONS: The results obtained by comparing the strain 1845 genome with the genomes of bacteria infecting monocots can help to identify the genes that define specific nature of the virulence of P. syringae strains.}, }
@article {pmid28095778, year = {2017}, author = {Bosi, E and Fondi, M and Orlandini, V and Perrin, E and Maida, I and de Pascale, D and Tutino, ML and Parrilli, E and Lo Giudice, A and Filloux, A and Fani, R}, title = {The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {93}, doi = {10.1186/s12864-016-3382-y}, pmid = {28095778}, issn = {1471-2164}, mesh = {Antarctic Regions ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/genetics/metabolism ; Cold Temperature ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Membrane Transport Proteins/genetics/metabolism ; Phylogeny ; Pseudoalteromonas/classification/*genetics ; Secondary Metabolism/genetics ; }, abstract = {BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.<br><br>RESULTS: Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.<br><br>CONCLUSIONS: This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.}, }
@article {pmid28078297, year = {2016}, author = {Cao, DM and Lu, QF and Li, SB and Wang, JP and Chen, YL and Huang, YQ and Bi, HK}, title = {Comparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability.}, journal = {BioMed research international}, volume = {2016}, number = {}, pages = {6106029}, doi = {10.1155/2016/6106029}, pmid = {28078297}, issn = {2314-6141}, mesh = {Bacterial Proteins/*genetics ; Genome, Bacterial ; *Genomics ; Helicobacter Infections/*genetics/microbiology ; Helicobacter pylori/*genetics/pathogenicity ; Humans ; Molecular Sequence Annotation ; }, abstract = {The genus Helicobacter is a group of Gram-negative, helical-shaped pathogens consisting of at least 36 bacterial species. Helicobacter pylori (H. pylori), infecting more than 50% of the human population, is considered as the major cause of gastritis, peptic ulcer, and gastric cancer. However, the genetic underpinnings of H. pylori that are responsible for its large scale epidemic and gastrointestinal environment adaption within human beings remain unclear. Core-pan genome analysis was performed among 75 representative H. pylori and 24 non-pylori Helicobacter genomes. There were 1173 conserved protein families of H. pylori and 673 of all 99 Helicobacter genus strains. We found 79 genome unique regions, a total of 202,359bp, shared by at least 80% of the H. pylori but lacked in non-pylori Helicobacter species. The operons, genes, and sRNAs within the H. pylori unique regions were considered as potential ones associated with its pathogenicity and adaptability, and the relativity among them has been partially confirmed by functional annotation analysis. However, functions of at least 54 genes and 10 sRNAs were still unclear. Our analysis of protein-protein interaction showed that 30 genes within them may have the cooperation relationship.}, }
@article {pmid28057934, year = {2017}, author = {Zeng, H and Zhang, J and Li, C and Xie, T and Ling, N and Wu, Q and Ye, Y}, title = {The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40206}, doi = {10.1038/srep40206}, pmid = {28057934}, issn = {2045-2322}, abstract = {Cronobacter sakazakii is an important foodborne pathogens causing rare but life-threatening diseases in neonates and infants. CRISPR-Cas system is a new prokaryotic defense system that provides adaptive immunity against phages, latter play an vital role on the evolution and pathogenicity of host bacteria. In this study, we found that genome sizes of C. sakazakii strains had a significant positive correlation with total genome sizes of prophages. Prophages contributed to 16.57% of the genetic diversity (pan genome) of C. sakazakii, some of which maybe the potential virulence factors. Subtype I-E CRISPR-Cas system and five types of CRISPR arrays were found in the conserved site of C. sakazakii strains. CRISPR1 and CRISPR2 loci with high variable spacers were active and showed potential protection against phage attacks. The number of spacers from two active CRISPR loci in clinical strains was significant less than that of foodborne strains, it maybe a reason why clinical strains were found to have more prophages than foodborne strains. The frequently gain/loss of prophages and spacers in CRISPR loci is likely to drive the quick evolution of C. sakazakii. Our study provides a new insight into the co-evolution of phages and C. sakazakii.}, }
@article {pmid28057677, year = {2017}, author = {Pedersen, TL and Nookaew, I and Wayne Ussery, D and Månsson, M}, title = {PanViz: interactive visualization of the structure of functionally annotated pangenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {7}, pages = {1081-1082}, doi = {10.1093/bioinformatics/btw761}, pmid = {28057677}, issn = {1367-4811}, mesh = {Computer Graphics ; Gene Ontology ; *Genome ; Genomics ; Molecular Sequence Annotation ; *Software ; }, abstract = {Summary: PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes with gene ontology based navigation of gene groups. Furthermore it allows for rich and complex visual querying of gene groups in the pangenome. PanViz visualizations require no external programs and are easily sharable, allowing for rapid pangenome analyses.<br><br>PanViz is written entirely in JavaScript and is available on https://github.com/thomasp85/PanViz . A companion R package that facilitates the creation of PanViz visualizations from a range of data formats is released through Bioconductor and is available at https://bioconductor.org/packages/PanVizGenerator .<br><br>Contact: thomasp85@gmail.com.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28056800, year = {2017}, author = {López-Pérez, M and Ramon-Marco, N and Rodriguez-Valera, F}, title = {Networking in microbes: conjugative elements and plasmids in the genus Alteromonas.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {36}, doi = {10.1186/s12864-016-3461-0}, pmid = {28056800}, issn = {1471-2164}, mesh = {Alteromonas/classification/*genetics/metabolism ; Base Composition ; Computational Biology/methods ; *Conjugation, Genetic ; *Genome, Bacterial ; *Genomics/methods ; Open Reading Frames ; Phylogeny ; Plasmids/*genetics ; Polymorphism, Single Nucleotide ; Protein Interaction Mapping ; Protein Interaction Maps ; Proteome ; Proteomics/methods ; }, abstract = {BACKGROUND: To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time.<br><br>RESULTS: We have found nine different plasmids of sizes ranging from 85 to 600 Kb, most of them were found in a single strain. Networks of gene similarity could be established among six of the plasmids that were also connected with another cluster of plasmids found in Shewanella strains. The cargo genes found in these plasmids included cassettes found before in chromosome flexible genomic islands of Alteromonas strains. We describe also the plasmids pAMCP48-600 and pAMCP49-600, the largest found in Alteromonas thus far (ca. 600 Kb) and containing all the hallmarks to be classified as chromids. We found in them some housekeeping genes and a cluster that code for an exocellular polysaccharide. They could represent the transport vectors for the previously described replacement flexible genomic islands. Integrative and conjugative elements (ICEs) were more common than plasmids and showed similar patterns of variation with cargo genes coding for components of additive flexible genomic islands. A nearly identical ICE was found in A. mediterranea MED64 and Vibrio cholera AHV1003 isolated from a human pathogen, indicating the potential exchange of these genes across phylogenetic distances exceeding the family threshold.<br><br>CONCLUSION: We have seen evidence of how CEs can be vectors to transfer gene cassettes acquired in the chromosomal flexible genomic islands, both of the additive and replacement kind. These CEs showed evidence of how genetic material is exchanged among members of the same species but also (albeit less frequently) across genus and family barriers. These gradients of exchange frequency are probably one of the main drivers of species origin and maintenance in prokaryotes and also provide these taxa with large genetic diversity.}, }
@article {pmid28053228, year = {2017}, author = {Croucher, NJ and Campo, JJ and Le, TQ and Liang, X and Bentley, SD and Hanage, WP and Lipsitch, M}, title = {Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {3}, pages = {E357-E366}, doi = {10.1073/pnas.1613937114}, pmid = {28053228}, issn = {1091-6490}, support = {//Wellcome Trust/United Kingdom ; R01 AI048935/AI/NIAID NIH HHS/United States ; R01 AI066304/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; 098051//Wellcome Trust/United Kingdom ; 104169/Z/14/Z//Wellcome Trust/United Kingdom ; }, mesh = {Adhesins, Bacterial/immunology ; Adult ; Antibodies, Bacterial/immunology ; Antibody Formation/immunology ; Antigens, Bacterial/*immunology ; Bacterial Proteins/immunology ; Epitopes/immunology ; Humans ; Immunoglobulin G/immunology ; Membrane Proteins/immunology ; Membrane Transport Proteins/immunology ; Pneumococcal Infections/immunology ; Pneumococcal Vaccines/immunology ; Streptococcus pneumoniae/*immunology ; }, abstract = {Characterizing the immune response to pneumococcal proteins is critical in understanding this bacterium's epidemiology and vaccinology. Probing a custom-designed proteome microarray with sera from 35 healthy US adults revealed a continuous distribution of IgG affinities for 2,190 potential antigens from the species-wide pangenome. Reproducibly elevated IgG binding was elicited by 208 &quot;antibody binding targets&quot; (ABTs), which included 109 variants of the diverse pneumococcal surface proteins A and C (PspA and PspC) and zinc metalloprotease A and B (ZmpA and ZmpB) proteins. Functional analysis found ABTs were enriched in motifs for secretion and cell surface association, with extensive representation of cell wall synthesis machinery, adhesins, transporter solute-binding proteins, and degradative enzymes. ABTs were associated with stronger evidence for evolving under positive selection, although this varied between functional categories, as did rates of diversification through recombination. Particularly rapid variation was observed at some immunogenic accessory loci, including a phage protein and a phase-variable glycosyltransferase ubiquitous among the diverse set of genomic islands encoding the serine-rich PsrP glycoprotein. Nevertheless, many antigens were conserved in the core genome, and strains' antigenic profiles were generally stable. No strong evidence was found for any epistasis between antigens driving population dynamics, or redundancy between functionally similar accessory ABTs, or age stratification of antigen profiles. These results highlight the paradox of why substantial variation is observed in only a subset of epitopes. This result may indicate only some interactions between immunoglobulins and ABTs clear pneumococcal colonization or that acquired immunity to pneumococci is an accumulation of individually weak responses to ABTs evolving under different levels of functional constraint.}, }
@article {pmid28045086, year = {2017}, author = {Uchiya, KI and Tomida, S and Nakagawa, T and Asahi, S and Nikai, T and Ogawa, K}, title = {Comparative genome analyses of Mycobacterium avium reveal genomic features of its subspecies and strains that cause progression of pulmonary disease.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {39750}, doi = {10.1038/srep39750}, pmid = {28045086}, issn = {2045-2322}, abstract = {Pulmonary disease caused by nontuberculous mycobacteria (NTM) is increasing worldwide. Mycobacterium avium is the most clinically significant NTM species in humans and animals, and comprises four subspecies: M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS), M. avium subsp. paratuberculosis (MAP), and M. avium subsp. hominissuis (MAH). To improve our understanding of the genetic landscape and diversity of M. avium and its role in disease, we performed a comparative genome analysis of 79 M. avium strains. Our analysis demonstrated that MAH is an open pan-genome species. Phylogenetic analysis based on single nucleotide variants showed that MAH had the highest degree of sequence variability among the subspecies, and MAH strains isolated in Japan and those isolated abroad possessed distinct phylogenetic features. Furthermore, MAP strains, MAS and MAA strains isolated from birds, and many MAH strains that cause the progression of pulmonary disease were grouped in each specific cluster. Comparative genome analysis revealed the presence of genetic elements specific to each lineage, which are thought to be acquired via horizontal gene transfer during the evolutionary process, and identified potential genetic determinants accounting for the pathogenic and host range characteristics of M. avium.}, }
@article {pmid28043631, year = {2016}, author = {Otchere, ID and Harris, SR and Busso, SL and Asante-Poku, A and Osei-Wusu, S and Koram, K and Parkhill, J and Gagneux, S and Yeboah-Manu, D}, title = {The First population structure and comparative genomics analysis of Mycobacterium africanum strains from Ghana reveals higher diversity of Lineage 5.}, journal = {International journal of mycobacteriology}, volume = {5 Suppl 1}, number = {}, pages = {S80-S81}, doi = {10.1016/j.ijmyco.2016.09.051}, pmid = {28043631}, issn = {2212-554X}, abstract = {OBJECTIVE/BACKGROUND: Mycobacterium africanum (MAF) remains an important TB causing pathogen in West Africa; however, little is known about its population structure and actual diversity which may have implications for diagnostics and vaccines. We carried out comparative genomics analysis of candidate Mycobacterium tuberculosis (MTB) and MAF using whole genome sequencing.<br><br>METHODS: Clinical MTB complex strains (n=187) comprising L4 (n=22), L5 (n=126), and L6 (n=39) isolated over 8years from Ghana were whole genome sequenced. The reads were mapped onto a reference genome for phylogenetic and functional genomics analysis. A maximum likelihood tree with 100 bootstraps was constructed from the single nucleotide polymorphisms (SNPs) found using RAxML and clustered with hierBAPS. A total of 147 (18 L4, 36 L6, and 93 L5) of the genomes were de novo assembled and annotated for comparative pangenome analysis using Roary.<br><br>RESULTS: The population structure of MAF revealed at least five clusters of L5 as compared to three for L6. We also identified a group of three multi-drug-resistants (MDRs) within a single cluster of L5 strains from Southern Ghana isolated in 2013. Among the global collection of MTB complex, there were four Ghana-specific L5 clusters of which one (L5.1.1) had traits of clonal expansion. From the 5947pan genes extracted from the collection, 3215 (54.1%) were core to all the 147 genomes whereas 719 (12.1%) were found in single genomes. Most of the variable genes were PE-PGRS/PPE (1,281) duplicates of other genes (431). The genome degradation was more pronounced in Lineages 4 and 6 as compared to Lineage 5. We identified the absence of some unique genes among specific lineages and/or clades with possible clinical implications. For example, mpt64 and mlaD encoding respectively an immunogenic protein and a mammalian cell entry protein were missing from all L6 genomes. In addition, all L5 strains had an amino acid substitution I43N within the mpt64 gene. Analysis of SNPs within some genes encoding proteins for substrate metabolism, ion transport and secretory systems showed higher proportion of SNPs among L6 compared to L5 and L4. We also identified a number of lineage/sublineage specific SNPs and indels that may be utilized in rapid PCR based genotyping of MTB complex.<br><br>CONCLUSION: This work emphasizes on the possibility that the mpt64-based rapid diagnostic kit would not be effective in MAF endemic settings. More mutations in ESAT-6 secretory system of MAF compared to MTB sensu stricto can affect efficacy of ESAT-6-based vaccines in the future.}, }
@article {pmid28018331, year = {2016}, author = {Liu, YY and Chen, CC and Chiou, CS}, title = {Construction of a Pan-Genome Allele Database of Salmonella enterica Serovar Enteritidis for Molecular Subtyping and Disease Cluster Identification.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2010}, doi = {10.3389/fmicb.2016.02010}, pmid = {28018331}, issn = {1664-302X}, abstract = {We built a pan-genome allele database with 395 genomes of Salmonella enterica serovar Enteritidis and developed computer tools for analysis of whole genome sequencing (WGS) data of bacterial isolates for disease cluster identification. A web server (http://wgmlst.imst.nsysu.edu.tw) was set up with the database and the tools, allowing users to upload WGS data to generate whole genome multilocus sequence typing (wgMLST) profiles and to perform cluster analysis of wgMLST profiles. The usefulness of the database in disease cluster identification was demonstrated by analyzing a panel of genomes from 55 epidemiologically well-defined S. Enteritidis isolates provided by the Minnesota Department of Health. The wgMLST-based cluster analysis revealed distinct clades that were concordant with the epidemiologically defined outbreaks. Thus, using a common pan-genome allele database, wgMLST can be a promising WGS-based subtyping approach for disease surveillance and outbreak investigation across laboratories.}, }
@article {pmid28011701, year = {2017}, author = {van Vliet, AH}, title = {Use of pan-genome analysis for the identification of lineage-specific genes of Helicobacter pylori.}, journal = {FEMS microbiology letters}, volume = {364}, number = {2}, pages = {}, doi = {10.1093/femsle/fnw296}, pmid = {28011701}, issn = {1574-6968}, mesh = {*Genes, Bacterial ; *Genetic Variation ; *Genome, Bacterial ; Genomic Islands ; Helicobacter Infections/microbiology ; Helicobacter pylori/classification/*genetics/isolation &amp; purification ; Humans ; Metabolic Networks and Pathways/genetics ; Multilocus Sequence Typing ; Virulence Factors/genetics ; }, abstract = {The human bacterial pathogen Helicobacter pylori has a highly variable genome, with significant allelic and sequence diversity between isolates and even within well-characterised strains, hampering comparative genomics of H. pylori In this study, pan-genome analysis has been used to identify lineage-specific genes of H. pylori A total of 346 H. pylori genomes spanning the hpAfrica1, hpAfrica2, hpAsia2, hpEurope, hspAmerind and hspEAsia multilocus sequence typing (MLST) lineages were searched for genes specifically overrepresented or underrepresented in MLST lineages or associated with the cag pathogenicity island. The only genes overrepresented in cag-positive genomes were the cag pathogenicity island genes themselves. In contrast, a total of 125 genes were either overrepresented or underrepresented in one or more MLST lineages. Of these 125 genes, alcohol/aldehyde-reducing enzymes linked with acid resistance and production of toxic aldehydes were found to be overrepresented in African lineages. Conversely, the FecA2 ferric citrate receptor was missing from hspAmerind genomes, but present in all other lineages. This work shows the applicability of pan-genome analysis for identification of lineage-specific genes of H. pylori, facilitating further investigation to allow linkage of differential distribution of genes with disease outcome or virulence of H. pylori.}, }
@article {pmid27993146, year = {2016}, author = {Brynildsrud, O and Bohlin, J and Scheffer, L and Eldholm, V}, title = {Erratum to: Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {262}, doi = {10.1186/s13059-016-1132-8}, pmid = {27993146}, issn = {1474-760X}, }
@article {pmid27988045, year = {2017}, author = {Benamar, S and Cassir, N and Merhej, V and Jardot, P and Robert, C and Raoult, D and La Scola, B}, title = {Multi-spacer typing as an effective method to distinguish the clonal lineage of Clostridium butyricum strains isolated from stool samples during a series of necrotizing enterocolitis cases.}, journal = {The Journal of hospital infection}, volume = {95}, number = {3}, pages = {300-305}, doi = {10.1016/j.jhin.2016.10.026}, pmid = {27988045}, issn = {1532-2939}, mesh = {Adult ; Aged ; Child ; Child, Preschool ; Clostridium Infections/epidemiology/*microbiology ; Clostridium butyricum/*classification/genetics/isolation &amp; purification ; Cluster Analysis ; Enterocolitis, Necrotizing/epidemiology/*microbiology ; Feces/microbiology ; *Genotype ; Humans ; Infant ; Infant, Newborn ; Molecular Epidemiology ; Molecular Typing/*methods ; }, abstract = {BACKGROUND: Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease with high morbidity and mortality that predominantly affects preterm neonates during outbreaks. In a previous study, the present authors identified 15 Clostridium butyricum isolates from stool samples during a series of NEC cases involving four neonatal intensive care units. A clonal lineage of these strains was observed by in-silico multi-locus sequence typing.<br><br>AIM: To confirm the previous findings by sequencing a larger number of C. butyricum genomes and using other genotyping approaches.<br><br>METHODS: The previously isolated 15 C. butyricum strains were characterized and compared with 17 other commensal and environmental C. butyricum strains using whole-genome sequencing (WGS). In addition, the clustering was analysed using multi-spacer sequence typing (MST).<br><br>FINDINGS: The core genome of C. butyricum was composed of 1251 genes, and its pan-genome consisted of 12,628 genes with high variability between strains. It was possible to distinguish the clonal lineage of strains from a series of NEC cases, forming three clades with geographical clustering. The results obtained using WGS and MST approaches were congruent.<br><br>CONCLUSION: MST is a fast, cheap and effective genotyping method for investigating NEC outbreaks associated with C. butyricum.}, }
@article {pmid27940610, year = {2017}, author = {Sun, C and Hu, Z and Zheng, T and Lu, K and Zhao, Y and Wang, W and Shi, J and Wang, C and Lu, J and Zhang, D and Li, Z and Wei, C}, title = {RPAN: rice pan-genome browser for ∼3000 rice genomes.}, journal = {Nucleic acids research}, volume = {45}, number = {2}, pages = {597-605}, doi = {10.1093/nar/gkw958}, pmid = {27940610}, issn = {1362-4962}, mesh = {Computational Biology/methods ; Databases, Genetic ; *Genome, Plant ; *Genomics/methods ; Molecular Sequence Annotation ; Oryza/*genetics ; *Software ; Web Browser ; }, abstract = {A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k.}, }
@article {pmid27938326, year = {2016}, author = {Walkowiak, S and Rowland, O and Rodrigue, N and Subramaniam, R}, title = {Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {1014}, doi = {10.1186/s12864-016-3371-1}, pmid = {27938326}, issn = {1471-2164}, mesh = {Alleles ; Computational Biology/methods ; Fusarium/*classification/*genetics/metabolism ; Genes, Fungal ; Genetic Variation ; *Genome, Fungal ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing ; INDEL Mutation ; Polymorphism, Single Nucleotide ; Pseudogenes ; Secondary Metabolism ; Selection, Genetic ; }, abstract = {BACKGROUND: The Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely related, these species and individuals within species have distinct phenotypic differences in toxin production and pathogenicity, with some isolates reported as non-pathogenic on certain hosts. In this report, we compare genomes and gene content of six new isolates from the species complex, including the first available genomes of F. asiaticum and F. meridionale, with four other genomes reported in previous studies.<br><br>RESULTS: A comparison of genome structure and gene content revealed a 93-99% overlap across all ten genomes. We identified more than 700 k base pairs (kb) of single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) within common regions of the genome, which validated the species and genetic populations reported within species. We constructed a non-redundant pan gene list containing 15,297 genes from the ten genomes and among them 1827 genes or 12% were absent in at least one genome. These genes were co-localized in telomeric regions and select regions within chromosomes with a corresponding increase in SNPs and indels. Many are also predicted to encode for proteins involved in secondary metabolism and other functions associated with disease. Genes that were common between isolates contained high levels of nucleotide variation and may be pseudogenes, allelic, or under diversifying selection.<br><br>CONCLUSIONS: The genomic resources we have contributed will be useful for the identification of genes that contribute to the phenotypic variation and niche specialization that have been reported among members of the F. graminearum species complex.}, }
@article {pmid27933096, year = {2016}, author = {Beller, T and Ohlebusch, E}, title = {Erratum to: A representation of a compressed de Bruijn graph for pan-genome analysis that enables search.}, journal = {Algorithms for molecular biology : AMB}, volume = {11}, number = {}, pages = {28}, doi = {10.1186/s13015-016-0090-8}, pmid = {27933096}, issn = {1748-7188}, abstract = {[This corrects the article DOI: 10.1186/s13015-016-0083-7.].}, }
@article {pmid27924951, year = {2016}, author = {Bakshi, U and Sarkar, M and Paul, S and Dutta, C}, title = {Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach - Identification of pathogen-specific and habitat-specific genes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38648}, doi = {10.1038/srep38648}, pmid = {27924951}, issn = {2045-2322}, mesh = {Base Composition ; Enterococcus faecalis/classification/pathogenicity/*physiology ; Genes, Bacterial ; Genetic Variation ; Genome Size ; *Genome, Bacterial ; *Genomic Islands ; *Genomics ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Open Reading Frames ; Phylogeny ; Plasmids ; Virulence/*genetics ; Virulence Factors/genetics ; }, abstract = {Enterococcus faecalis, a leading nosocomial pathogen and yet a prominent member of gut microbiome, lacks clear demarcation between pathogenic and non-pathogenic strains at genome level. Here we present the comparative genome analysis of 36 E. faecalis strains with different pathogenic features and from different body-habitats. This study begins by addressing the genome dynamics, which shows that the pan-genome of E. faecalis is still open, though the core genome is nearly saturated. We identified eight uncharacterized strains as potential pathogens on the basis of their co-segregation with reported pathogens in gene presence-absence matrix and Pathogenicity Island (PAI) distribution. A ~7.4 kb genomic-cassette, which is itself a part of PAI, is found to exist in all reported and potential pathogens, but not in commensals and other uncharacterized strains. This region encodes four genes and among them, products of two hypothetical genes are predicted to be intrinsically disordered that may serve as novel targets for therapeutic measures. Exclusive existence of 215, 129, 4 and 1 genes in the blood, gastrointestinal tract, urogenital tract, oral cavity and lymph node derived E. faecalis genomes respectively suggests possible employment of distinct habitat-specific genetic strategies in the adaptation of E. faecalis in human host.}, }
@article {pmid27924153, year = {2016}, author = {Kim, JY and Song, HS and Kim, YB and Kwon, J and Choi, JS and Cho, YJ and Kim, BY and Rhee, JK and Myoung, J and Nam, YD and Roh, SW}, title = {Genome sequence of a commensal bacterium, Enterococcus faecalis CBA7120, isolated from a Korean fecal sample.}, journal = {Gut pathogens}, volume = {8}, number = {}, pages = {62}, doi = {10.1186/s13099-016-0145-x}, pmid = {27924153}, issn = {1757-4749}, abstract = {BACKGROUND: Enterococcus faecalis, the type strain of the genus Enterococcus, is not only a commensal bacterium in the gastrointestinal tract in vertebrates and invertebrates, but also causes serious disease as an opportunistic pathogen. To date, genome sequences have been published for over four hundred E. faecalis strains; however, pathogenicity of these microbes remains complicated. To increase our knowledge of E. faecalis virulence factors, we isolated strain CBA7120 from the feces of an 81-year-old female from the Republic of Korea and performed a comparative genomic analysis.<br><br>RESULTS: The genome sequence of E. faecalis CBA7120 is 3,134,087 bp in length, with a G + C content of 37.35 mol%, and is comprised of four contigs with an N50 value of 2,922,046 bp. The genome showed high similarity with other strains of E. faecalis, including OG1RF, T13, 12107 and T20, based on OrthoANI values. Strain CBA7120 contains 374 pan-genome orthologous groups (POGs) as singletons, including &quot;Phages, Prophages, Transposable elements, Plasmids,&quot; &quot;Carbohydrates,&quot; &quot;DNA metabolism,&quot; and &quot;Virulence, Disease and Defense&quot; subsystems. Genes related to multidrug resistance efflux pumps were annotated in the genome.<br><br>CONCLUSIONS: The comparative genomic analysis of E. faecalis strains presented in this study was performed using a variety of analysis methods and will facilitate future identification of hypothetical proteins.}, }
@article {pmid27922098, year = {2016}, author = {Koehorst, JJ and van Dam, JC and van Heck, RG and Saccenti, E and Dos Santos, VA and Suarez-Diez, M and Schaap, PJ}, title = {Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38699}, doi = {10.1038/srep38699}, pmid = {27922098}, issn = {2045-2322}, mesh = {*Computational Biology/methods ; *Energy Metabolism ; *Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Pseudomonas/classification/*genetics/*metabolism ; Workflow ; }, abstract = {Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.}, }
@article {pmid27919552, year = {2017}, author = {Carter, MQ}, title = {Decoding the Ecological Function of Accessory Genome.}, journal = {Trends in microbiology}, volume = {25}, number = {1}, pages = {6-8}, doi = {10.1016/j.tim.2016.11.012}, pmid = {27919552}, issn = {1878-4380}, mesh = {Animals ; Cattle ; Escherichia coli Infections/microbiology/*transmission ; Escherichia coli O157/*genetics/isolation &amp; purification/metabolism/*pathogenicity ; Escherichia coli Proteins/*genetics ; Food Microbiology ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; Humans ; Phosphoproteins/*genetics ; Shiga Toxin/*metabolism ; Virulence Factors/genetics ; }, abstract = {Shiga toxin-producing Escherichia coli O157:H7 primarily resides in cattle asymptomatically, and can be transmitted to humans through food. A study by Lupolova et al. applied a machine-learning approach to complex pan-genome information and predicted that only a small subset of bovine isolates have the potential to cause diseases in humans.}, }
@article {pmid27887642, year = {2016}, author = {Brynildsrud, O and Bohlin, J and Scheffer, L and Eldholm, V}, title = {Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {238}, doi = {10.1186/s13059-016-1108-8}, pmid = {27887642}, issn = {1474-760X}, abstract = {Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary .}, }
@article {pmid27881098, year = {2016}, author = {Jironkin, A and Brown, RJ and Underwood, A and Chalker, VJ and Spiller, OB}, title = {Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {964}, doi = {10.1186/s12864-016-3284-z}, pmid = {27881098}, issn = {1471-2164}, mesh = {Alleles ; Cluster Analysis ; Genes, Bacterial ; *Genome, Bacterial ; *Genomics/methods ; Genotype ; Humans ; Multilocus Sequence Typing ; Mycoplasma hominis/*classification/*genetics/isolation &amp; purification ; Phylogeny ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; }, abstract = {BACKGROUND: Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, which would aid in understanding pathogen epidemiology and transmission. Due to availability and costs of whole genome sequencing and the challenges in obtaining adequate M. hominis DNA, the use of whole genome sequence analysis to provide clinical guidance is unpractical for this bacterial species as well as other fastidious organisms.<br><br>RESULTS: This study identified pan-genome set of 700 genes found to be present in four published reference genomes. A subset of 417 genes was identified to be core genome for 18 isolates and 1 reference. Leave-one-out analysis of the core genes highlighted set of 48 genes that are required to recapture the original phylogenetic relationships observed using whole genome SNP analysis. Three 7-locus MLST schemas with high diversity index (97%) and low dN/dS ratios (0.1, 0.13, and 0.11) were derived that could be used to confer good discrimination between strains and could be of practical use in future studies direct on clinical specimens.<br><br>CONCLUSIONS: The genes proposed in this study could be utilised to design a cost-effective and rapid PCR-based MLST assay that could be applied directly to clinical isolates, without prior isolation. This study includes additional genomic analysis revealing high levels of genetic heterogeneity among this species. This provides a novel and evidence based approach for the development of MLST schema that accurately represent genomic phylogeny for use in epidemiology and transmission studies.}, }
@article {pmid27880983, year = {2017}, author = {Weller-Stuart, T and De Maayer, P and Coutinho, T}, title = {Pantoea ananatis: genomic insights into a versatile pathogen.}, journal = {Molecular plant pathology}, volume = {18}, number = {9}, pages = {1191-1198}, doi = {10.1111/mpp.12517}, pmid = {27880983}, issn = {1364-3703}, mesh = {Biotechnology/methods ; Genomics/methods ; Pantoea/*genetics ; Quorum Sensing/physiology ; Type VI Secretion Systems/metabolism ; }, abstract = {Pantoea ananatis, a bacterium that is well known for its phytopathogenic characteristics, has been isolated from a myriad of ecological niches and hosts. Infection of agronomic crops, such as maize and rice, can result in substantial economic losses. In the last few years, much of the research performed on P. ananatis has been based on the sequencing and analysis of the genomes of strains isolated from different environments and with different lifestyles. In this review, we summarize the advances made in terms of pathogenicity determinants of phytopathogenic strains of P. ananatis and how this bacterium is able to adapt and survive in such a wide variety of habitats. The diversity and adaptability of P. ananatis can largely be attributed to the plasticity of its genome and the integration of mobile genetic elements on both the chromosome and plasmid. Furthermore, we discuss the recent interest in this species in various biotechnological applications.<br><br>TAXONOMY: Domain Bacteria; Class Gammaproteobacteria; Family Enterobacteriaceae; genus Pantoea; species ananatis.<br><br>DISEASE SYMPTOMS: Pantoea ananatis causes disease on a wide range of plants, and symptoms can range from dieback and stunted growth in Eucalyptus seedlings to chlorosis and bulb rotting in onions.<br><br>DISEASE CONTROL: Currently, the only methods of control of P. ananatis on most plant hosts are the use of resistant clones and cultivars or the eradication of infected plant material. The use of lytic bacteriophages on certain host plants, such as rice, has also achieved a measure of success.}, }
@article {pmid27864136, year = {2017}, author = {Zhi, XY and Jiang, Z and Yang, LL and Huang, Y}, title = {The underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {246-255}, doi = {10.1016/j.ympev.2016.11.009}, pmid = {27864136}, issn = {1095-9513}, mesh = {Actinomycetales/*classification/*genetics ; Animals ; Gene Transfer, Horizontal ; *Genetic Speciation ; Genetic Variation ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/genetics ; *Phylogeny ; }, abstract = {The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach. Genetic variations have occurred throughout the whole evolutionary history of the Corynebacteriaceae. Gene loss has been the primary force causing genetic changes, not only in terms of the number of protein families affected, but also because of its continuity on the time series. The variation in metabolism caused by these genetic changes mainly occurred for membrane transporters, two-component systems, and metabolism related to amino acids and carbohydrates. Interestingly, horizontal gene transfer (HGT) not only caused changes related to pathogenicity, but also triggered the acquisition of antimicrobial resistance. The Darwinian theory of evolution did not adequately explain the effects of dispersive HGT and/or gene loss in the evolution of the Corynebacteriaceae. These findings provide new insight into the evolution and speciation of Corynebacteriaceae and advance our understanding of the genetic innovation in microbial populations.}, }
@article {pmid27861551, year = {2016}, author = {Malki, K and Shapiro, JW and Price, TK and Hilt, EE and Thomas-White, K and Sircar, T and Rosenfeld, AB and Kuffel, G and Zilliox, MJ and Wolfe, AJ and Putonti, C}, title = {Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166757}, doi = {10.1371/journal.pone.0166757}, pmid = {27861551}, issn = {1932-6203}, mesh = {Adult ; Computational Biology/methods ; DNA Transposable Elements ; Female ; Gardnerella/*genetics/virology ; Genes, Viral ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; Open Reading Frames ; Phylogeny ; Prophages/*genetics ; Urinary Bladder/*microbiology ; }, abstract = {Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from the bladder reveal a large pangenome, as well as evidence of high frequency horizontal gene transfer. Prophage gene sequences were found to be abundant amongst the strains isolated from the bladder, as well as amongst publicly available Gardnerella genomes from the vagina and endometrium, motivating an in depth examination of these sequences. Amongst the 39 Gardnerella strains examined here, there were more than 400 annotated prophage gene sequences that we could cluster into 95 homologous groups; 49 of these groups were unique to a single strain. While many of these prophages exhibited no sequence similarity to any lytic phage genome, estimation of the rate of phage acquisition suggests both vertical and horizontal acquisition. Furthermore, bioinformatic evidence indicates that prophage acquisition is ongoing within both vaginal and bladder Gardnerella populations. The abundance of prophage sequences within the strains examined here suggests that phages could play an important role in the species' evolutionary history and in its interactions within the complex communities found in the female urinary and reproductive tracts.}, }
@article {pmid27851981, year = {2017}, author = {Yuvaraj, I and Sridhar, J and Michael, D and Sekar, K}, title = {PanGeT: Pan-genomics tool.}, journal = {Gene}, volume = {600}, number = {}, pages = {77-84}, doi = {10.1016/j.gene.2016.11.025}, pmid = {27851981}, issn = {1879-0038}, mesh = {Evolution, Molecular ; Genome, Bacterial ; Genomics/*statistics &amp; numerical data ; Mycobacterium/classification/genetics ; Proteome/genetics ; Salmonella enterica/classification/genetics ; *Software ; Species Specificity ; }, abstract = {A decade after the concept of Pan-genome was first introduced; research in this field has spread its tentacles to areas such as pathogenesis of diseases, bacterial evolutionary studies and drug resistance. Gene content-based differentiation of virulent and a virulent strains of bacteria and identification of pathogen specific genes is imperative to understand their physiology and gain insights into the mechanism of genome evolution. Subsequently, this will aid in identifying diagnostic targets and in developing and selecting vaccines. The root of pan-genomic studies, however, is to identify the core genes, dispensable genes and strain specific genes across the genomes belonging to a clade. To this end, we have developed a tool, &quot;PanGeT - Pan-genomics Tool&quot; to compute the 'pan-genome' based on comparisons at the genome as well as the proteome levels. This automated tool is implemented using LaTeX libraries for effective visualization of overall pan-genome through graphical plots. Links to retrieve sequence information and functional annotations have also been provided. PanGeT can be downloaded from http://pranag.physics.iisc.ernet.in/PanGeT/ or https://github.com/PanGeTv1/PanGeT.}, }
@article {pmid27834372, year = {2016}, author = {Golicz, AA and Bayer, PE and Barker, GC and Edger, PP and Kim, H and Martinez, PA and Chan, CK and Severn-Ellis, A and McCombie, WR and Parkin, IA and Paterson, AH and Pires, JC and Sharpe, AG and Tang, H and Teakle, GR and Town, CD and Batley, J and Edwards, D}, title = {The pangenome of an agronomically important crop plant Brassica oleracea.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13390}, doi = {10.1038/ncomms13390}, pmid = {27834372}, issn = {2041-1723}, support = {BB/E017479/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Brassica/*genetics ; Chromosome Mapping ; Chromosomes, Plant ; Crops, Agricultural/*genetics ; Gene Expression Regulation, Plant ; Genetic Variation ; *Genome, Plant ; Phylogeny ; Plant Proteins/genetics/metabolism ; Species Specificity ; }, abstract = {There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.}, }
@article {pmid27833590, year = {2016}, author = {Haack, FS and Poehlein, A and Kröger, C and Voigt, CA and Piepenbring, M and Bode, HB and Daniel, R and Schäfer, W and Streit, WR}, title = {Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1668}, doi = {10.3389/fmicb.2016.01668}, pmid = {27833590}, issn = {1664-302X}, abstract = {Janthinobacterium and Duganella are well-known for their antifungal effects. Surprisingly, almost nothing is known on molecular aspects involved in the close bacterium-fungus interaction. To better understand this interaction, we established the genomes of 11 Janthinobacterium and Duganella isolates in combination with phylogenetic and functional analyses of all publicly available genomes. Thereby, we identified a core and pan genome of 1058 and 23,628 genes. All strains encoded secondary metabolite gene clusters and chitinases, both possibly involved in fungal growth suppression. All but one strain carried a single gene cluster involved in the biosynthesis of alpha-hydroxyketone-like autoinducer molecules, designated JAI-1. Genome-wide RNA-seq studies employing the background of two isolates and the corresponding JAI-1 deficient strains identified a set of 45 QS-regulated genes in both isolates. Most regulated genes are characterized by a conserved sequence motif within the promoter region. Among the most strongly regulated genes were secondary metabolite and type VI secretion system gene clusters. Most intriguing, co-incubation studies of J. sp. HH102 or its corresponding JAI-1 synthase deletion mutant with the plant pathogen Fusarium graminearum provided first evidence of a QS-dependent interaction with this pathogen.}, }
@article {pmid27829029, year = {2016}, author = {Mansfeldt, CB and Heavner, GW and Rowe, AR and Hayete, B and Church, BW and Richardson, RE}, title = {Inferring Gene Networks for Strains of Dehalococcoides Highlights Conserved Relationships between Genes Encoding Core Catabolic and Cell-Wall Structural Proteins.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166234}, doi = {10.1371/journal.pone.0166234}, pmid = {27829029}, issn = {1932-6203}, mesh = {Cell Wall/*genetics ; Cell Wall Skeleton/*genetics ; Chloroflexi/*genetics/metabolism ; Consensus Sequence/genetics ; Gene Regulatory Networks/*genetics ; Metabolism/*genetics ; Oligonucleotide Array Sequence Analysis ; }, abstract = {The interpretation of high-throughput gene expression data for non-model microorganisms remains obscured because of the high fraction of hypothetical genes and the limited number of methods for the robust inference of gene networks. Therefore, to elucidate gene-gene and gene-condition linkages in the bioremediation-important genus Dehalococcoides, we applied a Bayesian inference strategy called Reverse Engineering/Forward Simulation (REFS™) on transcriptomic data collected from two organohalide-respiring communities containing different Dehalococcoides mccartyi strains: the Cornell University mixed community D2 and the commercially available KB-1® bioaugmentation culture. In total, 49 and 24 microarray datasets were included in the REFS™ analysis to generate an ensemble of 1,000 networks for the Dehalococcoides population in the Cornell D2 and KB-1® culture, respectively. Considering only linkages that appeared in the consensus network for each culture (exceeding the determined frequency cutoff of ≥ 60%), the resulting Cornell D2 and KB-1® consensus networks maintained 1,105 nodes (genes or conditions) with 974 edges and 1,714 nodes with 1,455 edges, respectively. These consensus networks captured multiple strong and biologically informative relationships. One of the main highlighted relationships shared between these two cultures was a direct edge between the transcript encoding for the major reductive dehalogenase (tceA (D2) or vcrA (KB-1®)) and the transcript for the putative S-layer cell wall protein (DET1407 (D2) or KB1_1396 (KB-1®)). Additionally, transcripts for two key oxidoreductases (a [Ni Fe] hydrogenase, Hup, and a protein with similarity to a formate dehydrogenase, &quot;Fdh&quot;) were strongly linked, generalizing a strong relationship noted previously for Dehalococcoides mccartyi strain 195 to multiple strains of Dehalococcoides. Notably, the pangenome array utilized when monitoring the KB-1® culture was capable of resolving signals from multiple strains, and the network inference engine was able to reconstruct gene networks in the distinct strain populations.}, }
@article {pmid27826029, year = {2016}, author = {Sváb, D and Bálint, B and Maróti, G and Tóth, I}, title = {Cytolethal distending toxin producing Escherichia coli O157:H43 strain T22 represents a novel evolutionary lineage within the O157 serogroup.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {46}, number = {}, pages = {110-117}, doi = {10.1016/j.meegid.2016.11.003}, pmid = {27826029}, issn = {1567-7257}, mesh = {Animals ; Bacterial Toxins/*genetics ; Cattle ; Escherichia coli O157/*classification/*genetics ; Evolution, Molecular ; Genome, Bacterial/genetics ; Genomics ; Milk/microbiology ; Phylogeny ; }, abstract = {Enterohemorrhagic Escherichia coli (EHEC) O157:H7/NM strains are significant foodborne pathogens intensively studied, while other sero- and pathotypes of the O157 serogroup only began to receive more attention. Here we report the first genome sequence of a cytolethal distending toxin (CDT-V) producing E. coli O157:H43 strain (T22) isolated from cattle. The genome consists of a 4.9Mb chromosome assembled into three contigs and one plasmid of 82.4kb. Comparative genomic investigations conducted with the core genomes of representative E. coli strains in GenBank (n=62) confirmed the separation of T22 from the EHEC and enteropathogenic (EPEC) O157 lineages. Gene content based pangenome analysis revealed as many as 261 T22-specific coding sequences without orthologs in EDL933 EHEC O157 prototypic and two phylogenetically related commensal E. coli strains. The genome sequence revealed 10 prophage-like regions which harbor several virulence-associated genes including cdt and heat-labile enterotoxin (LT-II) encoding operons. Our results indicate that the evolutionary path of T22 is largely independent from that of EHEC and EPEC O157:H7/NM strains. Thus, the CDT-producing T22 E. coli O157:H43 strain represents a unique lineage of E. coli O157.}, }
@article {pmid27824078, year = {2016}, author = {Liu, YY and Chiou, CS and Chen, CC}, title = {PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36213}, doi = {10.1038/srep36213}, pmid = {27824078}, issn = {2045-2322}, mesh = {Alleles ; Bacterial Typing Techniques/methods ; Databases, Genetic ; Genome, Bacterial ; Internet ; Multilocus Sequence Typing/*methods ; Salmonella typhimurium/*genetics ; Whole Genome Sequencing/*methods ; }, abstract = {With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subtyping of bacterial isolates. To use WGS as a general subtyping method for disease outbreak investigation and surveillance, the layout of WGS-based typing must be comparable among laboratories. Whole genome multilocus sequence typing (wgMLST) is an approach that achieves this requirement. To apply wgMLST as a standard subtyping approach, a pan-genome allele database (PGAdb) for the population of a bacterial organism must first be established. We present a free web service tool, PGAdb-builder (http://wgmlstdb.imst.nsysu.edu.tw), for the construction of bacterial PGAdb. The effectiveness of PGAdb-builder was tested by constructing a pan-genome allele database for Salmonella enterica serovar Typhimurium, with the database being applied to create a wgMLST tree for a panel of epidemiologically well-characterized S. Typhimurium isolates. The performance of the wgMLST-based approach was as high as that of the SNP-based approach in Leekitcharoenphon's study used for discerning among epidemiologically related and non-related isolates.}, }
@article {pmid27815276, year = {2017}, author = {Qumar, S and Majid, M and Kumar, N and Tiwari, SK and Semmler, T and Devi, S and Baddam, R and Hussain, A and Shaik, S and Ahmed, N}, title = {Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {1}, pages = {}, doi = {10.1128/AEM.02305-16}, pmid = {27815276}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cephalosporins/pharmacology ; Chickens/*microbiology ; DNA, Bacterial/*genetics ; *Drug Resistance, Multiple, Bacterial ; Fluoroquinolones/pharmacology ; Food Microbiology ; *Genome, Bacterial ; Genomic Islands ; Helicobacter/drug effects/*genetics/isolation &amp; purification ; Helicobacter Infections/epidemiology/microbiology/*veterinary ; High-Throughput Nucleotide Sequencing ; Humans ; India/epidemiology ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Phylogeny ; Poultry Diseases/epidemiology/*microbiology ; Prophages/genetics/isolation &amp; purification ; beta-Lactamases/biosynthesis/genetics ; }, abstract = {Some life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in the livestock industry has led to an increased prevalence of multidrug-resistant bacteria with epidemic potential. Here, we present a functional molecular epidemiological analysis entailing the phenotypic and whole-genome sequence-based characterization of 11 H. pullorum isolates from broiler and free-range chickens sampled from retail wet markets in Hyderabad City, India. Antimicrobial susceptibility tests revealed all of the isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides, and macrolides. The isolates were also found to be extended-spectrum β-lactamase producers and were even resistant to clavulanic acid. Whole-genome sequencing and comparative genomic analysis of these isolates revealed the presence of five or six well-characterized antimicrobial resistance genes, including those encoding a resistance-nodulation-division efflux pump(s). Phylogenetic analysis combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates from free-range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n = 16), together with the genomes of 17 other Helicobacter species, revealed a high number (8,560) of H. pullorum-specific protein-encoding genes, with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain-specific gene content in isolates from free-range chickens (average, 34) compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1 to 9) and a significant presence of genomic islands (0 to 4) were observed in free-range and broiler chicken isolates. Taken together, these observations provide significant baseline data for functional molecular infection epidemiology of nonpyloric Helicobacter species such as H. pullorum by unraveling their evolution in chickens and their possible zoonotic transmission to humans.<br><br>IMPORTANCE: Globally, the poultry industry is expanding with an ever-growing consumer base for chicken meat. Given this, food-associated transmission of multidrug-resistant bacteria represents an important health care issue. Our study involves a critical baseline approach directed at genome sequence-based epidemiology and transmission dynamics of H. pullorum, a poultry pathogen having established zoonotic potential. We believe our studies would facilitate the development of surveillance systems that ensure the safety of food for humans and guide public health policies related to the use of antibiotics in animal feed in countries such as India. We sequenced 11 new genomes of H. pullorum as a part of this study. These genomes would provide much value in addition to the ongoing comparative genomic studies of helicobacters.}, }
@article {pmid27806993, year = {2017}, author = {Shippy, DC and Lemke, JJ and Berry, A and Nelson, K and Hines, ME and Talaat, AM}, title = {Superior Protection from Live-Attenuated Vaccines Directed against Johne's Disease.}, journal = {Clinical and vaccine immunology : CVI}, volume = {24}, number = {1}, pages = {}, doi = {10.1128/CVI.00478-16}, pmid = {27806993}, issn = {1556-679X}, mesh = {Adaptive Immunity ; Animals ; Bacterial Load ; Bacterial Shedding ; Bacterial Vaccines/administration &amp; dosage/*immunology ; Female ; Genes, Bacterial ; Goat Diseases/*prevention &amp; control ; Goats ; Histocytochemistry ; Immunity, Cellular ; Male ; Mutation ; Mycobacterium avium subsp. paratuberculosis/*immunology/isolation &amp; purification ; Paratuberculosis/microbiology/pathology/*prevention &amp; control ; Treatment Outcome ; Vaccines, Attenuated/administration &amp; dosage/immunology ; Virulence Factors/genetics ; }, abstract = {Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) is the etiological agent of Johne's disease in ruminants. Johne's disease is an important enteric infection causing large economic losses associated with infected herds. In an attempt to fight this infection, we created two novel live-attenuated vaccine candidates with mutations in sigH and lipN (pgsH and pgsN, respectively). Earlier reports in mice suggested these vaccines are promising candidates to fight Johne's disease in ruminants. In this study, we tested the performances of the two constructs as vaccine candidates using the goat model of Johne's disease. Both vaccines appeared to provide significant immunity to goats against challenge from wild-type M. paratuberculosis The pgsH and pgsN constructs showed a significant reduction in histopathological lesions and tissue colonization compared to nonvaccinated goats and those vaccinated with an inactivated vaccine. Unlike the inactivated vaccine, the pgsN construct was able to eliminate fecal shedding from challenged animals, a feature that is highly desirable to control Johne's disease in infected herds. Furthermore, strong initial cell-mediated immune responses were elicited in goats vaccinated with pgsN that were not demonstrated in other vaccine groups. Overall, the results indicate the potential use of live-attenuated vaccines to control intracellular pathogens, including M. paratuberculosis, and warrant further testing in cattle, the main target for Johne's disease control programs.}, }
@article {pmid27773726, year = {2017}, author = {He, EM and Chen, CW and Guo, Y and Hsu, MH and Zhang, L and Chen, HL and Zhao, GP and Chiu, CH and Zhou, Y}, title = {The genome of serotype VI Streptococcus agalactiae serotype VI and comparative analysis.}, journal = {Gene}, volume = {597}, number = {}, pages = {59-65}, doi = {10.1016/j.gene.2016.10.030}, pmid = {27773726}, issn = {1879-0038}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Cattle ; Dogs ; *Genome, Bacterial ; Genomic Islands/genetics ; Humans ; Phylogeny ; Sequence Analysis, DNA ; Streptococcus agalactiae/*genetics/isolation &amp; purification/*pathogenicity ; }, abstract = {Streptococcus agalactiae (GBS) causes serious infections in humans and other species. A total of 25 complete GBS genomes, including the first sequenced serotype VI genome (GBS-M002), were compared in this study. The power law model suggested that the pan-genome of GBS is open, with approximately 1300 genes in the core genome of GBS, accounting for approximately 60% of the average genome content. GBS-M002 has 73 specific genes and is one of the five strains containing >60 specific genes. Based on COG (Cluster of Orthologous Groups of proteins) functional classification, 24% of the genes related to defense mechanisms are specific among the strains. A phylogenetic tree shows that GBS-M002 is closely related to certain strains of serotypes III and V from humans and to isolates of unknown serotype from dog and bovine hosts, suggesting the universal infection potential of GBS from humans to other mammal and fish hosts.}, }
@article {pmid27638249, year = {2016}, author = {Anastasi, E and MacArthur, I and Scortti, M and Alvarez, S and Giguère, S and Vázquez-Boland, JA}, title = {Pangenome and Phylogenomic Analysis of the Pathogenic Actinobacterium Rhodococcus equi.}, journal = {Genome biology and evolution}, volume = {8}, number = {10}, pages = {3140-3148}, doi = {10.1093/gbe/evw222}, pmid = {27638249}, issn = {1759-6653}, support = {BB/J004227/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/genetics ; Carbohydrate Metabolism/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Membrane Transport Proteins/genetics ; *Phylogeny ; Polymorphism, Genetic ; Rhodococcus equi/classification/*genetics ; }, abstract = {We report a comparative study of 29 representative genomes of the animal pathogen Rhodococcus equi The analyses showed that R. equi is genetically homogeneous and clonal, with a large core genome accounting for ≈80% of an isolates' gene content. An open pangenome, even distribution of accessory genes among the isolates, and absence of significant core-genome recombination, indicated that gene gain/loss is a main driver of R. equi genome evolution. Traits previously predicted to be important in R. equi physiology, virulence and niche adaptation were part of the core genome. This included the lack of a phosphoenolpyruvate:carbohydrate transport system (PTS), unique among the rhodococci except for the closely related Rhodococcus defluvii, reflecting selective PTS gene loss in the R. equi-R. defluvii sublineage. Thought to be asaccharolytic, rbsCB and glcP non-PTS sugar permease homologues were identified in the core genome and, albeit inefficiently, R. equi utilized their putative substrates, ribose and (irregularly) glucose. There was no correlation between R. equi whole-genome phylogeny and host or geographical source, with evidence of global spread of genomovars. The distribution of host-associated virulence plasmid types was consistent with the exchange of the plasmids (and corresponding host shifts) across the R. equi population, and human infection being zoonotically acquired. Phylogenomic analyses demonstrated that R. equi occupies a central position in the Rhodococcus phylogeny, not supporting the recently proposed transfer of the species to a new genus.}, }
@article {pmid27339259, year = {2016}, author = {Coutinho, FH and Dutilh, BE and Thompson, CC and Thompson, FL}, title = {Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features.}, journal = {Archives of microbiology}, volume = {198}, number = {10}, pages = {973-986}, doi = {10.1007/s00203-016-1256-y}, pmid = {27339259}, issn = {1432-072X}, mesh = {Cyanobacteria/*classification/genetics/physiology ; Genome, Bacterial/genetics ; Genomics ; Nucleic Acid Hybridization ; Oceans and Seas ; Phylogeny ; *Water Microbiology ; }, abstract = {Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.}, }
@article {pmid27769991, year = {2018}, author = {, }, title = {Computational pan-genomics: status, promises and challenges.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {1}, pages = {118-135}, doi = {10.1093/bib/bbw089}, pmid = {27769991}, issn = {1477-4054}, abstract = {Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.}, }
@article {pmid27768818, year = {2017}, author = {Molina-Santiago, C and Udaondo, Z and Gómez-Lozano, M and Molin, S and Ramos, JL}, title = {Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene.}, journal = {Environmental microbiology}, volume = {19}, number = {2}, pages = {645-658}, doi = {10.1111/1462-2920.13585}, pmid = {27768818}, issn = {1462-2920}, mesh = {Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Gene Expression Regulation, Bacterial/*physiology ; Pseudomonas putida/*drug effects/genetics/*metabolism ; Solvents/*pharmacology ; Toluene/*pharmacology ; *Transcriptome ; }, abstract = {Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan-genome analysis has revealed that 30% of genes belong to the core-genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA-seq analysis compared the short- and long-term responses of the toluene-sensitive KT2440 strain and the highly tolerant DOT-T1E strain. The sensitive strain activates a larger number of genes in a higher magnitude than DOT-T1E. This is expected because KT2440 bears one toluene tolerant pump, while DOT-T1E encodes three of these pumps. Both strains activate membrane modifications to reduce toluene membrane permeability. The KT2440 strain activates the TCA cycle to generate energy, while avoiding energy-intensive processes such as flagellar biosynthesis. This suggests that KT2440 responds to toluene by focusing on survival mechanisms. The DOT-T1E strain activates toluene degradation pathways, using toluene as source of energy. Among the unique genes encoded by DOT-T1E is a 70 kb island composed of genes of unknown function induced in response to toluene.}, }
@article {pmid27765811, year = {2016}, author = {Li, G and Shen, M and Le, S and Tan, Y and Li, M and Zhao, X and Shen, W and Yang, Y and Wang, J and Zhu, H and Li, S and Rao, X and Hu, F and Lu, S}, title = {Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing.}, journal = {Bioscience reports}, volume = {36}, number = {6}, pages = {}, doi = {10.1042/BSR20160282}, pmid = {27765811}, issn = {1573-4935}, mesh = {Bacterial Proteins/*genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Genomic Islands/genetics ; Genomics/methods ; Phylogeny ; Pseudomonas aeruginosa/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin-antitoxin (T-A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.}, }
@article {pmid27765012, year = {2016}, author = {Sternes, PR and Borneman, AR}, title = {Erratum to: 'Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni'.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {813}, doi = {10.1186/s12864-016-2811-2}, pmid = {27765012}, issn = {1471-2164}, }
@article {pmid27734920, year = {2016}, author = {Bolotin, E and Hershberg, R}, title = {Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35168}, doi = {10.1038/srep35168}, pmid = {27734920}, issn = {2045-2322}, mesh = {Bacteria/*genetics ; Bacterial Proteins/genetics ; Evolution, Molecular ; Genes, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Phylogeny ; }, abstract = {Gene loss is a major contributor to the evolution of bacterial gene content. Gene loss may occur as a result of shifts in environment leading to changes in the intensity and/or directionality of selection applied for the maintenance of specific genes. Gene loss may also occur in a more neutral manner, when gene functions are lost that were not subject to strong selection to be maintained, irrespective of changes to environment. Here, we used a pangenome-based approach to investigate patterns of gene loss across 15 bacterial species. We demonstrate that gene loss tends to occur mostly within a pool of genes that are less constrained within species, even in those strains from which they are not lost, and less conserved across bacterial species. Our results indicate that shifts in selection, resulting from shifts in environment are not required to explain the majority of gene loss events occurring within a diverse collection of bacterial species. Caution should therefore be taken when attributing differences in gene content to differences in environment.}, }
@article {pmid27733845, year = {2016}, author = {Shin, J and Song, Y and Jeong, Y and Cho, BK}, title = {Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1531}, doi = {10.3389/fmicb.2016.01531}, pmid = {27733845}, issn = {1664-302X}, abstract = {Acetogens are obligate anaerobic bacteria capable of reducing carbon dioxide (CO2) to multicarbon compounds coupled to the oxidation of inorganic substrates, such as hydrogen (H2) or carbon monoxide (CO), via the Wood-Ljungdahl pathway. Owing to the metabolic capability of CO2 fixation, much attention has been focused on understanding the unique pathways associated with acetogens, particularly their metabolic coupling of CO2 fixation to energy conservation. Most known acetogens are phylogenetically and metabolically diverse bacteria present in 23 different bacterial genera. With the increased volume of available genome information, acetogenic bacterial genomes can be analyzed by comparative genome analysis. Even with the genetic diversity that exists among acetogens, the Wood-Ljungdahl pathway, a central metabolic pathway, and cofactor biosynthetic pathways are highly conserved for autotrophic growth. Additionally, comparative genome analysis revealed that most genes in the acetogen-specific core genome were associated with the Wood-Ljungdahl pathway. The conserved enzymes and those predicted as missing can provide insight into biological differences between acetogens and allow for the discovery of promising candidates for industrial applications.}, }
@article {pmid27722863, year = {2016}, author = {Cui, Y and Song, Y}, title = {Genome and Evolution of Yersinia pestis.}, journal = {Advances in experimental medicine and biology}, volume = {918}, number = {}, pages = {171-192}, doi = {10.1007/978-94-024-0890-4_6}, pmid = {27722863}, issn = {0065-2598}, mesh = {*Evolution, Molecular ; Gene Silencing ; Genome, Bacterial/*genetics ; Mutation Rate ; *Pandemics ; Plague/epidemiology/*microbiology ; Yersinia pestis/classification/*genetics/pathogenicity/physiology ; }, abstract = {This chapter summarizes researches on genome and evolution features of Yersinia pestis, the young pathogen that evolved from Y. pseudotuberculosis at least 5000 years ago. Y. pestis is a highly clonal bacterial species with closed pan-genome. Comparative genomic analysis revealed that genome of Y. pestis experienced highly frequent rearrangement and genome decay events during the evolution. The genealogy of Y. pestis includes five major branches, and four of them seemed raised from a &quot;big bang&quot; node that is associated with the Black Death. Although whole genome-wide variation of Y. pestis reflected a neutral evolutionary process, the branch length in the genealogical tree revealed over dispersion, which was supposedly caused by varied historical molecular clock that is associated with demographical effect by alternate cycles of enzootic disease and epizootic disease in sylvatic plague foci. In recent years, palaeomicrobiology researches on victims of the Black Death, and Justinian's plague verified that two historical pandemics were indeed caused by Y. pestis, but the etiological lineages might be extinct today.}, }
@article {pmid27712915, year = {2016}, author = {Zhang, X and She, S and Dong, W and Niu, J and Xiao, Y and Liang, Y and Liu, X and Zhang, X and Fan, F and Yin, H}, title = {Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {8}, pages = {493-502}, doi = {10.1016/j.syapm.2016.08.007}, pmid = {27712915}, issn = {1618-0984}, mesh = {Acidithiobacillus/classification/*genetics/*metabolism ; Adaptation, Physiological/*genetics ; Carbon/*metabolism ; Genome, Bacterial/genetics ; Genomics ; Hydrogen-Ion Concentration ; Metabolic Networks and Pathways/*genetics ; Metals, Heavy/metabolism ; Nitrogen/*metabolism ; Sulfur/*metabolism ; }, abstract = {Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.}, }
@article {pmid27711162, year = {2016}, author = {Pucker, B and Holtgräwe, D and Rosleff Sörensen, T and Stracke, R and Viehöver, P and Weisshaar, B}, title = {A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0164321}, doi = {10.1371/journal.pone.0164321}, pmid = {27711162}, issn = {1932-6203}, mesh = {Arabidopsis/genetics ; Chromosome Mapping ; DNA Copy Number Variations ; DNA, Plant/chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Expressed Sequence Tags ; *Genome, Plant ; High-Throughput Nucleotide Sequencing ; INDEL Mutation ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Arabidopsis thaliana is the most important model organism for fundamental plant biology. The genome diversity of different accessions of this species has been intensively studied, for example in the 1001 genome project which led to the identification of many small nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels). In addition, presence/absence variation (PAV), copy number variation (CNV) and mobile genetic elements contribute to genomic differences between A. thaliana accessions. To address larger genome rearrangements between the A. thaliana reference accession Columbia-0 (Col-0) and another accession of about average distance to Col-0, we created a de novo next generation sequencing (NGS)-based assembly from the accession Niederzenz-1 (Nd-1). The result was evaluated with respect to assembly strategy and synteny to Col-0. We provide a high quality genome sequence of the A. thaliana accession (Nd-1, LXSY01000000). The assembly displays an N50 of 0.590 Mbp and covers 99% of the Col-0 reference sequence. Scaffolds from the de novo assembly were positioned on the basis of sequence similarity to the reference. Errors in this automatic scaffold anchoring were manually corrected based on analyzing reciprocal best BLAST hits (RBHs) of genes. Comparison of the final Nd-1 assembly to the reference revealed duplications and deletions (PAV). We identified 826 insertions and 746 deletions in Nd-1. Randomly selected candidates of PAV were experimentally validated. Our Nd-1 de novo assembly allowed reliable identification of larger genic and intergenic variants, which was difficult or error-prone by short read mapping approaches alone. While overall sequence similarity as well as synteny is very high, we detected short and larger (affecting more than 100 bp) differences between Col-0 and Nd-1 based on bi-directional comparisons. The de novo assembly provided here and additional assemblies that will certainly be published in the future will allow to describe the pan-genome of A. thaliana.}, }
@article {pmid27697167, year = {2017}, author = {Stefanovic, E and Fitzgerald, G and McAuliffe, O}, title = {Advances in the genomics and metabolomics of dairy lactobacilli: A review.}, journal = {Food microbiology}, volume = {61}, number = {}, pages = {33-49}, doi = {10.1016/j.fm.2016.08.009}, pmid = {27697167}, issn = {1095-9998}, mesh = {Dairy Products/*microbiology ; Food Microbiology ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Genomics ; Lactobacillus/classification/*genetics/*metabolism/physiology ; *Metabolic Engineering ; *Metabolome ; Metabolomics ; Phylogeny ; }, abstract = {The Lactobacillus genus represents the largest and most diverse genera of all the lactic acid bacteria (LAB), encompassing species with applications in industrial, biotechnological and medical fields. The increasing number of available Lactobacillus genome sequences has allowed understanding of genetic and metabolic potential of this LAB group. Pangenome and core genome studies are available for numerous species, demonstrating the plasticity of the Lactobacillus genomes and providing the evidence of niche adaptability. Advancements in the application of lactobacilli in the dairy industry lie in exploring the genetic background of their commercially important characteristics, such as flavour development potential or resistance to the phage attack. The integration of available genomic and metabolomic data through the generation of genome scale metabolic models has enabled the development of computational models that predict the behaviour of organisms under specific conditions and present a route to metabolic engineering. Lactobacilli are recognised as potential cell factories, confirmed by the successful production of many compounds. In this review, we discuss the current knowledge of genomics, metabolomics and metabolic engineering of the prevalent Lactobacillus species associated with the production of fermented dairy foods. In-depth understanding of their characteristics opens the possibilities for their future knowledge-based applications.}, }
@article {pmid27696900, year = {2016}, author = {Yu, D and Yin, Z and Li, B and Jin, Y and Ren, H and Zhou, J and Zhou, W and Liang, L and Yue, J}, title = {Gene flow, recombination, and positive selection in Stenotrophomonas maltophilia: mechanisms underlying the diversity of the widespread opportunistic pathogen.}, journal = {Genome}, volume = {59}, number = {12}, pages = {1063-1075}, doi = {10.1139/gen-2016-0073}, pmid = {27696900}, issn = {1480-3321}, mesh = {Bacterial Proteins/genetics ; Evolution, Molecular ; *Gene Flow ; Genetic Variation ; Genome, Bacterial ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Opportunistic Infections/microbiology ; Phylogeny ; *Recombination, Genetic ; *Selection, Genetic ; Stenotrophomonas maltophilia/classification/*genetics ; }, abstract = {Stenotrophomonas maltophilia is a global multidrug-resistant human opportunistic pathogen in clinical environments. Stenotrophomonas maltophilia is also ubiquitous in aqueous environments, soil, and plants. Various molecular typing methods have revealed that S. maltophilia exhibits high levels of phenotypic and genotypic diversity. However, information regarding the genomic diversity within S. maltophilia and the corresponding genetic mechanisms resulting in said diversity remain scarce. The genome sequences of 17 S. maltophilia strains were selected to investigate the mechanisms contributing to genetic diversity at the genome level. The core and large pan-genomes of the species were first estimated, resulting in a large, open pan-genome. A species phylogeny was also reconstructed based on 344 orthologous genes with one copy per genome, and the contribution of four evolutionary mechanisms to the species genome diversity was quantified: 15%-35% of the genes showed evidence for recombination, 0%-25% of the genes in one genome were likely gained, 0%-44% of the genes in some genomes were likely lost, and less than 0.3% of the genes in a genome were under positive selection pressures. We observed that, among the four main mechanisms, homologous recombination plays a key role in maintaining diversity in S. maltophilia. In this study, we provide an overview of evolution in S. maltophilia to provide a better understanding of its evolutionary dynamics and its relationship with genome diversity.}, }
@article {pmid27663497, year = {2017}, author = {Lanza, VF and Baquero, F and de la Cruz, F and Coque, TM}, title = {AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {2}, pages = {283-285}, doi = {10.1093/bioinformatics/btw601}, pmid = {27663497}, issn = {1367-4811}, mesh = {Bacteria/genetics ; *Genome, Bacterial ; Genomics/*methods ; *Metagenome ; *Phylogeny ; Proteome ; *Software ; }, abstract = {AcCNET (Accessory genome Constellation Network) is a Perl application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels. Using the proteomes extracted from the analysed genomes, AcCNET creates a bipartite network compatible with standard network analysis platforms. AcCNET allows merging phylogenetic and functional information about the concerned genomes, thus improving the capability of current methods of network analysis. The AcCNET bipartite network opens a new perspective to explore the pangenome of bacterial species, focusing on the accessory genome behind the idiosyncrasy of a particular strain and/or population.<br><br>AcCNET is available under GNU General Public License version 3.0 (GPLv3) from http://sourceforge.net/projects/accnet CONTACT: : valfernandez.vf@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid27659070, year = {2016}, author = {Shen, M and Le, S and Jin, X and Li, G and Tan, Y and Li, M and Zhao, X and Shen, W and Yang, Y and Wang, J and Zhu, H and Li, S and Rao, X and Hu, F and Lu, S}, title = {Characterization and Comparative Genomic Analyses of Pseudomonas aeruginosa Phage PaoP5: New Members Assigned to PAK_P1-like Viruses.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34067}, doi = {10.1038/srep34067}, pmid = {27659070}, issn = {2045-2322}, abstract = {As a potential alternative to antibiotics, phages can be used to treat multi-drug resistant bacteria. As such, the biological characteristics of phages should be investigated to utilize them as effective antimicrobial agents. In this study, phage PaoP5, a lytic virus that infects Pseudomonas aeruginosa PAO1, was isolated and genomically characterized. PaoP5 comprises an icosahedral head with an apex diameter of 69 nm and a contractile tail with a length of 120 nm. The PaoP5 genome is a linear dsDNA molecule containing 93,464 base pairs (bp) with 49.51% G + C content of 11 tRNA genes and a 1,200 bp terminal redundancy. A total of 176 protein-coding genes were predicted in the PaoP5 genome. Nine PaoP5 structural proteins were identified. Three hypothetical proteins were determined as structural. Comparative genomic analyses revealed that seven new Pseudomonas phages, namely, PaoP5, K8, C11, vB_PaeM_C2-10_Ab02, vB_PaeM_C2-10_Ab08, vB_PaeM_C2-10_Ab10, and vB_PaeM_C2-10_Ab15, were similar to PAK_P1-like viruses. Phylogenetic and pan-genome analyses suggested that the new phages should be assigned to PAK_P1-like viruses, which possess approximately 100 core genes and 150 accessory genes. This work presents a detailed and comparative analysis of PaoP5 to enhance our understanding of phage biology.}, }
@article {pmid27634541, year = {2016}, author = {Hassan, A and Naz, A and Obaid, A and Paracha, RZ and Naz, K and Awan, FM and Muhmmad, SA and Janjua, HA and Ahmad, J and Ali, A}, title = {Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {732}, doi = {10.1186/s12864-016-2951-4}, pmid = {27634541}, issn = {1471-2164}, mesh = {Acinetobacter baumannii/classification/*genetics/immunology/*metabolism ; Amino Acid Sequence ; Antigens, Bacterial/chemistry/genetics/immunology/metabolism ; Computational Biology/methods ; Epitope Mapping ; Epitopes/chemistry/genetics/immunology ; Evolution, Molecular ; *Genome, Bacterial ; *Genomics/methods ; Models, Molecular ; Molecular Sequence Annotation ; Peptides/chemistry/genetics/immunology/metabolism ; Phylogeny ; Protein Conformation ; Protein Interaction Mapping ; Protein Interaction Maps ; *Proteome ; *Proteomics/methods ; Vaccines, Subunit/genetics/immunology ; Virulence/genetics ; }, abstract = {BACKGROUND: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets.<br><br>RESULTS: The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control.<br><br>CONCLUSION: The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.}, }
@article {pmid27633769, year = {2016}, author = {Joseph, SJ and Cox, D and Wolff, B and Morrison, SS and Kozak-Muiznieks, NA and Frace, M and Didelot, X and Castillo-Ramirez, S and Winchell, J and Read, TD and Dean, D}, title = {Dynamics of genome change among Legionella species.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {33442}, doi = {10.1038/srep33442}, pmid = {27633769}, issn = {2045-2322}, support = {MR/K010174/1//Medical Research Council/United Kingdom ; R01 AI098843/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Secretion Systems/genetics ; Base Sequence ; CRISPR-Cas Systems/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial ; *Genome, Bacterial ; Genomics ; Legionella/*genetics ; Phylogeny ; Recombination, Genetic/genetics ; Selection, Genetic ; Species Specificity ; }, abstract = {Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires' Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1-17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD-causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence.}, }
@article {pmid27607357, year = {2016}, author = {van Opijnen, T and Dedrick, S and Bento, J}, title = {Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome.}, journal = {PLoS pathogens}, volume = {12}, number = {9}, pages = {e1005869}, doi = {10.1371/journal.ppat.1005869}, pmid = {27607357}, issn = {1553-7374}, support = {R01 AI110724/AI/NIAID NIH HHS/United States ; U01 AI124302/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Daptomycin/*pharmacology ; Drug Resistance, Bacterial/drug effects/*genetics ; Gene Expression Regulation, Bacterial/*drug effects ; Gene Regulatory Networks/*physiology ; *Genome, Bacterial ; Streptococcus pneumoniae/*genetics/growth &amp; development ; }, abstract = {The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.}, }
@article {pmid27595771, year = {2016}, author = {Gómez-Garzón, C and Hernández-Santana, A and Dussán, J}, title = {Comparative genomics reveals Lysinibacillus sphaericus group comprises a novel species.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {709}, doi = {10.1186/s12864-016-3056-9}, pmid = {27595771}, issn = {1471-2164}, mesh = {Bacillus/*classification/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genomics/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {BACKGROUND: Early in the 1990s, it was recognized that Lysinibacillus sphaericus, one of the most popular and effective entomopathogenic bacteria, was a highly heterogeneous group. Many authors have even proposed it comprises more than one species, but the lack of phenotypic traits that guarantee an accurate differentiation has not allowed this issue to be clarified. Now that genomic technologies are rapidly advancing, it is possible to address the problem from a whole genome perspective, getting insights into the phylogeny, evolutive history and biology itself.<br><br>RESULTS: The genome of the Colombian strain L. sphaericus OT4b.49 was sequenced, assembled and annotated, obtaining 3 chromosomal contigs and no evidence of plasmids. Using these sequences and the 13 other L. sphaericus genomes available on the NCBI database, we carried out comparative genomic analyses that included whole genome alignments, searching for mobile elements, phylogenomic metrics (TETRA, ANI and in-silico DDH) and pan-genome assessments. The results support the hypothesis about this species as a very heterogeneous group. The entomopathogenic lineage is actually a single and independent species with 3728 core genes and 2153 accessory genes, whereas each non-toxic strain seems to be a separate species, though without a clear circumscription. Toxin-encoding genes, binA, B and mtx1, 2, 3 could be acquired via horizontal gene transfer in a single evolutionary event. The non-toxic strain OT4b.31 is the most related with the type strain KCTC 3346.<br><br>CONCLUSIONS: The current L. sphaericus is actually a sensu lato due to a sub-estimation of diversity accrued using traditional non-genomics based classification strategies. The toxic lineage is the most studied with regards to its larvicidal activity, which is a greatly conserved trait among these strains and thus, their differentiating feature. Further studies are needed in order to establish a univocal classification of the non-toxic strains that, according to our results, seem to be a paraphyletic group.}, }
@article {pmid27587666, year = {2016}, author = {Sheikhizadeh, S and Schranz, ME and Akdel, M and de Ridder, D and Smit, S}, title = {PanTools: representation, storage and exploration of pan-genomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {17}, pages = {i487-i493}, doi = {10.1093/bioinformatics/btw455}, pmid = {27587666}, issn = {1367-4811}, mesh = {*Algorithms ; Arabidopsis ; Computational Biology/methods ; Escherichia coli ; *Genome ; Genome, Bacterial ; Genomics ; *High-Throughput Nucleotide Sequencing ; Humans ; Software ; }, abstract = {MOTIVATION: Next-generation sequencing technology is generating a wealth of highly similar genome sequences for many species, paving the way for a transition from single-genome to pan-genome analyses. Accordingly, genomics research is going to switch from reference-centric to pan-genomic approaches. We define the pan-genome as a comprehensive representation of multiple annotated genomes, facilitating analyses on the similarity and divergence of the constituent genomes at the nucleotide, gene and genome structure level. Current pan-genomic approaches do not thoroughly address scalability, functionality and usability.<br><br>RESULTS: We introduce a generalized De Bruijn graph as a pan-genome representation, as well as an online algorithm to construct it. This representation is stored in a Neo4j graph database, which makes our approach scalable to large eukaryotic genomes. Besides the construction algorithm, our software package, called PanTools, currently provides functionality for annotating pan-genomes, adding sequences, grouping genes, retrieving gene sequences or genomic regions, reconstructing genomes and comparing and querying pan-genomes. We demonstrate the performance of the tool using datasets of 62 E. coli genomes, 93 yeast genomes and 19 Arabidopsis thaliana genomes.<br><br>The Java implementation of PanTools is publicly available at http://www.bif.wur.nl<br><br>CONTACT: sandra.smit@wur.nl.}, }
@article {pmid27574119, year = {2017}, author = {Millman, A and Dar, D and Shamir, M and Sorek, R}, title = {Computational prediction of regulatory, premature transcription termination in bacteria.}, journal = {Nucleic acids research}, volume = {45}, number = {2}, pages = {886-893}, doi = {10.1093/nar/gkw749}, pmid = {27574119}, issn = {1362-4962}, support = {260432//European Research Council/International ; }, mesh = {Bacteria/*genetics ; *Computer Simulation ; *Gene Expression Regulation, Bacterial ; Machine Learning ; *Models, Biological ; Nucleic Acid Conformation ; RNA, Messenger/chemistry/genetics ; ROC Curve ; *Transcription Termination, Genetic ; }, abstract = {A common strategy for regulation of gene expression in bacteria is conditional transcription termination. This strategy is frequently employed by 5'UTR cis-acting RNA elements (riboregulators), including riboswitches and attenuators. Such riboregulators can assume two mutually exclusive RNA structures, one of which forms a transcriptional terminator and results in premature termination, and the other forms an antiterminator that allows read-through into the coding sequence to produce a full-length mRNA. We developed a machine-learning based approach, which, given a 5'UTR of a gene, predicts whether it can form the two alternative structures typical to riboregulators employing conditional termination. Using a large positive training set of riboregulators derived from 89 human microbiome bacteria, we show high specificity and sensitivity for our classifier. We further show that our approach allows the discovery of previously unidentified riboregulators, as exemplified by the detection of new LeuA leaders and T-boxes in Streptococci Finally, we developed PASIFIC (www.weizmann.ac.il/molgen/Sorek/PASIFIC/), an online web-server that, given a user-provided 5'UTR sequence, predicts whether this sequence can adopt two alternative structures conforming with the conditional termination paradigm. This webserver is expected to assist in the identification of new riboswitches and attenuators in the bacterial pan-genome.}, }
@article {pmid27536275, year = {2016}, author = {Sun, S and Xiao, J and Zhang, H and Zhang, Z}, title = {Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1180}, doi = {10.3389/fmicb.2016.01180}, pmid = {27536275}, issn = {1664-302X}, abstract = {Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains. We further explore the forces in influencing codon usage and investigate the difference of the major force between core and strain-specific genes. Our results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biased codon usage as genes are present in an increased number of strains. Together, our results provide important insights for better understanding genome plasticity and complexity as well as evolutionary mechanisms behind codon usage bias.}, }
@article {pmid27504980, year = {2016}, author = {Uchiyama, I and Albritton, J and Fukuyo, M and Kojima, KK and Yahara, K and Kobayashi, I}, title = {A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0159419}, doi = {10.1371/journal.pone.0159419}, pmid = {27504980}, issn = {1932-6203}, mesh = {Chromosomes, Bacterial/genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Genomic Islands/*genetics ; Genomics/*methods ; Helicobacter pylori/*genetics ; Multigene Family/genetics ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; }, abstract = {Genomes of a given bacterial species can show great variation in gene content and thus systematic analysis of the entire gene repertoire, termed the pan-genome, is important for understanding bacterial intra-species diversity, population genetics, and evolution. Here, we analyzed the pan-genome from 30 completely sequenced strains of the human gastric pathogen Helicobacter pylori belonging to various phylogeographic groups, focusing on 991 accessory (not fully conserved) orthologous groups (OGs). We developed a method to evaluate the mobility of genes within a genome, using the gene order in the syntenically conserved regions as a reference, and classified the 991 accessory OGs into five classes: Core, Stable, Intermediate, Mobile, and Unique. Phylogenetic networks based on the gene content of Core and Stable classes are highly congruent with that created from the concatenated alignment of fully conserved core genes, in contrast to those of Intermediate and Mobile classes, which show quite different topologies. By clustering the accessory OGs on the basis of phylogenetic pattern similarity and chromosomal proximity, we identified 60 co-occurring gene clusters (CGCs). In addition to known genomic islands, including cag pathogenicity island, bacteriophages, and integrating conjugative elements, we identified some novel ones. One island encodes TerY-phosphorylation triad, which includes the eukaryote-type protein kinase/phosphatase gene pair, and components of type VII secretion system. Another one contains a reverse-transcriptase homolog, which may be involved in the defense against phage infection through altruistic suicide. Many of the CGCs contained restriction-modification (RM) genes. Different RM systems sometimes occupied the same (orthologous) locus in the strains. We anticipate that our method will facilitate pan-genome studies in general and help identify novel genomic islands in various bacterial species.}, }
@article {pmid27499133, year = {2016}, author = {Pinosio, S and Giacomello, S and Faivre-Rampant, P and Taylor, G and Jorge, V and Le Paslier, MC and Zaina, G and Bastien, C and Cattonaro, F and Marroni, F and Morgante, M}, title = {Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation.}, journal = {Molecular biology and evolution}, volume = {33}, number = {10}, pages = {2706-2719}, doi = {10.1093/molbev/msw161}, pmid = {27499133}, issn = {1537-1719}, mesh = {DNA Copy Number Variations ; Genes, Plant ; Genome, Plant ; Genome-Wide Association Study ; Genomics ; INDEL Mutation ; Populus/*genetics ; Structure-Activity Relationship ; }, abstract = {Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome.}, }
@article {pmid27476200, year = {2016}, author = {Provorov, NA and Andronov, EE}, title = {[Evolution of Root Nodule Bacteria: Reconstruction of the Speciation Processes Resulting from Genomic Rearrangements in a Symbiotic System].}, journal = {Mikrobiologiia}, volume = {85}, number = {2}, pages = {115-125}, pmid = {27476200}, issn = {0026-3656}, mesh = {*Bacteria/genetics/metabolism ; *Evolution, Molecular ; Genome, Bacterial/*physiology ; Root Nodules, Plant/*microbiology ; Symbiosis/*physiology ; }, abstract = {The processes of speciation and macroevolution of root nodule bacteria (rhizobia), based on deep rearrangements of their genomes and occurring in the N₂-fixing symbiotic system, are reconstructed. At the first stage of rhizobial evolution, transformation of free-living diazotrophs (related to Rhodopseudomonas) to symbiotic N₂-fixers (Bradyrhizobium) occurred due to the acquisition of the fix gene system, which is responsible for providing nitrogenase with electrons and reducing equivalents, as well as for oxygen-dependent regulation of nitrogenase synthesis in planta, and then of the nod genes responsible for the synthesis of the lipo- chito-oligosaccharide Nod factors, which induce root nodule development. The subsequent rearrangements of bacterial genomes included: (1) increased volume of hereditary information supported by species, genera (pan-genome), and individual strains; (2) transition from the unitary genome to a multicomponent one; and (3) enhanced levels of bacterial genetic plasticity and horizontal gene transfer, resulting in formation of new genera, of which Mesorhizobium, Rhizobium, and Sinorhizobium are the largest, and of over 100 species. Rhizobial evolution caused by development and diversification of the Nod factor synthesizing systems may result in both increased host specificity range (transition of Bradyrhizobium from autotrophic to symbiotrophic carbon metabolism in interaction with a broad spectrum of legumes) and to its contraction (transition of Rhizobium and Sinorhizobium to &quot;altruistic&quot; interaction with legumes of the galegoid clade). Reconstruction of the evolutionary pathway from symbiotic N₂-fixers to their free-living ancestors makes it possible to initiate the studies based on up-to-date genome screening technologies and aimed at the issues of genetic integration of organisms into supracpecies complexes, ratios of the macro- and microevolutionary mechanisms, and developmetn of cooperative adaptations based on altruistic relationship between the symbiotic partners.}, }
@article {pmid27461509, year = {2016}, author = {Breurec, S and Criscuolo, A and Diancourt, L and Rendueles, O and Vandenbogaert, M and Passet, V and Caro, V and Rocha, EP and Touchon, M and Brisse, S}, title = {Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30379}, doi = {10.1038/srep30379}, pmid = {27461509}, issn = {2045-2322}, support = {281605//European Research Council/International ; }, mesh = {Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Transposable Elements ; Evolution, Molecular ; Flavobacteriaceae/classification/*genetics/pathogenicity ; Gene Transfer, Horizontal ; *Genetic Variation ; *Genome, Bacterial ; *Phylogeny ; Virulence/genetics ; }, abstract = {Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.}, }
@article {pmid27460800, year = {2016}, author = {Ray, A and Kinch, LN and de Souza Santos, M and Grishin, NV and Orth, K and Salomon, D}, title = {Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus.}, journal = {mBio}, volume = {7}, number = {4}, pages = {}, doi = {10.1128/mBio.01077-16}, pmid = {27460800}, issn = {2150-7511}, support = {K99 AI116948/AI/NIAID NIH HHS/United States ; R01 AI056404/AI/NIAID NIH HHS/United States ; R01 GM094575/GM/NIGMS NIH HHS/United States ; T32 DK007745/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Aquatic Organisms/chemistry ; Cell Survival/drug effects ; Cytoskeleton/metabolism ; Epithelial Cells/microbiology/physiology ; HeLa Cells ; Hemolysin Proteins/*analysis/secretion ; Humans ; Macrophages/microbiology/physiology ; Mice ; *Proteomics ; RAW 264.7 Cells ; Vibrio/*chemistry ; Virulence Factors/*analysis ; }, abstract = {UNLABELLED: Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells.<br><br>IMPORTANCE: The pan-genome of the genus Vibrio is a potential reservoir of unidentified toxins that can provide insight into how members of this genus have successfully risen as emerging pathogens worldwide. We focused on Vibrio proteolyticus, a marine bacterium that was previously implicated in virulence toward marine animals, and characterized its interaction with eukaryotic cells. We found that this bacterium causes actin cytoskeleton rearrangements and leads to cell death. Using a proteomics approach, we identified a previously unstudied member of the leukocidin family of pore-forming toxins as the virulence factor responsible for the observed cytotoxicity in eukaryotic cells, as well as a plethora of additional putative virulence factors secreted by this bacterium. Our findings reveal a functional new clan of the leukocidin toxin superfamily and establish this pathogen as a reservoir of potential toxins that can be used for biomedical applications.}, }
@article {pmid27446038, year = {2016}, author = {Tian, X and Zhang, Z and Yang, T and Chen, M and Li, J and Chen, F and Yang, J and Li, W and Zhang, B and Zhang, Z and Wu, J and Zhang, C and Long, L and Xiao, J}, title = {Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {998}, doi = {10.3389/fmicb.2016.00998}, pmid = {27446038}, issn = {1664-302X}, abstract = {Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.}, }
@article {pmid27446024, year = {2016}, author = {Zheng, Q and Lin, W and Liu, Y and Chen, C and Jiao, N}, title = {A Comparison of 14 Erythrobacter Genomes Provides Insights into the Genomic Divergence and Scattered Distribution of Phototrophs.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {984}, doi = {10.3389/fmicb.2016.00984}, pmid = {27446024}, issn = {1664-302X}, abstract = {Aerobic anoxygenic phototrophic bacteria (AAPB) are bacteriochlorophyll a (Bchl a)-containing microbial functional population. Erythrobacter is the first genus that was identified to contain AAPB species. Here, we compared 14 Erythrobacter genomes: seven phototrophic strains and seven non- phototrophic strains. Interestingly, AAPB strains are scattered in this genus based on their phylogenetic relationships. All 14 strains could be clustered into three groups based on phylo-genomic analysis, average genomic nucleotide identity and the phylogeny of signature genes (16S rRNA and virB4 genes). The AAPB strains were distributed in three groups, and gain and loss of phototrophic genes co-occurred in the evolutionary history of the genus Erythrobacter. The organization and structure of photosynthesis gene clusters (PGCs) in seven AAPB genomes displayed high synteny of major regions except for few insertions. The 14 Erythrobacter genomes had a large range of genome sizes, from 2.72 to 3.60 M, and the sizes of the core and pan- genomes were 1231 and 8170 orthologous clusters, respectively. Integrative and conjugative elements (ICEs) were frequently identified in genomes we studied, which might play significant roles in shaping or contributing to the pan-genome of Erythrobacter. Our findings suggest the ongoing evolutionary divergence of Erythrobacter genomes and the scattered distribution characteristic of PGC.}, }
@article {pmid27437028, year = {2016}, author = {Beller, T and Ohlebusch, E}, title = {A representation of a compressed de Bruijn graph for pan-genome analysis that enables search.}, journal = {Algorithms for molecular biology : AMB}, volume = {11}, number = {}, pages = {20}, doi = {10.1186/s13015-016-0083-7}, pmid = {27437028}, issn = {1748-7188}, abstract = {BACKGROUND: Recently, Marcus et al. (Bioinformatics 30:3476-83, 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an [Formula: see text] time algorithm called splitMEM that constructs this graph directly (i.e., without using the uncompressed de Bruijn graph) based on a suffix tree, where n is the total length of the genomes and g is the length of the longest genome. Baier et al. (Bioinformatics 32:497-504, 2016) improved their result.<br><br>RESULTS: In this paper, we propose a new space-efficient representation of the compressed de Bruijn graph that adds the possibility to search for a pattern (e.g. an allele-a variant form of a gene) within the pan-genome. The ability to search within the pan-genome graph is of utmost importance and is a design goal of pan-genome data structures.}, }
@article {pmid27420027, year = {2017}, author = {Porter, SS and Chang, PL and Conow, CA and Dunham, JP and Friesen, ML}, title = {Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {248-262}, doi = {10.1038/ismej.2016.88}, pmid = {27420027}, issn = {1751-7370}, mesh = {Acclimatization ; Adaptation, Physiological/genetics ; Bacterial Proteins/genetics/*metabolism ; Chromosome Mapping ; Ecotype ; Genetic Variation ; Genome-Wide Association Study ; Genomics ; Mesorhizobium/classification/genetics/isolation &amp; purification/*physiology ; Secologanin Tryptamine Alkaloids/*metabolism ; Soil Microbiology ; }, abstract = {The genetic variants that underlie microbial environmental adaptation are key components of models of microbial diversification. Characterizing adaptive variants and the pangenomic context in which they evolve remains a frontier in understanding how microbial diversity is generated. The genomics of rhizobium adaptation to contrasting soil environments is ecologically and agriculturally important because these bacteria are responsible for half of all current biologically fixed nitrogen, yet they live the majority of their lives in soil. Our study uses whole-genome sequencing to describe the pan-genome of a focal clade of wild mesorhizobia that show contrasting levels of nickel adaptation despite high relatedness (99.8% identity at 16S). We observe ecotypic specialization within an otherwise genomically cohesive population, rather than finding distinct specialized bacterial lineages in contrasting soil types. This finding supports recent reports that heterogeneous environments impose selection that maintains differentiation only at a small fraction of the genome. Our work further uses a genome-wide association study to propose candidate genes for nickel adaptation. Several candidates show homology to genetic systems involved in nickel tolerance and one cluster of candidates correlates perfectly with soil origin, which validates our approach of ascribing genomic variation to adaptive divergence.}, }
@article {pmid27363390, year = {2016}, author = {Thakur, S and Guttman, DS}, title = {A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.}, journal = {BMC bioinformatics}, volume = {17}, number = {1}, pages = {260}, doi = {10.1186/s12859-016-1142-2}, pmid = {27363390}, issn = {1471-2105}, mesh = {Algorithms ; Amino Acid Sequence ; Cluster Analysis ; Computational Biology ; *Genome ; Genomics/*methods ; Markov Chains ; Molecular Sequence Annotation ; Prokaryotic Cells/*metabolism ; Reproducibility of Results ; Sequence Homology, Nucleic Acid ; *Software ; }, abstract = {BACKGROUND: Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation.<br><br>RESULTS: We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available.<br><br>CONCLUSION: DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/ .}, }
@article {pmid27358423, year = {2016}, author = {Ceapa, C and Davids, M and Ritari, J and Lambert, J and Wels, M and Douillard, FP and Smokvina, T and de Vos, WM and Knol, J and Kleerebezem, M}, title = {The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {1889-1905}, doi = {10.1093/gbe/evw123}, pmid = {27358423}, issn = {1759-6653}, support = {250172//European Research Council/International ; }, mesh = {CRISPR-Cas Systems ; Carbohydrate Metabolism/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Lactobacillus rhamnosus/*genetics ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.}, }
@article {pmid27341059, year = {2016}, author = {Bou Khalil, JY and Andreani, J and Raoult, D and La Scola, B}, title = {A Rapid Strategy for the Isolation of New Faustoviruses from Environmental Samples Using Vermamoeba vermiformis.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {112}, pages = {}, doi = {10.3791/54104}, pmid = {27341059}, issn = {1940-087X}, mesh = {Amoeba ; Genotype ; Viruses/*isolation &amp; purification ; }, abstract = {The isolation of giant viruses is of great interest in this new era of virology, especially since these giant viruses are related to protists. Giant viruses may be potentially pathogenic for many species of protists. They belong to the recently described order of Megavirales. The new lineage Faustovirus that has been isolated from sewage samples is distantly related to the mammalian pathogen African swine fever virus. This virus is also specific to its amoebal host, Vermamoeba vermiformis, a protist common in health care water systems. It is crucial to continue isolating new Faustovirus genotypes in order to enlarge its genotype collection and study its pan-genome. We developed new strategies for the isolation of additional strains by improving the use of antibiotic and antifungal combinations in order to avoid bacterial and fungal contaminations of the amoeba co-culture and favoring the virus multiplication. We also implemented a new starvation medium to maintain V. vermiformis in optimal conditions for viruses co-culture. Finally, we used flow cytometry rather than microscopic observation, which is time-consuming, to detect the cytopathogenic effect. We obtained two isolates from sewage samples, proving the efficiency of this method and thus widening the collection of Faustoviruses, to better understand their environment, host specificity and genetic content.}, }
@article {pmid27316954, year = {2016}, author = {Perez, M and Juniper, SK}, title = {Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {17}, pages = {5197-5205}, doi = {10.1128/AEM.00953-16}, pmid = {27316954}, issn = {1098-5336}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Gammaproteobacteria/classification/genetics/*isolation &amp; purification/*physiology ; Host Specificity ; Hydrothermal Vents/microbiology ; Polychaeta/classification/*microbiology/physiology ; Seawater/microbiology ; Symbiosis ; }, abstract = {UNLABELLED: The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms Oasisia alvinae, Riftia pachyptila, Tevnia jerichonana, and Ridgeia piscesae belong to the same phylotype of gammaproteobacteria, &quot;Candidatus Endoriftia persephone.&quot; Comparisons of symbiont genomes between the East Pacific Rise tubeworms R. pachyptila and T. jerichonana confirmed that these two hosts share the same symbionts. Two Ridgeia symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced Riftia and Tevnia symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that &quot;Ca Endoriftia persephone&quot; symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity.<br><br>IMPORTANCE: Remarkably, the intracellular symbionts of four to six species of eastern Pacific vent tubeworms all belong to the same phylotype of gammaproteobacteria, &quot;Candidatus Endoriftia persephone.&quot; Understanding the structure, dynamism, and interconnectivity of &quot;Ca Endoriftia persephone&quot; populations is important to advancing our knowledge of the ecology and evolution of their host worms, which are often keystone species in vent communities. In this paper, we present the first genomes for symbionts associated with the species R. piscesae, from the Juan de Fuca Ridge. We then combine these genomes with published symbiont genomes from the East Pacific Rise tubeworms R. pachyptila and T. jerichonana to develop a portrait of the &quot;Ca Endoriftia persephone&quot; pangenome and an initial outline of symbiont population structure in the different host species. Our study is the first to apply genome-wide comparisons of &quot;Ca Endoriftia persephone&quot; assemblies in the context of population genetics and molecular evolution.}, }
@article {pmid27286824, year = {2016}, author = {Bosi, E and Monk, JM and Aziz, RK and Fondi, M and Nizet, V and Palsson, BØ}, title = {Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {26}, pages = {E3801-9}, doi = {10.1073/pnas.1523199113}, pmid = {27286824}, issn = {1091-6490}, support = {R01 GM098105/GM/NIGMS NIH HHS/United States ; U01 AI124316/AI/NIAID NIH HHS/United States ; U54 HD071600/HD/NICHD NIH HHS/United States ; }, mesh = {*Genome, Bacterial ; Models, Molecular ; Species Specificity ; Staphylococcus aureus/*genetics/growth &amp; development/metabolism/pathogenicity ; Virulence Factors/genetics ; }, abstract = {Staphylococcus aureus is a preeminent bacterial pathogen capable of colonizing diverse ecological niches within its human host. We describe here the pangenome of S. aureus based on analysis of genome sequences from 64 strains of S. aureus spanning a range of ecological niches, host types, and antibiotic resistance profiles. Based on this set, S. aureus is expected to have an open pangenome composed of 7,411 genes and a core genome composed of 1,441 genes. Metabolism was highly conserved in this core genome; however, differences were identified in amino acid and nucleotide biosynthesis pathways between the strains. Genome-scale models (GEMs) of metabolism were constructed for the 64 strains of S. aureus These GEMs enabled a systems approach to characterizing the core metabolic and panmetabolic capabilities of the S. aureus species. All models were predicted to be auxotrophic for the vitamins niacin (vitamin B3) and thiamin (vitamin B1), whereas strain-specific auxotrophies were predicted for riboflavin (vitamin B2), guanosine, leucine, methionine, and cysteine, among others. GEMs were used to systematically analyze growth capabilities in more than 300 different growth-supporting environments. The results identified metabolic capabilities linked to pathogenic traits and virulence acquisitions. Such traits can be used to differentiate strains responsible for mild vs. severe infections and preference for hosts (e.g., animals vs. humans). Genome-scale analysis of multiple strains of a species can thus be used to identify metabolic determinants of virulence and increase our understanding of why certain strains of this deadly pathogen have spread rapidly throughout the world.}, }
@article {pmid27252683, year = {2016}, author = {Bezuidt, OK and Pierneef, R and Gomri, AM and Adesioye, F and Makhalanyane, TP and Kharroub, K and Cowan, DA}, title = {The Geobacillus Pan-Genome: Implications for the Evolution of the Genus.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {723}, doi = {10.3389/fmicb.2016.00723}, pmid = {27252683}, issn = {1664-302X}, abstract = {The genus Geobacillus is comprised of a diverse group of spore-forming Gram-positive thermophilic bacterial species and is well known for both its ecological diversity and as a source of novel thermostable enzymes. Although the mechanisms underlying the thermophilicity of the organism and the thermostability of its macromolecules are reasonably well understood, relatively little is known of the evolutionary mechanisms, which underlie the structural and functional properties of members of this genus. In this study, we have compared 29 Geobacillus genomes, with a specific focus on the elements, which comprise the conserved core and flexible genomes. Based on comparisons of conserved core and flexible genomes, we present evidence of habitat delineation with specific Geobacillus genomes linked to specific niches. Our analysis revealed that Geobacillus and Anoxybacillus share a high proportion of genes. Moreover, the results strongly suggest that horizontal gene transfer is a major factor deriving the evolution of Geobacillus from Bacillus, with genetic contributions from other phylogenetically distant taxa.}, }
@article {pmid27230650, year = {2016}, author = {Rodríguez-Blanco, A and Lemos, ML and Osorio, CR}, title = {Unveiling the pan-genome of the SXT/R391 family of ICEs: molecular characterisation of new variable regions of SXT/R391-like ICEs detected in Pseudoalteromonas sp. and Vibrio scophthalmi.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {8}, pages = {1141-1152}, doi = {10.1007/s10482-016-0716-3}, pmid = {27230650}, issn = {1572-9699}, mesh = {Animals ; Aquaculture ; Bacterial Proteins/genetics ; Base Sequence ; *Conjugation, Genetic ; DNA Replication ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Fishes/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Phylogeny ; Pseudoalteromonas/*genetics ; Sequence Analysis, DNA ; Vibrio/*genetics ; }, abstract = {Integrating conjugative elements (ICEs) of the SXT/R391 family have been identified in fish-isolated bacterial strains collected from marine aquaculture environments of the northwestern Iberian Peninsula. Here we analysed the variable regions of two ICEs, one preliminarily characterised in a previous study (ICEVscSpa3) and one newly identified (ICEPspSpa1). Bacterial strains harboring these ICEs were phylogenetically assigned to Vibrio scophthalmi and Pseudoalteromonas sp., thus constituting the first evidence of SXT/R391-like ICEs in the genus Pseudoalteromonas to date. Variable DNA regions, which confer element-specific properties to ICEs of this family, were characterised. Interestingly, the two ICEs contained 29 genes not found in variable DNA insertions of previously described ICEs. Most notably, variable gene content for ICEVscSpa3 showed similarity to genes potentially involved in housekeeping functions of replication, nucleotide metabolism and transcription. For these genes, closest homologues were found clustered in the genome of Pseudomonas psychrotolerans L19, suggesting a transfer as a block to ICEVscSpa3. Genes encoding antibiotic resistance, restriction modification systems and toxin/antitoxin systems were absent from hotspots of ICEVscSpa3. In contrast, the variable gene content of ICEPspSpa1 included genes involved in restriction/modification functions in two different hotspots and genes related to ICE maintenance. The present study unveils a relatively large number of novel genes in SXT/R391-ICEs, and demonstrates the major role of ICE elements as contributors to horizontal gene transfer.}, }
@article {pmid27189997, year = {2016}, author = {Kubasova, T and Cejkova, D and Matiasovicova, J and Sekelova, Z and Polansky, O and Medvecky, M and Rychlik, I and Juricova, H}, title = {Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids in Salmonella Typhimurium.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {1661-1671}, doi = {10.1093/gbe/evw105}, pmid = {27189997}, issn = {1759-6653}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial/drug effects ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Humans ; Plasmids/genetics ; Salmonella Infections/*genetics/microbiology ; Salmonella typhimurium/drug effects/*genetics/pathogenicity ; Sequence Analysis, DNA ; }, abstract = {Conjugative plasmids from the IncHI1 incompatibility group play an important role in transferring antibiotic resistance in Salmonella Typhimurium. However, knowledge of their genome structure or gene expression is limited. In this study, we determined the complete nucleotide sequences of four IncHI1 plasmids transferring resistance to antibiotics by two different next generation sequencing protocols and protein expression by mass spectrometry. Sequence data including additional 11 IncHI1 plasmids from GenBank were used for the definition of the IncHI1 plasmid core-genome and pan-genome. The core-genome consisted of approximately 123 kbp and 122 genes while the total pan-genome represented approximately 600 kbp. When the core-genome sequences were used for multiple alignments, the 15 tested IncHI1 plasmids were separated into two main lineages. GC content in core-genome genes was around 46% and 50% in accessory genome genes. A multidrug resistance region present in all 4 sequenced plasmids extended over 20 kbp and, except for tet(B), the genes responsible for antibiotic resistance were those with the highest GC content. IncHI1 plasmids therefore represent replicons that evolved in low GC content bacteria. From their original host, they spread to Salmonella and during this spread these plasmids acquired multiple accessory genes including those coding for antibiotic resistance. Antibiotic-resistance genes belonged to genes with the highest level of expression and were constitutively expressed even in the absence of antibiotics. This is the likely mechanism that facilitates host cell survival when antibiotics suddenly emerge in the environment.}, }
@article {pmid27189983, year = {2016}, author = {López-Pérez, M and Rodriguez-Valera, F}, title = {Pangenome Evolution in the Marine Bacterium Alteromonas.}, journal = {Genome biology and evolution}, volume = {8}, number = {5}, pages = {1556-1570}, doi = {10.1093/gbe/evw098}, pmid = {27189983}, issn = {1759-6653}, mesh = {Alteromonas/*genetics ; Aquatic Organisms/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Genome, Bacterial ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7-83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9-5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed.}, }
@article {pmid27118061, year = {2016}, author = {Sternes, PR and Borneman, AR}, title = {Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {308}, doi = {10.1186/s12864-016-2604-7}, pmid = {27118061}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Amino Acids/biosynthesis ; Carbohydrate Metabolism ; Fermentation ; Food Microbiology ; *Genetic Variation ; *Genome, Bacterial ; Genomics/*methods ; Lactic Acid/metabolism ; Molecular Sequence Data ; Oenococcus/*genetics ; Wine/*microbiology ; }, abstract = {BACKGROUND: Oenococcus oeni is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermentation that is often required for many types of wine. Expanding the understanding of strain-dependent genetic variations in its small and streamlined genome is important for realising its full potential in industrial fermentation processes.<br><br>RESULTS: Whole genome comparison was performed on 191 strains of O. oeni; from this rich source of genomic information consensus pan-genome assemblies of the invariant (core) and variable (flexible) regions of this organism were established. Genetic variation in amino acid biosynthesis and sugar transport and utilisation was found to be common between strains. Furthermore, we characterised previously-unreported intra-specific genetic variations in the natural competence of this microbe.<br><br>CONCLUSION: By assembling a consensus pan-genome from a large number of strains, this study provides a tool for researchers to readily compare protein-coding genes across strains and infer functional relationships between genes in conserved syntenic regions. This establishes a foundation for further genetic, and thus phenotypic, research of this industrially-important species.}, }
@article {pmid27114887, year = {2016}, author = {Asenjo, F and Olmos, A and Henríquez-Piskulich, P and Polanco, V and Aldea, P and Ugalde, JA and Trombert, AN}, title = {Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1950}, doi = {10.7717/peerj.1950}, pmid = {27114887}, issn = {2167-8359}, abstract = {Background. The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease of Firmicutes populations, such as the Lactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain of Lactobacillus kunkeei (L. kunkeei strain MP2) from the gut of Chilean honey bees. L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, the L. kunkeei genetic background and perform a comparative genome analysis with other Lactobacillus species. Methods. L. kunkeei MP2 was originally isolated from the guts of Chilean A. mellifera individuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology. De novo assembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons between L. kunkeei MP2 with other L. kunkeei, and Lactobacillus strains were done using Roary. Results. The complete genome of L. kunkeei MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16 L. kunkeei strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of L. kunkeei MP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with other Lactobacillus species, identified several unique genes of L. kunkeei MP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs). Discussion. The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability in L. kunkeei. Its versatility and ability to survive in different ecological niches (bee guts, flowers, fruits among others) could be given by its genetic capacity to change and adapt to different environments. L. kunkeei could be a new source of Lactobacillus with beneficial properties. Indeed, L. kunkeei MP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.}, }
@article {pmid27087830, year = {2016}, author = {Holley, G and Wittler, R and Stoye, J}, title = {Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.}, journal = {Algorithms for molecular biology : AMB}, volume = {11}, number = {}, pages = {3}, doi = {10.1186/s13015-016-0066-8}, pmid = {27087830}, issn = {1748-7188}, abstract = {BACKGROUND: High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high number of sequences sampled from each genome. Such a highly redundant collection of very similar sequences is called a pan-genome. It can be transformed into a set of sequences &quot;colored&quot; by the genomes to which they belong. A colored de Bruijn graph (C-DBG) extracts from the sequences all colored k-mers, strings of length k, and stores them in vertices.<br><br>RESULTS: In this paper, we present an alignment-free, reference-free and incremental data structure for storing a pan-genome as a C-DBG: the bloom filter trie (BFT). The data structure allows to store and compress a set of colored k-mers, and also to efficiently traverse the graph. Bloom filter trie was used to index and query different pangenome datasets. Compared to another state-of-the-art data structure, BFT was up to two times faster to build while using about the same amount of main memory. For querying k-mers, BFT was about 52-66 times faster while using about 5.5-14.3 times less memory.<br><br>CONCLUSION: We present a novel succinct data structure called the Bloom Filter Trie for indexing a pan-genome as a colored de Bruijn graph. The trie stores k-mers and their colors based on a new representation of vertices that compress and index shared substrings. Vertices use basic data structures for lightweight substrings storage as well as Bloom filters for efficient trie and graph traversals. Experimental results prove better performance compared to another state-of-the-art data structure.<br><br>AVAILABILITY: https://www.github.com/GuillaumeHolley/BloomFilterTrie.}, }
@article {pmid27075453, year = {2016}, author = {Ghatak, S and Blom, J and Das, S and Sanjukta, R and Puro, K and Mawlong, M and Shakuntala, I and Sen, A and Goesmann, A and Kumar, A and Ngachan, SV}, title = {Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {7}, pages = {945-956}, doi = {10.1007/s10482-016-0693-6}, pmid = {27075453}, issn = {1572-9699}, mesh = {Aeromonas caviae/drug effects/*genetics/pathogenicity ; Aeromonas hydrophila/drug effects/*genetics/pathogenicity ; Aeromonas veronii/drug effects/*genetics/pathogenicity ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; Genotype ; Homologous Recombination ; Humans ; Microbial Sensitivity Tests ; Phylogeny ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.}, }
@article {pmid27071527, year = {2016}, author = {Chaudhari, NM and Gupta, VK and Dutta, C}, title = {BPGA- an ultra-fast pan-genome analysis pipeline.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {24373}, doi = {10.1038/srep24373}, pmid = {27071527}, issn = {2045-2322}, mesh = {*Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Phylogeny ; Software ; Streptococcus pyogenes/classification/genetics ; }, abstract = {Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift in microbial genomics from few genome comparisons to large-scale pan-genome studies at different scales of phylogenetic resolution. Pan-genome studies provide a framework for estimating the genomic diversity of the dataset, determining core (conserved), accessory (dispensable) and unique (strain-specific) gene pool of a species, tracing horizontal gene-flux across strains and providing insight into species evolution. The existing pan genome software tools suffer from various limitations like limited datasets, difficult installation/requirements, inadequate functional features etc. Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules. In addition to the routine pan genome analyses, BPGA introduces a number of novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny, exclusive presence/absence of genes in specific strains, subset analysis, atypical G + C content analysis and KEGG &amp;COG mapping of core, accessory and unique genes. Other notable features include minimum running prerequisites, freedom to select the gene clustering method, ultra-fast execution, user friendly command line interface and high-quality graphics outputs. The performance of BPGA has been evaluated using a dataset of complete genome sequences of 28 Streptococcus pyogenes strains.}, }
@article {pmid27071075, year = {2016}, author = {Castillo, D and Christiansen, RH and Dalsgaard, I and Madsen, L and Espejo, R and Middelboe, M}, title = {Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0152515}, doi = {10.1371/journal.pone.0152515}, pmid = {27071075}, issn = {1932-6203}, mesh = {Biofilms/growth &amp; development ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Drug Resistance, Bacterial/genetics ; Flavobacterium/*genetics/*pathogenicity ; Sequence Analysis, DNA/*methods ; Virulence/*genetics ; }, abstract = {Flavobacterium psychrophilum is a fish pathogen in salmonid aquaculture worldwide that causes cold water disease (CWD) and rainbow trout fry syndrome (RTFS). Comparative genome analyses of 11 F. psychrophilum isolates representing temporally and geographically distant populations were used to describe the F. psychrophilum pan-genome and to examine virulence factors, prophages, CRISPR arrays, and genomic islands present in the genomes. Analysis of the genomic DNA sequences were complemented with selected phenotypic characteristics of the strains. The pan genome analysis showed that F. psychrophilum could hold at least 3373 genes, while the core genome contained 1743 genes. On average, 67 new genes were detected for every new genome added to the analysis, indicating that F. psychrophilum possesses an open pan genome. The putative virulence factors were equally distributed among isolates, independent of geographic location, year of isolation and source of isolates. Only one prophage-related sequence was found which corresponded to the previously described prophage 6H, and appeared in 5 out of 11 isolates. CRISPR array analysis revealed two different loci with dissimilar spacer content, which only matched one sequence in the database, the temperate bacteriophage 6H. Genomic Islands (GIs) were identified in F. psychrophilum isolates 950106-1/1 and CSF 259-93, associated with toxins and antibiotic resistance. Finally, phenotypic characterization revealed a high degree of similarity among the strains with respect to biofilm formation and secretion of extracellular enzymes. Global scale dispersion of virulence factors in the genomes and the abilities for biofilm formation, hemolytic activity and secretion of extracellular enzymes among the strains suggested that F. psychrophilum isolates have a similar mode of action on adhesion, colonization and destruction of fish tissues across large spatial and temporal scales of occurrence. Overall, the genomic characterization and phenotypic properties may provide new insights to the mechanisms of pathogenicity in F. psychrophilum.}, }
@article {pmid27065955, year = {2016}, author = {Rivers, AR and Burns, AS and Chan, LK and Moran, MA}, title = {Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {380}, doi = {10.3389/fmicb.2016.00380}, pmid = {27065955}, issn = {1664-302X}, abstract = {In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon (C) and nitrogen (N) limitation. RNAseq analysis identified 99 putative sRNAs. Sixty-nine were cis-encoded and located antisense to a presumed target gene. Thirty were trans-encoded and initial target prediction was performed computationally. The most prevalent functional roles of genes anti-sense to the cis-sRNAs were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Most sRNAs were transcribed equally under both C and N limitation, and may be involved in a general stress response. However, 14 were regulated differentially between the C and N treatments and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi cis-sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome.}, }
@article {pmid27048805, year = {2016}, author = {Hemme, CL and Green, SJ and Rishishwar, L and Prakash, O and Pettenato, A and Chakraborty, R and Deutschbauer, AM and Van Nostrand, JD and Wu, L and He, Z and Jordan, IK and Hazen, TC and Arkin, AP and Kostka, JE and Zhou, J}, title = {Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02234-15}, doi = {10.1128/mBio.02234-15}, pmid = {27048805}, issn = {2150-7511}, mesh = {Gammaproteobacteria/*genetics/metabolism ; *Gene Transfer, Horizontal ; Groundwater/analysis/*microbiology ; Metals, Heavy/*analysis/metabolism ; Microbiota ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {UNLABELLED: Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.<br><br>IMPORTANCE: Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.}, }
@article {pmid27042991, year = {2016}, author = {Blanc-Mathieu, R and Ogata, H}, title = {DNA repair genes in the Megavirales pangenome.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {94-100}, doi = {10.1016/j.mib.2016.03.011}, pmid = {27042991}, issn = {1879-0364}, mesh = {DNA Repair/*genetics ; DNA, Viral/genetics ; Eukaryota/genetics/virology ; Evolution, Molecular ; Genome, Viral/genetics ; Giant Viruses/classification/*genetics/*metabolism ; }, abstract = {The order 'Megavirales' represents a group of eukaryotic viruses with a large genome encoding a few hundred up to two thousand five hundred genes. Several members of Megavirales possess genes involved in major DNA repair pathways. Some of these genes were likely inherited from an ancient virus world and some others were derived from the genomes of their hosts. Here we examine molecular phylogenies of key DNA repair enzymes in light of recent hypotheses on the origin of Megavirales, and propose that the last common ancestors of the individual families of the order Megavirales already possessed DNA repair functions to achieve and maintain a moderately large genome and that this repair capacity gradually increased, in a family-dependent manner, during their recent evolution.}, }
@article {pmid27037122, year = {2016}, author = {Patel, IR and Gangiredla, J and Lacher, DW and Mammel, MK and Jackson, SA and Lampel, KA and Elkins, CA}, title = {FDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {11}, pages = {3384-3394}, doi = {10.1128/AEM.04077-15}, pmid = {27037122}, issn = {1098-5336}, mesh = {Escherichia coli/*classification/*genetics ; Genetic Variation ; Genotyping Techniques/*methods ; Microarray Analysis/*methods ; Molecular Epidemiology/*methods ; Serotyping/*methods ; United States ; United States Food and Drug Administration ; Virulence Factors/*analysis/genetics ; }, abstract = {UNLABELLED: Most Escherichia coli strains are nonpathogenic. However, for clinical diagnosis and food safety analysis, current identification methods for pathogenic E. coli either are time-consuming and/or provide limited information. Here, we utilized a custom DNA microarray with informative genetic features extracted from 368 sequence sets for rapid and high-throughput pathogen identification. The FDA Escherichia coli Identification (FDA-ECID) platform contains three sets of molecularly informative features that together stratify strain identification and relatedness. First, 53 known flagellin alleles, 103 alleles of wzx and wzy, and 5 alleles of wzm provide molecular serotyping utility. Second, 41,932 probe sets representing the pan-genome of E. coli provide strain-level gene content information. Third, approximately 125,000 single nucleotide polymorphisms (SNPs) of available whole-genome sequences (WGS) were distilled to 9,984 SNPs capable of recapitulating the E. coli phylogeny. We analyzed 103 diverse E. coli strains with available WGS data, including those associated with past foodborne illnesses, to determine robustness and accuracy. The array was able to accurately identify the molecular O and H serotypes, potentially correcting serological failures and providing better resolution for H-nontypeable/nonmotile phenotypes. In addition, molecular risk assessment was possible with key virulence marker identifications. Epidemiologically, each strain had a unique comparative genomic fingerprint that was extended to an additional 507 food and clinical isolates. Finally, a 99.7% phylogenetic concordance was established between microarray analysis and WGS using SNP-level data for advanced genome typing. Our study demonstrates FDA-ECID as a powerful tool for epidemiology and molecular risk assessment with the capacity to profile the global landscape and diversity of E. coli<br><br>IMPORTANCE: This study describes a robust, state-of-the-art platform developed from available whole-genome sequences of E. coli and Shigella spp. by distilling useful signatures for epidemiology and molecular risk assessment into one assay. The FDA-ECID microarray contains features that enable comprehensive molecular serotyping and virulence profiling along with genome-scale genotyping and SNP analysis. Hence, it is a molecular toolbox that stratifies strain identification and pathogenic potential in the contexts of epidemiology and phylogeny. We applied this tool to strains from food, environmental, and clinical sources, resulting in significantly greater phylogenetic and strain-specific resolution than previously reported for available typing methods.}, }
@article {pmid27035119, year = {2016}, author = {Duranti, S and Milani, C and Lugli, GA and Mancabelli, L and Turroni, F and Ferrario, C and Mangifesta, M and Viappiani, A and Sánchez, B and Margolles, A and van Sinderen, D and Ventura, M}, title = {Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23971}, doi = {10.1038/srep23971}, pmid = {27035119}, issn = {2045-2322}, mesh = {Animals ; Bifidobacterium adolescentis/*genetics/isolation &amp; purification ; Carbohydrates/chemistry ; Cattle ; DNA, Bacterial/genetics ; Diet ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Genetic Variation ; Genome, Bacterial ; Genomics ; Humans ; Intestines/*microbiology ; Milk/microbiology ; Open Reading Frames ; Polysaccharides/chemistry ; Rumen/microbiology ; }, abstract = {Bifidobacteria are members of the human gut microbiota, being numerically dominant in the colon of infants, while also being prevalent in the large intestine of adults. In this study, we determined and analyzed the pan-genome of Bifidobacterium adolescentis, which is one of many bacteria found in the human adult gut microbiota. In silico analysis of the genome sequences of eighteen B. adolescentis strains isolated from various environments, such as human milk, human feces and bovine rumen, revealed a high level of genetic variability, resulting in an open pan-genome. Compared to other bifidobacterial taxa such as Bifidobacterium bifidum and Bifidobacterium breve, the more extensive B. adolescentis pan-genome supports the hypothesis that the genetic arsenal of this taxon expanded so as to become more adaptable to the variable and changing ecological niche of the gut. These increased genetic capabilities are particularly evident for genes required for dietary glycan-breakdown.}, }
@article {pmid27014232, year = {2016}, author = {Patil, PP and Midha, S and Kumar, S and Patil, PB}, title = {Genome Sequence of Type Strains of Genus Stenotrophomonas.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {309}, doi = {10.3389/fmicb.2016.00309}, pmid = {27014232}, issn = {1664-302X}, abstract = {Genomic resource of type strains and historically important strains of genus Stenotrophomonas allowed us to reveal the existence of 18 distinct species by applying modern phylogenomic criterions. Apart from Stenotrophomonas maltophilia, S. africana represents another species of clinical importance. Interestingly, Pseudomonas hibsicola, P. beteli, and S. pavani that are of plant origin are closer to S. maltophilia than the majority of the environmental isolates. The genus has an open pan-genome. By providing the case study on genes encoding metallo-β-lactamase and Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) regions, we have tried to show the importance of this genomic dataset in understanding its ecology.}, }
@article {pmid27006628, year = {2015}, author = {Guimarães, LC and Florczak-Wyspianska, J and de Jesus, LB and Viana, MV and Silva, A and Ramos, RT and Soares, Sde C and Soares, Sde C}, title = {Inside the Pan-genome - Methods and Software Overview.}, journal = {Current genomics}, volume = {16}, number = {4}, pages = {245-252}, doi = {10.2174/1389202916666150423002311}, pmid = {27006628}, issn = {1389-2029}, abstract = {The number of genomes that have been deposited in databases has increased exponentially after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence data; this circumstance has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics. In comparative genomics, the genetic content of an organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences, identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be &quot;open&quot; as long as new genes are added significantly to the total repertoire for each new additional genome and &quot;closed&quot; when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous gene identification.}, }
@article {pmid26999001, year = {2016}, author = {Scholz, M and Ward, DV and Pasolli, E and Tolio, T and Zolfo, M and Asnicar, F and Truong, DT and Tett, A and Morrow, AL and Segata, N}, title = {Strain-level microbial epidemiology and population genomics from shotgun metagenomics.}, journal = {Nature methods}, volume = {13}, number = {5}, pages = {435-438}, doi = {10.1038/nmeth.3802}, pmid = {26999001}, issn = {1548-7105}, support = {HHSN272200900018C/AI/NIAID NIH HHS/United States ; }, mesh = {Escherichia coli/classification/genetics/isolation &amp; purification/pathogenicity ; Gene Expression Profiling ; Genome, Bacterial ; Germany ; Humans ; Intestinal Mucosa/*microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbial Consortia/*genetics ; *Phylogeny ; Skin/*microbiology ; Software ; Species Specificity ; }, abstract = {Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.}, }
@article {pmid26983005, year = {2016}, author = {Ross, DE and Marshall, CW and May, HD and Norman, RS}, title = {Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151214}, doi = {10.1371/journal.pone.0151214}, pmid = {26983005}, issn = {1932-6203}, mesh = {Epsilonproteobacteria/classification/*genetics ; *Genome, Bacterial ; *Microbiota ; Phylogeny ; }, abstract = {Sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and contain metabolic versatility that enables reduction of a wide range of electron acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and nitrite. Here we describe the assembly of a Sulfurospirillum genome obtained from the metagenome of an electrosynthetic microbiome. The ubiquity and persistence of this organism in microbial electrosynthesis systems suggest it plays an important role in reactor stability and performance. Understanding why this organism is present and elucidating its genetic repertoire provide a genomic and ecological foundation for future studies where Sulfurospirillum are found, especially in electrode-associated communities. Metabolic comparisons and in-depth analysis of unique genes revealed potential ecological niche-specific capabilities within the Sulfurospirillum genus. The functional similarities common to all genomes, i.e., core genome, and unique gene clusters found only in a single genome were identified. Based upon 16S rRNA gene phylogenetic analysis and average nucleotide identity, the Sulfurospirillum draft genome was found to be most closely related to Sulfurospirillum cavolei. Characterization of the draft genome described herein provides pathway-specific details of the metabolic significance of the newly described Sulfurospirillum cavolei MES and, importantly, yields insight to the ecology of the genus as a whole. Comparison of eleven sequenced Sulfurospirillum genomes revealed a total of 6246 gene clusters in the pan-genome. Of the total gene clusters, 18.5% were shared among all eleven genomes and 50% were unique to a single genome. While most Sulfurospirillum spp. reduce nitrate to ammonium, five of the eleven Sulfurospirillum strains encode for a nitrous oxide reductase (nos) cluster with an atypical nitrous-oxide reductase, suggesting a utility for this genus in reduction of the nitrous oxide, and as a potential sink for this potent greenhouse gas.}, }
@article {pmid26978387, year = {2016}, author = {Dornas, FP and Assis, FL and Aherfi, S and Arantes, T and Abrahão, JS and Colson, P and La Scola, B}, title = {A Brazilian Marseillevirus Is the Founding Member of a Lineage in Family Marseilleviridae.}, journal = {Viruses}, volume = {8}, number = {3}, pages = {76}, doi = {10.3390/v8030076}, pmid = {26978387}, issn = {1999-4915}, mesh = {Brazil ; Cluster Analysis ; DNA Viruses/*genetics/*isolation &amp; purification ; DNA, Viral/*chemistry/*genetics ; *Evolution, Molecular ; Gene Order ; *Genome, Viral ; Open Reading Frames ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; Synteny ; }, abstract = {In 2003, Acanthamoeba polyphaga mimivirus (APMV) was discovered as parasitizing Acanthamoeba. It was revealed to exhibit remarkable features, especially odd genomic characteristics, and founded viral family Mimiviridae. Subsequently, a second family of giant amoebal viruses was described, Marseilleviridae, whose prototype member is Marseillevirus, discovered in 2009. Currently, the genomes of seven different members of this family have been fully sequenced. Previous phylogenetic analysis suggested the existence of three Marseilleviridae lineages: A, B and C. Here, we describe a new member of this family, Brazilian Marseillevirus (BrMV), which was isolated from a Brazilian sample and whose genome was fully sequenced and analyzed. Surprisingly, data from phylogenetic analyses and comparative genomics, including mean amino acid identity between BrMV and other Marseilleviridae members and the analyses of the core genome and pan-genome of marseilleviruses, indicated that this virus can be assigned to a new Marseilleviridae lineage. Even if the BrMV genome is one of the smallest among Marseilleviridae members, it harbors the second largest gene content into this family. In addition, the BrMV genome encodes 29 ORFans. Here, we describe the isolation and genome analyses of the BrMV strain, and propose its classification as the prototype virus of a new lineage D within the family Marseilleviridae.}, }
@article {pmid26953603, year = {2016}, author = {de Barsy, M and Frandi, A and Panis, G and Théraulaz, L and Pillonel, T and Greub, G and Viollier, PH}, title = {Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum.}, journal = {The ISME journal}, volume = {10}, number = {9}, pages = {2129-2144}, doi = {10.1038/ismej.2016.23}, pmid = {26953603}, issn = {1751-7370}, mesh = {Animals ; Bacterial Proteins/genetics ; Cercopithecus aethiops ; Chlamydiales/*genetics ; Chromatin Immunoprecipitation ; Genome, Bacterial/*genetics ; Genomics ; Phylogeny ; Reproducibility of Results ; Transcription Factors/*genetics ; Vero Cells ; Verrucomicrobia/*genetics ; }, abstract = {Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved.}, }
@article {pmid26941766, year = {2016}, author = {Figueroa, M and Upadhyaya, NM and Sperschneider, J and Park, RF and Szabo, LJ and Steffenson, B and Ellis, JG and Dodds, PN}, title = {Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {205}, doi = {10.3389/fpls.2016.00205}, pmid = {26941766}, issn = {1664-462X}, abstract = {The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.}, }
@article {pmid26930352, year = {2016}, author = {Pang, B and Du, P and Zhou, Z and Diao, B and Cui, Z and Zhou, H and Kan, B}, title = {The Transmission and Antibiotic Resistance Variation in a Multiple Drug Resistance Clade of Vibrio cholerae Circulating in Multiple Countries in Asia.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0149742}, doi = {10.1371/journal.pone.0149742}, pmid = {26930352}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/pharmacology ; Asia/epidemiology ; Cholera/epidemiology/microbiology/*transmission ; Disease Outbreaks ; Drug Resistance, Microbial/drug effects/*genetics ; Drug Resistance, Multiple/drug effects/*genetics ; Epidemics ; Genetic Variation ; Genome, Bacterial/genetics ; Phylogeny ; Sequence Analysis, DNA ; Vibrio cholerae/classification/*genetics/physiology ; }, abstract = {Vibrio cholerae has caused massive outbreaks and even trans-continental epidemics. In 2008 and 2010, at least 3 remarkable cholera outbreaks occurred in Hainan, Anhui and Jiangsu provinces of China. To address the possible transmissions and the relationships to the 7th pandemic strains of those 3 outbreaks, we sequenced the whole genomes of the outbreak isolates and compared with the global isolates from the 7th pandemic. The three outbreaks in this study were caused by a cluster of V. cholerae in clade 3.B which is parallel to the clade 3.C that was transmitted from Nepal to Haiti and caused an outbreak in 2010. Pan-genome analysis provided additional evolution information on the mobile element and acquired multiple antibiotic resistance genes. We suggested that clade 3.B should be monitored because the multiple antibiotic resistant characteristics of this clade and the 'amplifier' function of China in the global transmission of current Cholera pandemic. We also show that dedicated whole genome sequencing analysis provided more information than the previous techniques and should be applied in the disease surveillance networks.}, }
@article {pmid26915094, year = {2016}, author = {Garrido-Sanz, D and Meier-Kolthoff, JP and Göker, M and Martín, M and Rivilla, R and Redondo-Nieto, M}, title = {Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0150183}, doi = {10.1371/journal.pone.0150183}, pmid = {26915094}, issn = {1932-6203}, mesh = {Base Sequence ; DNA, Bacterial/genetics ; Denitrification/physiology ; *Genetic Variation ; Genome, Bacterial/*genetics ; Genomics ; Phylogeny ; Pseudomonas fluorescens/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Siderophores/biosynthesis ; Soil Microbiology ; }, abstract = {The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.}, }
@article {pmid26912404, year = {2016}, author = {Earl, JP and de Vries, SP and Ahmed, A and Powell, E and Schultz, MP and Hermans, PW and Hill, DJ and Zhou, Z and Constantinidou, CI and Hu, FZ and Bootsma, HJ and Ehrlich, GD}, title = {Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution.}, journal = {Genome biology and evolution}, volume = {8}, number = {4}, pages = {955-974}, doi = {10.1093/gbe/evw039}, pmid = {26912404}, issn = {1759-6653}, support = {AI080935/AI/NIAID NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC005659/DC/NIDCD NIH HHS/United States ; DC02148/DC/NIDCD NIH HHS/United States ; DC05659/DC/NIDCD NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Line ; Evolution, Molecular ; *Genome, Bacterial ; Genomics ; Humans ; Moraxella (Branhamella) catarrhalis/*genetics/growth &amp; development ; Moraxellaceae Infections/microbiology ; Multigene Family ; Phylogeny ; Virulence Factors/genetics ; }, abstract = {The bacterial speciesMoraxella catarrhalishas been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS]) with separate evolutionary histories based on several molecular typing methods, whereas 16S ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR-lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages-the SR, SS, and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for ß-lactamase genes. The four divergent strains aresui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size. Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored.}, }
@article {pmid26903955, year = {2016}, author = {Gómez-Lunar, Z and Hernández-González, I and Rodríguez-Torres, MD and Souza, V and Olmedo-Álvarez, G}, title = {Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {58}, doi = {10.3389/fmicb.2016.00058}, pmid = {26903955}, issn = {1664-302X}, abstract = {Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution). Our aim was to compare the genomes and relevant phenotypes of three Bacillus coahuilensis strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin (México), to unveil the environmental challenges that this species cope with, and the microevolutionary differences in these genotypes. Since the strains were isolated from a low P environment, we placed emphasis on the search of different phosphorus acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of coding DNA sequences, of which 82% (2,893) constituted the core genome, and 18% corresponded to accessory genes. Most of the genes in this last group were associated with mobile genetic elements (MGEs) or were annotated as hypothetical proteins. Ten percent of the pangenome consisted of strain-specific genes. Alignment of the three B. coahuilensis genomes indicated a high level of synteny and revealed the presence of several genomic islands. Unexpectedly, one of these islands contained genes that encode the 2-keto-3-deoxymannooctulosonic acid (Kdo) biosynthesis enzymes, a feature associated to cell walls of Gram-negative bacteria. Some microevolutionary changes were clearly associated with MGEs. Our analysis revealed inconsistencies between phenotype and genotype, which we suggest result from the impossibility to map regulatory features to genome analysis. Experimental results revealed variability in the types and numbers of auxotrophies between the strains that could not consistently be explained by in silico metabolic models. Several intraspecific differences in preferences for carbohydrate and phosphorus utilization were observed. Regarding phosphorus recycling, scavenging, and storage, variations were found between the three genomes. The three strains exhibited differences regarding alkaline phosphatase that revealed that in addition to gene gain and loss, regulation adjustment of gene expression also has contributed to the intraspecific diversity of B. coahuilensis.}, }
@article {pmid26903952, year = {2016}, author = {Benamar, S and Reteno, DG and Bandaly, V and Labas, N and Raoult, D and La Scola, B}, title = {Faustoviruses: Comparative Genomics of New Megavirales Family Members.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {3}, doi = {10.3389/fmicb.2016.00003}, pmid = {26903952}, issn = {1664-302X}, abstract = {An emerging interest for the giant virus discovery process, genome sequencing and analysis has allowed an expansion of the number of known Megavirales members. Using the protist Vermamoeba sp. as cell support, a new giant virus named Faustovirus has been isolated. In this study, we describe the genome sequences of nine Faustoviruses and build a genomic comparison in order to have a comprehensive overview of genomic composition and diversity among this new virus family. The average sequence length of these viruses is 467,592.44 bp (ranging from 455,803 to 491,024 bp), making them the fourth largest Megavirales genome after Mimiviruses, Pandoraviruses, and Pithovirus sibericum. Faustovirus genomes displayed an average G+C content of 37.14 % (ranging from 36.22 to 39.59%) which is close to the G+C content range of the Asfarviridae genomes (38%). The proportion of best matches and the phylogenetic analysis suggest a shared origin with Asfarviridae without belonging to the same family. The core-gene-based phylogeny of Faustoviruses study has identified four lineages. These results were confirmed by the analysis of amino acids and COGs category distribution. The diversity of the gene composition of these lineages is mainly explained by gene deletion or acquisition and some exceptions for gene duplications. The high proportion of best matches from Bacteria and Phycodnaviridae on the pan-genome and unique genes may be explained by an interaction occurring after the separation of the lineages. The Faustovirus core-genome appears to consolidate the surrounding of 207 genes whereas the pan-genome is described as an open pan-genome, its enrichment via the discovery of new Faustoviruses is required to better seize all the genomic diversity of this family.}, }
@article {pmid26899827, year = {2016}, author = {Roisin, S and Gaudin, C and De Mendonça, R and Bellon, J and Van Vaerenbergh, K and De Bruyne, K and Byl, B and Pouseele, H and Denis, O and Supply, P}, title = {Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {6}, pages = {520-526}, doi = {10.1016/j.cmi.2016.01.024}, pmid = {26899827}, issn = {1469-0691}, mesh = {Belgium/epidemiology ; Cross Infection/*epidemiology/microbiology ; *Disease Outbreaks ; *Genome, Bacterial ; Hospitals ; Humans ; Infant, Newborn ; Molecular Epidemiology ; *Multilocus Sequence Typing ; *Polymorphism, Single Nucleotide ; Staphylococcal Infections/*epidemiology/microbiology ; Staphylococcus aureus/*classification/genetics/isolation &amp; purification ; }, abstract = {We used a two-step whole genome sequencing analysis for resolving two concurrent outbreaks in two neonatal services in Belgium, caused by exfoliative toxin A-encoding-gene-positive (eta+) methicillin-susceptible Staphylococcus aureus with an otherwise sporadic spa-type t209 (ST-109). Outbreak A involved 19 neonates and one healthcare worker in a Brussels hospital from May 2011 to October 2013. After a first episode interrupted by decolonization procedures applied over 7 months, the outbreak resumed concomitantly with the onset of outbreak B in a hospital in Asse, comprising 11 neonates and one healthcare worker from mid-2012 to January 2013. Pan-genome multilocus sequence typing, defined on the basis of 42 core and accessory reference genomes, and single-nucleotide polymorphisms mapped on an outbreak-specific de novo assembly were used to compare 28 available outbreak isolates and 19 eta+/spa-type t209 isolates identified by routine or nationwide surveillance. Pan-genome multilocus sequence typing showed that the outbreaks were caused by independent clones not closely related to any of the surveillance isolates. Isolates from only ten cases with overlapping stays in outbreak A, including four pairs of twins, showed no or only a single nucleotide polymorphism variation, indicating limited sequential transmission. Detection of larger genomic variation, even from the start of the outbreak, pointed to sporadic seeding from a pre-existing exogenous source, which persisted throughout the whole course of outbreak A. Whole genome sequencing analysis can provide unique fine-tuned insights into transmission pathways of complex outbreaks even at their inception, which, with timely use, could valuably guide efforts for early source identification.}, }
@article {pmid26885654, year = {2016}, author = {Ding, T and Case, KA and Omolo, MA and Reiland, HA and Metz, ZP and Diao, X and Baumler, DJ}, title = {Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0149423}, doi = {10.1371/journal.pone.0149423}, pmid = {26885654}, issn = {1932-6203}, mesh = {Computer Simulation ; Enterobacteriaceae/*genetics/growth &amp; development ; Genes, Bacterial ; *Genome, Bacterial ; Host-Pathogen Interactions/*genetics ; Humans ; Metabolome/*genetics ; Salmonella/genetics ; }, abstract = {Microorganisms have evolved to occupy certain environmental niches, and the metabolic genes essential for growth in these locations are retained in the genomes. Many microorganisms inhabit niches located in the human body, sometimes causing disease, and may retain genes essential for growth in locations such as the bloodstream and urinary tract, or growth during intracellular invasion of the hosts' macrophage cells. Strains of Escherichia coli (E. coli) and Salmonella spp. are thought to have evolved over 100 million years from a common ancestor, and now cause disease in specific niches within humans. Here we have used a genome scale metabolic model representing the pangenome of E. coli which contains all metabolic reactions encoded by genes from 16 E. coli genomes, and have simulated environmental conditions found in the human bloodstream, urinary tract, and macrophage to determine essential metabolic genes needed for growth in each location. We compared the predicted essential genes for three E. coli strains and one Salmonella strain that cause disease in each host environment, and determined that essential gene retention could be accurately predicted using this approach. This project demonstrated that simulating human body environments such as the bloodstream can successfully lead to accurate computational predictions of essential/important genes.}, }
@article {pmid26859489, year = {2016}, author = {Alcaraz, LD and Martínez-Sánchez, S and Torres, I and Ibarra-Laclette, E and Herrera-Estrella, L}, title = {The Metagenome of Utricularia gibba's Traps: Into the Microbial Input to a Carnivorous Plant.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148979}, doi = {10.1371/journal.pone.0148979}, pmid = {26859489}, issn = {1932-6203}, support = {55007646//Howard Hughes Medical Institute/United States ; }, mesh = {Carnivory ; DNA, Plant/genetics ; Gene Library ; Genome, Plant/*genetics ; Lamiales/*genetics/microbiology ; *Metagenome ; Microbiota ; Plant Structures/*genetics/microbiology ; }, abstract = {The genome and transcriptome sequences of the aquatic, rootless, and carnivorous plant Utricularia gibba L. (Lentibulariaceae), were recently determined. Traps are necessary for U. gibba because they help the plant to survive in nutrient-deprived environments. The U. gibba's traps (Ugt) are specialized structures that have been proposed to selectively filter microbial inhabitants. To determine whether the traps indeed have a microbiome that differs, in composition or abundance, from the microbiome in the surrounding environment, we used whole-genome shotgun (WGS) metagenomics to describe both the taxonomic and functional diversity of the Ugt microbiome. We collected U. gibba plants from their natural habitat and directly sequenced the metagenome of the Ugt microbiome and its surrounding water. The total predicted number of species in the Ugt was more than 1,100. Using pan-genome fragment recruitment analysis, we were able to identify to the species level of some key Ugt players, such as Pseudomonas monteilii. Functional analysis of the Ugt metagenome suggests that the trap microbiome plays an important role in nutrient scavenging and assimilation while complementing the hydrolytic functions of the plant.}, }
@article {pmid26857276, year = {2016}, author = {Scholz, CF and Brüggemann, H and Lomholt, HB and Tettelin, H and Kilian, M}, title = {Genome stability of Propionibacterium acnes: a comprehensive study of indels and homopolymeric tracts.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20662}, doi = {10.1038/srep20662}, pmid = {26857276}, issn = {2045-2322}, mesh = {*Databases, Nucleic Acid ; *Genome, Bacterial ; *Genomic Instability ; *INDEL Mutation ; Propionibacterium acnes/*genetics ; }, abstract = {We present a species-wide comparative analysis of 90 genomes of Propionibacterium acnes that represent the known diversity of the species. Our results are augmented by six high-quality genomes and a manual investigation of all gene-sized indels found in the strains. Overall, the order of genes is conserved throughout the species. A public sybil database for easy comparative analysis of the 90 genomes was established. The analysis of indels revealed a total of 66 loci of non-core genes that correlate with phylogenetic clades. No gene was strain-specific in agreement with our conclusion that the P. acnes pan-genome is closed. An exhaustive search for homopolymeric tracts (HPTs) identified a total of 54 variable-length HPTs almost exclusively of guanine/cytosines located between genes or affecting the reading frame of genes. The repeat variation was consistent with phylogenetic clades suggesting slow accumulation over time rather than active modification. By transcriptome analysis we demonstrate how an HPT variation can affect the gene expression levels. Selected cases of both indels and HPTs are described. The catalogued data and the public P. acnes Sybil database provide a solid foundation for generating hypotheses and facilitate comparative genetic analyses in future P. acnes research.}, }
@article {pmid26854360, year = {2016}, author = {D'Amato, F and Eldin, C and Raoult, D}, title = {The contribution of genomics to the study of Q fever.}, journal = {Future microbiology}, volume = {11}, number = {2}, pages = {253-272}, doi = {10.2217/fmb.15.137}, pmid = {26854360}, issn = {1746-0921}, mesh = {Animals ; Axenic Culture ; Computer Simulation ; Coxiella burnetii/*genetics/pathogenicity ; Disease Outbreaks ; Genetic Variation ; *Genome, Bacterial ; *Genomics ; Genotype ; Humans ; Mice ; Phylogeny ; Q Fever/diagnosis/*microbiology/physiopathology/therapy ; Real-Time Polymerase Chain Reaction ; Virulence/genetics ; Zoonoses ; }, abstract = {Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis that can result in large outbreaks. The birth of genomics and sequencing of C. burnetii strains has revolutionized many fields of study of this infection. Accurate genotyping methods and comparative genomic analysis have enabled description of the diversity of strains around the world and their link with pathogenicity. Genomics has also permitted the development of qPCR tools and axenic culture medium, facilitating the diagnosis of Q fever. Moreover, several pathophysiological mechanisms can now be predicted and therapeutic strategies can be determined thanks to in silico genome analysis. An extensive pan-genomic analysis will allow for a comprehensive view of the clonal diversity of C. burnetii and its link with virulence.}, }
@article {pmid26839740, year = {2016}, author = {Coutinho, F and Tschoeke, DA and Thompson, F and Thompson, C}, title = {Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1522}, doi = {10.7717/peerj.1522}, pmid = {26839740}, issn = {2167-8359}, abstract = {Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages.}, }
@article {pmid26754847, year = {2016}, author = {Mosquera-Rendón, J and Rada-Bravo, AM and Cárdenas-Brito, S and Corredor, M and Restrepo-Pineda, E and Benítez-Páez, A}, title = {Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {45}, doi = {10.1186/s12864-016-2364-4}, pmid = {26754847}, issn = {1471-2164}, mesh = {Biofilms/growth &amp; development ; *Evolution, Molecular ; Genome, Bacterial ; Genotype ; Humans ; *Phylogeny ; Pseudomonas Infections/*genetics/microbiology ; Pseudomonas aeruginosa/*genetics/pathogenicity ; }, abstract = {BACKGROUND: Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains.<br><br>RESULTS: The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15 % of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates.<br><br>CONCLUSIONS: We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.}, }
@article {pmid26748339, year = {2016}, author = {Dumas, E and Christina Boritsch, E and Vandenbogaert, M and Rodríguez de la Vega, RC and Thiberge, JM and Caro, V and Gaillard, JL and Heym, B and Girard-Misguich, F and Brosch, R and Sapriel, G}, title = {Mycobacterial Pan-Genome Analysis Suggests Important Role of Plasmids in the Radiation of Type VII Secretion Systems.}, journal = {Genome biology and evolution}, volume = {8}, number = {2}, pages = {387-402}, doi = {10.1093/gbe/evw001}, pmid = {26748339}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Mycobacterium/classification/*genetics ; Phylogeny ; Plasmids/*genetics ; Synteny ; Type IV Secretion Systems/*genetics ; }, abstract = {In mycobacteria, various type VII secretion systems corresponding to different ESX (ESAT-6 secretory) types, are contributing to pathogenicity, iron acquisition, and/or conjugation. In addition to the known chromosomal ESX loci, the existence of plasmid-encoded ESX systems was recently reported. To investigate the potential role of ESX-encoding plasmids on mycobacterial evolution, we analyzed a large representative collection of mycobacterial genomes, including both chromosomal and plasmid-borne sequences. Data obtained for chromosomal ESX loci confirmed the previous five classical ESX types and identified a novel mycobacterial ESX-4-like type, termed ESX-4-bis. Moreover, analysis of the plasmid-encoded ESX loci showed extensive diversification, with at least seven new ESX profiles, identified. Three of them (ESX-P clusters 1-3) were found in multiple plasmids, while four corresponded to singletons. Our phylogenetic and gene-order-analyses revealed two main groups of ESX types: 1) ancestral types, including ESX-4 and ESX-4-like systems from mycobacterial and non-mycobacterial actinobacteria and 2) mycobacteria-specific ESX systems, including ESX-1-2-3-5 systems and the plasmid-encoded ESX types. Synteny analysis revealed that ESX-P systems are part of phylogenetic groups that derived from a common ancestor, which diversified and resulted in the different ESX types through extensive gene rearrangements. A converging body of evidence, derived from composition bias-, phylogenetic-, and synteny analyses points to a scenario in which ESX-encoding plasmids have been a major driving force for acquisition and diversification of type VII systems in mycobacteria, which likely played (and possibly still play) important roles in the adaptation to new environments and hosts during evolution of mycobacterial pathogenesis.}, }
@article {pmid26724943, year = {2016}, author = {Yang, X and Li, Y and Zang, J and Li, Y and Bie, P and Lu, Y and Wu, Q}, title = {Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.}, journal = {Molecular genetics and genomics : MGG}, volume = {291}, number = {2}, pages = {905-912}, doi = {10.1007/s00438-015-1154-z}, pmid = {26724943}, issn = {1617-4623}, mesh = {Animals ; Brucella/*genetics/pathogenicity ; Computational Biology ; Energy Metabolism/*genetics ; Genes, Essential ; *Genome, Bacterial ; Humans ; Zoonoses/*genetics/microbiology ; }, abstract = {Brucella spp. are facultative intracellular pathogens, that cause a contagious zoonotic disease, that can result in such outcomes as abortion or sterility in susceptible animal hosts and grave, debilitating illness in humans. For deciphering the survival mechanism of Brucella spp. in vivo, 42 Brucella complete genomes from NCBI were analyzed for the pan-genome and core genome by identification of their composition and function of Brucella genomes. The results showed that the total 132,143 protein-coding genes in these genomes were divided into 5369 clusters. Among these, 1710 clusters were associated with the core genome, 1182 clusters with strain-specific genes and 2477 clusters with dispensable genomes. COG analysis indicated that 44 % of the core genes were devoted to metabolism, which were mainly responsible for energy production and conversion (COG category C), and amino acid transport and metabolism (COG category E). Meanwhile, approximately 35 % of the core genes were in positive selection. In addition, 1252 potential essential genes were predicted in the core genome by comparison with a prokaryote database of essential genes. The results suggested that the core genes in Brucella genomes are relatively conservation, and the energy and amino acid metabolism play a more important role in the process of growth and reproduction in Brucella spp. This study might help us to better understand the mechanisms of Brucella persistent infection and provide some clues for further exploring the gene modules of the intracellular survival in Brucella spp.}, }
@article {pmid26717500, year = {2015}, author = {Chaves-Moreno, D and Wos-Oxley, ML and Jáuregui, R and Medina, E and Oxley, AP and Pieper, DH}, title = {Application of a Novel &quot;Pan-Genome&quot;-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0145861}, doi = {10.1371/journal.pone.0145861}, pmid = {26717500}, issn = {1932-6203}, mesh = {Computational Biology/methods ; Databases, Nucleic Acid ; Gene Library ; *Genome, Bacterial ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/*genetics ; *Transcriptome ; }, abstract = {Understanding the behaviour of opportunistic pathogens such as Staphylococcus aureus in their natural human niche holds great medical interest. With the development of sensitive molecular methods and deep-sequencing technology, it is now possible to robustly assess the global transcriptome of bacterial species in their human habitat. However, as the genomes of the colonizing strains are often not available compiling the pan-genome for the species of interest may provide an effective method to reliably and rapidly compile the transcriptome of a bacterial species. The pan-genome of S. aureus and its associated core and accessory components were compiled based on 25 genomes and comprises a total of 65,557 proteins clustering into 4,198 Orthologous Groups (OGs). The generated gene catalogue was used to assign RNAseq-derived sequence reads to S. aureus in a variety of in vitro and in vivo samples. In all cases, the number of reads that could be assigned to S. aureus was greater using the OG database than using a reference genome. Growth of two S. aureus strains in synthetic nasal medium confirmed that both strains experienced strong iron starvation. Traits such as purine metabolism appeared to be more affected in a typical nasal colonizer than in a strain representative of the S. aureus USA300 lineage. Mapping sequencing reads from a metatranscriptome generated from the human anterior nares allowed the identification of genes highly expressed by S. aureus in vivo. The OG database generated in this study represents a useful tool to obtain a snapshot of the functional attributes of S. aureus under different in vitro and in vivo conditions. The approach proved to be advantageous to assign sequencing reads to bacterial strains when RNAseq data is derived from samples where strain information and/or the corresponding genome/s are unavailable.}, }
@article {pmid26713670, year = {2016}, author = {Scott, RA and Lindow, SE}, title = {Transcriptional control of quorum sensing and associated metabolic interactions in Pseudomonas syringae strain B728a.}, journal = {Molecular microbiology}, volume = {99}, number = {6}, pages = {1080-1098}, doi = {10.1111/mmi.13289}, pmid = {26713670}, issn = {1365-2958}, mesh = {Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Plant Diseases/microbiology ; Promoter Regions, Genetic ; Pseudomonas syringae/*genetics/*metabolism ; Quorum Sensing/*genetics ; Regulon ; Transcription Factors/genetics/metabolism ; }, abstract = {Pseudomonas syringae pv. syringae cell densities fluctuate regularly during host plant colonization. Previously we identified nine genes dependent on the quorum-sensing-associated luxR homolog ahlR during epiphytic and apoplastic stages of host colonization. Yet their contributions to host colonization remain obscure, despite ahlR regulon presence within and beyond the P. syringae pan-genome. To elucidate AhIR regulon member functions, we characterized their regulation, interactions with each other, and contributions to the metabolome. We report Psyr_1625, encoding a functional pyruvate deydrogenase-E1 subunit PdhQ, is required to prevent the accumulation of pyruvate in rich media. Furthermore it is exquisitely regulated by both repression of its own promoter by QrpR within a novel clade of the MarR regulator family, and co-transcription on a 5kb transcript originating from the AhlR-driven ahlI promoter, that reads over ahlR and qrpR. Metabolites accumulated during expression of the second AhlR-driven operon (Psyr_1620-1616, paoABCDE), only in a pdhQ mutant background, in addition to pyruvate, are herein associated with derepression of QrpR-repressed pdhQ. AHL signaling, QrpR, and transcriptional read-through events integrate to ensure AHL-dependent expression of a novel metabolism in anticipation of environmental stress, while minimizing endogenously generated cytotoxicity.}, }
@article {pmid26659686, year = {2015}, author = {Couger, MB and Hanafy, RA and Mitacek, RM and Budd, C and French, DP and Hoff, WD and Elshahed, MS and Youssef, NH}, title = {The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens.}, journal = {Genome announcements}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/genomeA.01450-15}, pmid = {26659686}, issn = {2169-8287}, abstract = {We report the draft genome sequence of Xanthomonas sp. strain Mitacek01, isolated from an indoor environment vending machine surface with frequent human use in Stillwater, Oklahoma, USA, as part of the Student-Initiated Microbial Discovery project. The genome has a total size of 3,617,426 bp and a contig N50 of 1,906,967 bp.}, }
@article {pmid26657763, year = {2016}, author = {Ngugi, DK and Blom, J and Stepanauskas, R and Stingl, U}, title = {Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines.}, journal = {The ISME journal}, volume = {10}, number = {6}, pages = {1383-1399}, doi = {10.1038/ismej.2015.214}, pmid = {26657763}, issn = {1751-7370}, mesh = {*Adaptation, Physiological ; Bacteria/classification/*genetics/metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Indian Ocean ; Metabolic Networks and Pathways ; *Metagenomics ; Nitrites/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Salts ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine-seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean.}, }
@article {pmid26626322, year = {2015}, author = {Wegmann, U and MacKenzie, DA and Zheng, J and Goesmann, A and Roos, S and Swarbreck, D and Walter, J and Crossman, LC and Juge, N}, title = {The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1023}, doi = {10.1186/s12864-015-2216-7}, pmid = {26626322}, issn = {1471-2164}, support = {BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Secretion Systems/genetics ; Bacteriophages ; Basal Metabolism/genetics ; Chromosomes, Bacterial ; Gastrointestinal Tract/microbiology ; Gene Order ; Gene Transfer, Horizontal ; Genetic Structures ; *Genome, Bacterial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Lactobacillus reuteri/*genetics/isolation &amp; purification/metabolism/virology ; Multigene Family ; Phylogeny ; Pseudogenes ; Swine ; }, abstract = {BACKGROUND: Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown.<br><br>RESULTS: To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity.<br><br>CONCLUSIONS: This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.}, }
@article {pmid26615445, year = {2015}, author = {Goryunov, DV and Nagaev, BE and Nikolaev, MY and Alexeevski, AV and Troitsky, AV}, title = {Moss Phylogeny Reconstruction Using Nucleotide Pangenome of Complete Mitogenome Sequences.}, journal = {Biochemistry. Biokhimiia}, volume = {80}, number = {11}, pages = {1522-1527}, doi = {10.1134/S0006297915110152}, pmid = {26615445}, issn = {1608-3040}, mesh = {Bryophyta/classification/*genetics ; DNA, Mitochondrial/*metabolism ; Databases, Genetic ; Internet ; *Phylogeny ; User-Computer Interface ; }, abstract = {Stability of composition and sequence of genes was shown earlier in 13 mitochondrial genomes of mosses (Rensing, S. A., et al. (2008) Science, 319, 64-69). It is of interest to study the evolution of mitochondrial genomes not only at the gene level, but also on the level of nucleotide sequences. To do this, we have constructed a &quot;nucleotide pangenome&quot; for mitochondrial genomes of 24 moss species. The nucleotide pangenome is a set of aligned nucleotide sequences of orthologous genome fragments covering the totality of all genomes. The nucleotide pangenome was constructed using specially developed new software, NPG-explorer (NPGe). The stable part of the mitochondrial genome (232 stable blocks) is shown to be, on average, 45% of its length. In the joint alignment of stable blocks, 82% of positions are conserved. The phylogenetic tree constructed with the NPGe program is in good correlation with other phylogenetic reconstructions. With the NPGe program, 30 blocks have been identified with repeats no shorter than 50 bp. The maximal length of a block with repeats is 140 bp. Duplications in the mitochondrial genomes of mosses are rare. On average, the genome contains about 500 bp in large duplications. The total length of insertions and deletions was determined in each genome. The losses and gains of DNA regions are rather active in mitochondrial genomes of mosses, and such rearrangements presumably can be used as additional markers in the reconstruction of phylogeny.}, }
@article {pmid26615220, year = {2015}, author = {Brito, AF and Braconi, CT and Weidmann, M and Dilcher, M and Alves, JM and Gruber, A and Zanotto, PM}, title = {The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV).}, journal = {Genome biology and evolution}, volume = {8}, number = {1}, pages = {94-108}, doi = {10.1093/gbe/evv231}, pmid = {26615220}, issn = {1759-6653}, mesh = {Animals ; Baculoviridae/*genetics ; Base Sequence ; *Genome, Viral ; Genomic Instability ; Lepidoptera/*virology ; Molecular Sequence Data ; Open Reading Frames ; Polymorphism, Genetic ; Recombination, Genetic ; Ubiquitins/genetics ; Viral Proteins/genetics ; }, abstract = {The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.}, }
@article {pmid26597042, year = {2015}, author = {de Bruijn, I and Cheng, X and de Jager, V and Expósito, RG and Watrous, J and Patel, N and Postma, J and Dorrestein, PC and Kobayashi, D and Raaijmakers, JM}, title = {Comparative genomics and metabolic profiling of the genus Lysobacter.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {991}, doi = {10.1186/s12864-015-2191-z}, pmid = {26597042}, issn = {1471-2164}, mesh = {*Genomics ; Lysobacter/*genetics/*metabolism/physiology ; *Metabolomics ; Movement ; Multigene Family ; Rhizoctonia/physiology ; }, abstract = {BACKGROUND: Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses.<br><br>RESULTS: Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani.<br><br>CONCLUSIONS: Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.}, }
@article {pmid26593040, year = {2016}, author = {Golicz, AA and Batley, J and Edwards, D}, title = {Towards plant pangenomics.}, journal = {Plant biotechnology journal}, volume = {14}, number = {4}, pages = {1099-1105}, doi = {10.1111/pbi.12499}, pmid = {26593040}, issn = {1467-7652}, mesh = {Arabidopsis/genetics ; *Genome, Plant ; Genomics/*methods ; Soybeans/genetics ; Zea mays/genetics ; }, abstract = {As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.}, }
@article {pmid26585406, year = {2016}, author = {Kanehisa, M and Sato, Y and Morishima, K}, title = {BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences.}, journal = {Journal of molecular biology}, volume = {428}, number = {4}, pages = {726-731}, doi = {10.1016/j.jmb.2015.11.006}, pmid = {26585406}, issn = {1089-8638}, mesh = {Computational Biology/*methods ; *Genome ; Internet ; *Metagenome ; Sequence Analysis, DNA/*methods ; }, abstract = {BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG Web site (http://www.kegg.jp/blastkoala/). In BlastKOALA, the KO assignment is performed by a modified version of the internally used KOALA algorithm after the BLAST search against a non-redundant dataset of pangenome sequences at the species, genus or family level, which is generated from the KEGG GENES database by retaining the KO content of each taxonomic category. In GhostKOALA, which utilizes more rapid GHOSTX for database search and is suitable for metagenome annotation, the pangenome dataset is supplemented with Cd-hit clusters including those for viral genes. The result files may be downloaded and manipulated for further KEGG Mapper analysis, such as comparative pathway analysis using multiple BlastKOALA results.}, }
@article {pmid26578582, year = {2016}, author = {Winsor, GL and Griffiths, EJ and Lo, R and Dhillon, BK and Shay, JA and Brinkman, FS}, title = {Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D646-53}, doi = {10.1093/nar/gkv1227}, pmid = {26578582}, issn = {1362-4962}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacterial Proteins/analysis/chemistry ; *Databases, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Ontology ; *Genome, Bacterial ; Genomic Islands ; Internet ; *Molecular Sequence Annotation ; Pseudomonas/drug effects/*genetics/pathogenicity ; Virulence Factors ; }, abstract = {The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches.}, }
@article {pmid26578556, year = {2016}, author = {Sheppard, TK and Hitz, BC and Engel, SR and Song, G and Balakrishnan, R and Binkley, G and Costanzo, MC and Dalusag, KS and Demeter, J and Hellerstedt, ST and Karra, K and Nash, RS and Paskov, KM and Skrzypek, MS and Weng, S and Wong, ED and Cherry, JM}, title = {The Saccharomyces Genome Database Variant Viewer.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D698-702}, doi = {10.1093/nar/gkv1250}, pmid = {26578556}, issn = {1362-4962}, support = {U41 HG001315/HG/NHGRI NIH HHS/United States ; HG001315/HG/NHGRI NIH HHS/United States ; }, mesh = {*Databases, Genetic ; *Genetic Variation ; *Genome, Fungal ; Molecular Sequence Annotation ; Saccharomyces cerevisiae/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; User-Computer Interface ; }, abstract = {The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-