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16 Jan 2020 at 01:32
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Bibliography on: Pangenome


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RJR: Recommended Bibliography 16 Jan 2020 at 01:32 Created: 


Although the enforced stability of genomic content is ubiquitous among MCEs, the opposite is proving to be the case among prokaryotes, which exhibit remarkable and adaptive plasticity of genomic content. Early bacterial whole-genome sequencing efforts discovered that whenever a particular "species" was re-sequenced, new genes were found that had not been detected earlier — entirely new genes, not merely new alleles. This led to the concepts of the bacterial core-genome, the set of genes found in all members of a particular "species", and the flex-genome, the set of genes found in some, but not all members of the "species". Together these make up the species' pan-genome.

Created with PubMed® Query: pangenome or "pan-genome" or "pan genome" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2020-01-14

Nakamura K, Murase K, Sato MP, et al (2020)

Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28.

Microbial genomics [Epub ahead of print].

Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing Escherichia coli O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of stx genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.

RevDate: 2020-01-14

Tetz VV, GV Tetz (2020)

A new biological definition of life.

Biomolecular concepts, 11(1):1-6 pii:/j/bmc.2020.11.issue-1/bmc-2020-0001/bmc-2020-0001.xml.

Here we have proposed a new biological definition of life based on the function and reproduction of existing genes and creation of new ones, which is applicable to both unicellular and multicellular organisms. First, we coined a new term "genetic information metabolism" comprising functioning, reproduction, and creation of genes and their distribution among living and non-living carriers of genetic information. Encompassing this concept, life is defined as organized matter that provides genetic information metabolism. Additionally, we have articulated the general biological function of life as Tetz biological law: "General biological function of life is to provide genetic information metabolism" and formulated novel definition of life: "Life is an organized matter that provides genetic information metabolism". New definition of life and Tetz biological law allow to distinguish in a new way living and non-living objects on Earth and other planets based on providing genetic information metabolism.

RevDate: 2020-01-14

Song JM, Guan Z, Hu J, et al (2020)

Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus.

Nature plants pii:10.1038/s41477-019-0577-7 [Epub ahead of print].

Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2-149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.

RevDate: 2020-01-11

Zhang B, Zhu W, Diao S, et al (2019)

The poplar pangenome provides insights into the evolutionary history of the genus.

Communications biology, 2(1):215 pii:10.1038/s42003-019-0474-7.

The genus Populus comprises a complex amalgam of ancient and modern species that has become a prime model for evolutionary and taxonomic studies. Here we sequenced the genomes of 10 species from five sections of the genus Populus, identified 71 million genomic variations, and observed new correlations between the single-nucleotide polymorphism-structural variation (SNP-SV) density and indel-SV density to complement the SNP-indel density correlation reported in mammals. Disease resistance genes (R genes) with heterozygous loss-of-function (LOF) were significantly enriched in the 10 species, which increased the diversity of poplar R genes during evolution. Heterozygous LOF mutations in the self-incompatibility genes were closely related to the self-fertilization of poplar, suggestive of genomic control of self-fertilization in dioecious plants. The phylogenetic genome-wide SNPs tree also showed possible ancient hybridization among species in sections Tacamahaca, Aigeiros, and Leucoides. The pangenome resource also provided information for poplar genetics and breeding.

RevDate: 2020-01-11

Jaiswal AK, Tiwari S, Jamal SB, et al (2020)

The pan-genome of Treponema pallidum reveals differences in genome plasticity between subspecies related to venereal and non-venereal syphilis.

BMC genomics, 21(1):33 pii:10.1186/s12864-019-6430-6.

BACKGROUND: Spirochetal organisms of the Treponema genus are responsible for causing Treponematoses. Pathogenic treponemes is a Gram-negative, motile, spirochete pathogen that causes syphilis in human. Treponema pallidum subsp. endemicum (TEN) causes endemic syphilis (bejel); T. pallidum subsp. pallidum (TPA) causes venereal syphilis; T. pallidum subsp. pertenue (TPE) causes yaws; and T. pallidum subsp. Ccarateum causes pinta. Out of these four high morbidity diseases, venereal syphilis is mediated by sexual contact; the other three diseases are transmitted by close personal contact. The global distribution of syphilis is alarming and there is an increasing need of proper treatment and preventive measures. Unfortunately, effective measures are limited.

RESULTS: Here, the genome sequences of 53 T. pallidum strains isolated from different parts of the world and a diverse range of hosts were comparatively analysed using pan-genomic strategy. Phylogenomic, pan-genomic, core genomic and singleton analysis disclosed the close connection among all strains of the pathogen T. pallidum, its clonal behaviour and showed increases in the sizes of the pan-genome. Based on the genome plasticity analysis of the subsets containing the subspecies T pallidum subsp. pallidum, T. pallidum subsp. endemicum and T. pallidum subsp. pertenue, we found differences in the presence/absence of pathogenicity islands (PAIs) and genomic islands (GIs) on subsp.-based study.

CONCLUSIONS: In summary, we identified four pathogenicity islands (PAIs), eight genomic islands (GIs) in subsp. pallidum, whereas subsp. endemicum has three PAIs and seven GIs and subsp. pertenue harbours three PAIs and eight GIs. Concerning the presence of genes in PAIs and GIs, we found some genes related to lipid and amino acid biosynthesis that were only present in the subsp. of T. pallidum, compared to T. pallidum subsp. endemicum and T. pallidum subsp. pertenue.

RevDate: 2020-01-09

Nguyen ST, Ngoc HM, Nhat LD, et al (2020)

Genomic features, whole-genome phylogenetic and comparative genomic analysis of extreme-drug-resistant ventilator-associated-pneumonia Acinetobacter baumannii strain in a Vietnam hospital.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases pii:S1567-1348(20)30010-1 [Epub ahead of print].

OBJECTIVES: Acinetobacter baumannii is a major cause of ventilator-associated-pneumonia (VAP) worldwide due to its impressive propensity to rapidly acquire resistance elements to a wide range of antibacterial agents. We sought to explore the genomic features of this pathogen from a sputum specimen of a VAP male patient.

METHODS: Whole genome analysis of A. baumannii DMS06670 included de novo assembly; functional annotation, whole-genome-phylogenetic analysis, antibiotics genes identification, prophage regions, virulent factor and pan-genome analysis.

RESULTS: Assembly of whole-genome shotgun sequences of strain DMS06670 yielded an estimated genome size of 3.8 Mb with Sequence Type 447. Functional annotation and orthologous protein cluster analysis identified several potential antibiotic resistance genes was conducted (with 1 novel gene), prophage regions, virulent factors. The clusters of orthologous groups (COGs) analysis in protein sequence of the A. baumannii strain was compared with the other five genomes showed that the orthologous protein clusters responsible for multi-drug exist inside highly antimicrobial resistant strains. Whole-genome phylogenetic and in silico MLST analysis revealed that this A. baumannii strain is in the same clade as strains LAC-4 and BJAB0715. Comparative analysis of 23 available genomes of A. baumannii revealed a pan-genome consisting of 15,883 genes.

CONCLUSION: Our findings provide insight into the virulence-associated genes and then compared with the genomes of other A. baumannii strains by calculation of ANI values and pan-genome analysis. Functional studies of these pathogens are required to validate these findings.

RevDate: 2020-01-09

Rodriguez CI, JBH Martiny (2020)

Evolutionary relationships among bifidobacteria and their hosts and environments.

BMC genomics, 21(1):26 pii:10.1186/s12864-019-6435-1.

BACKGROUND: The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates.

RESULTS: We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes).

CONCLUSIONS: Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources. However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.

RevDate: 2020-01-03

Teijeiro RG, Belimov AA, IC Dodd (2019)

Microbial inoculum development for ameliorating crop drought stress: a case study of Variovorax paradoxus 5C-2.

New biotechnology pii:S1871-6784(19)30008-1 [Epub ahead of print].

Drought affects plant hormonal homeostasis, including root to shoot signalling. The plant is intimately connected below-ground with soil-dwelling microbes, including plant growth promoting rhizobacteria (PGPR) that can modulate plant hormonal homeostasis. Incorporating PGPR into the rhizosphere often delivers favourable results in greenhouse experiments, while field applications are much less predictable. We review the natural processes that affect the formation and dynamics of the rhizosphere, establishing a model for successful field application of PGPR utilizing an example microbial inoculum, Variovorax paradoxus 5C-2.

RevDate: 2020-01-03

Rasheed A, Takumi S, Hassan MA, et al (2020)

Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik pii:10.1007/s00122-019-03523-w [Epub ahead of print].

KEY MESSAGE: We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.

RevDate: 2020-01-03

Sulthana A, Lakshmi SG, RS Madempudi (2019)

High-quality draft genome and characterization of commercially potent probiotic Lactobacillus strains.

Genomics & informatics, 17(4):e43.

Lactobacillus acidophilus UBLA-34, L. paracasei UBLPC-35, L. plantarum UBLP-40, and L. reuteri UBLRU-87 were isolated from different varieties of fermented foods. To determine the probiotic safety at the strain level, the whole genome of the respective strains was sequenced, assembled, and characterized. Both the core-genome and pan-genome phylogeny showed that L. reuteri was closest to L. plantarum than to L. acidophilus, which was closest to L. paracasei. The genomic analysis of all the strains confirmed the absence of genes encoding putative virulence factors, antibiotic resistance, and the plasmids.

RevDate: 2020-01-01

Hu H, Yuan Y, Bayer PE, et al (2020)

Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach.

Methods in molecular biology (Clifton, N.J.), 2107:35-47.

A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows for comprehensive, species-wide characterization of genetic variations and mining of variable genes which may play important roles in phenotypes of interest. Recent advances in sequencing technologies have facilitated draft genome sequence construction and have made pangenome constructions feasible. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.

RevDate: 2019-12-31

Kim Y, Gu C, Kim HU, et al (2019)

Current status of pan-genome analysis for pathogenic bacteria.

Current opinion in biotechnology, 63:54-62 pii:S0958-1669(19)30138-7 [Epub ahead of print].

Biological knowledge accumulated over the decades and advances in computational methods have facilitated the implementation of pan-genome analysis that aims at better understanding of genotype-phenotype associations of a specific group of organisms. Pan-genome analysis has been shown to be an effective approach to better understand a clade of pathogenic bacteria because it helps developing various and tailored therapeutic strategies on the basis of their biological similarities and differences. Here, we review recent progress in the pan-genome analysis of pathogenic bacteria. In particular, we focus on computational tools that allow streamlined pan-genome analysis. Also, various applications of pan-genome analysis including those relevant to devising strategies for the prevention and treatment of pathogenic bacteria are reviewed.

RevDate: 2019-12-30

Coutinho FH, Edwards RA, F Rodríguez-Valera (2019)

Charting the diversity of uncultured viruses of Archaea and Bacteria.

BMC biology, 17(1):109 pii:10.1186/s12915-019-0723-8.

BACKGROUND: Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on the unknown viral diversity, revealing thousands of new viral nucleotide sequences at an unprecedented scale. However, these novel sequences have not been properly classified and the evolutionary associations between them were not resolved.

RESULTS: Here, we performed phylogenomic analysis of nearly 200,000 viral nucleotide sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. The pan-genome content of the identified lineages shed light on some of their infection strategies, potential to modulate host physiology, and mechanisms to escape host resistance systems. Furthermore, using GL-UVAB as a reference database for annotating metagenomes revealed elusive habitat distribution patterns of viral lineages and environmental drivers of community composition.

CONCLUSIONS: These findings provide insights about the genomic diversity and ecology of viruses of prokaryotes. The source code used in these analyses is freely available at https://sourceforge.net/projects/gluvab/.

RevDate: 2019-12-28

Golicz AA, Bayer PE, Bhalla PL, et al (2019)

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications.

Trends in genetics : TIG pii:S0168-9525(19)30246-X [Epub ahead of print].

The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities.

RevDate: 2019-12-28

Lee IPA, CP Andam (2019)

Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle.

BMC microbiology, 19(1):306 pii:10.1186/s12866-019-1664-7.

BACKGROUND: Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources.

RESULTS: The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production.

CONCLUSIONS: Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.

RevDate: 2019-12-24

Wang Y, Luo L, Li Q, et al (2019)

Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China.

BMC genomics, 20(1):1014 pii:10.1186/s12864-019-6399-1.

BACKGROUND: Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food products, food associated environments and sporadic listeriosis in China. Here, we performed a comparative genomic analysis of the L. monocytogenes ST87 clone by sequencing 71 strains representing a diverse range of sources, different geographical locations and isolation years.

RESULTS: The core genome and pan genome of ST87 contained 2667 genes and 3687 genes respectively. Phylogenetic analysis based on core genome SNPs divided the 71 strains into 10 clades. The clinical strains were distributed among multiple clades. Four clades contained strains from multiple geographic regions and showed high genetic diversity. The major gene content variation of ST87 genomes was due to putative prophages, with eleven hotspots of the genome that harbor prophages. All strains carry an intact CRISRP/Cas system. Two major CRISPR spacer profiles were found which were not clustered phylogenetically. A large plasmid of about 90 Kb, which carried heavy metal resistance genes, was found in 32.4% (23/71) of the strains. All ST87 strains harbored the Listeria pathogenicity island (LIPI)-4 and a unique 10-open read frame (ORF) genomic island containing a novel restriction-modification system.

CONCLUSION: Whole genome sequence analysis of L. monocytogenes ST87 enabled a clearer understanding of the population structure and the evolutionary history of ST87 L. monocytogenes in China. The novel genetic elements identified may contribute to its virulence and adaptation to different environmental niches. Our findings will be useful for the development of effective strategies for the prevention and treatment of listeriosis caused by this prevalent clone.

RevDate: 2019-12-21

Albert K, Rani A, DA Sela (2019)

Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum.

Microorganisms, 8(1): pii:microorganisms8010007.

Bifidobacterium longum colonizes mammalian gastrointestinal tracts where it could metabolize host-indigestible oligosaccharides. Although B. longum strains are currently segregated into three subspecies that reflect common metabolic capacities and genetic similarity, heterogeneity within subspecies suggests that these taxonomic boundaries may not be completely resolved. To address this, the B. longum pangenome was analyzed from representative strains isolated from a diverse set of sources. As a result, the B. longum pangenome is open and contains almost 17,000 genes, with over 85% of genes found in ≤28 of 191 strains. B. longum genomes share a small core gene set of only ~500 genes, or ~3% of the total pangenome. Although the individual B. longum subspecies pangenomes share similar relative abundances of clusters of orthologous groups, strains show inter- and intrasubspecies differences with respect to carbohydrate utilization gene content and growth phenotypes.

RevDate: 2019-12-18

Sitto F, FU Battistuzzi (2019)

Estimating PanGenomes with Roary.

Molecular biology and evolution pii:5652084 [Epub ahead of print].

A description of the genetic make-up of a species based on a single genome is often insufficient because it ignores the variability in gene repertoire among multiple strains. The estimation of the pangenome of a species is a solution to this issue as it provides an overview of genes that are shared by all strains and genes that are present in only some of the genomes. These different sets of genes can then be analyzed functionally to explore correlations with unique phenotypes and adaptations. This protocol presents the usage of Roary, a Linux-native pangenome application. Roary is a straightforward software that provides (i) an overview about core and accessory genes for those interested in general trends and, also, (ii) detailed information on gene presence/absence in each genome for in-depth analyses. Results are provided both in text and graphic format.

RevDate: 2019-12-18

Heo S, Lee JS, Lee JH, et al (2019)

Comparative genomic analysis of food-originated coagulase-negative Staphylococcus: Analysis of conserved core genes and diversity of the pan-genome.

Journal of microbiology and biotechnology pii:10.4014/jmb.1910.10049 [Epub ahead of print].

To shed light on the genetic differences among food-originated coagulase-negative Staphylococcus (CNS), we performed pan-genome analysis of five species: Staphylococcus carnosus (two strains), Staphylococcus equorum (two strains), Staphylococcus succinus (three strains), Staphylococcus xylosus (two strains), and Staphylococcus saprophyticus (one strain). The pan-genome size increases with each new strain and currently holds about 4,500 genes from 10 genomes. Specific genes were shown to be strain dependent but not species dependent. Most specific genes were of unknown function or encoded restriction31 modification enzymes, transposases, or prophages. Our results indicate that unique genes have been acquired or lost by convergent evolution within individual strains.

RevDate: 2019-12-17

Liang CY, Yang CH, Lai CH, et al (2019)

Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence.

Scientific reports, 9(1):19167 pii:10.1038/s41598-019-55795-3.

Bacteria of the genus Elizabethkingia are emerging infectious agents that can cause infection in humans. The number of published whole-genome sequences of Elizabethkingia is rapidly increasing. In this study, we used comparative genomics to investigate the genomes of the six species in the Elizabethkingia genus, namely E. meningoseptica, E. anophelis, E. miricola, E. bruuniana, E. ursingii, and E. occulta. In silico DNA-DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, and clusters of orthologous groups were evaluated. Of the 86 whole-genome sequences available in GenBank, 21 were complete genome sequences and 65 were shotgun sequences. In silico DNA-DNA hybridization clearly delineated the six Elizabethkingia species. Phylogenetic analysis confirmed that E. bruuniana, E. ursingii, and E. occulta were closer to E. miricola than to E. meningoseptica and E. anophelis. A total of 2,609 clusters of orthologous groups were identified among the six type strains of the Elizabethkingia genus. Metabolism-related clusters of orthologous groups accounted for the majority of gene families in KEGG analysis. New genes were identified that substantially increased the total repertoire of the pan genome after the addition of 86 Elizabethkingia genomes, which suggests that Elizabethkingia has shown adaptive evolution to environmental change. This study presents a comparative genomic analysis of Elizabethkingia, and the results of this study provide knowledge that facilitates a better understanding of this microorganism.

RevDate: 2019-12-17

D'Mello A, Ahearn CP, Murphy TF, et al (2019)

ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates.

BMC genomics, 20(1):981 pii:10.1186/s12864-019-6195-y.

BACKGROUND: Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering architecture using feature prediction programs or a machine learning approach. Filtering approaches may eliminate potential antigens based on limitations in the accuracy of prediction tools used. Machine learning approaches are heavily dependent on the selection of training datasets with experimentally validated antigens (positive control) and non-protective-antigens (negative control). The use of one or few bacterial proteomes does not assess PVC conservation among strains, an important feature of vaccine antigens.

RESULTS: We present ReVac, which implements both a panoply of feature prediction programs without filtering out proteins, and scoring of candidates based on predictions made on curated positive and negative control PVCs datasets. ReVac surveys several genomes assessing protein conservation, as well as DNA and protein repeats, which may result in variable expression of PVCs. ReVac's orthologous clustering of conserved genes, identifies core and dispensable genome components. This is useful for determining the degree of conservation of PVCs among the population of isolates for a given pathogen. Potential vaccine candidates are then prioritized based on conservation and overall feature-based scoring. We present the application of ReVac, applied to 69 Moraxella catarrhalis and 270 non-typeable Haemophilus influenzae genomes, prioritizing 64 and 29 proteins as PVCs, respectively.

CONCLUSION: ReVac's use of a scoring scheme ranks PVCs for subsequent experimental testing. It employs a redundancy-based approach in its predictions of features using several prediction tools. The protein's features are collated, and each protein is ranked based on the scoring scheme. Multi-genome analyses performed in ReVac allow for a comprehensive overview of PVCs from a pan-genome perspective, as an essential pre-requisite for any bacterial subunit vaccine design. ReVac prioritized PVCs of two human respiratory pathogens, identifying both novel and previously validated PVCs.

RevDate: 2019-12-16

Haro-Moreno JM, Rodriguez-Valera F, Rosselli R, et al (2019)

Ecogenomics of the SAR11 clade.

Environmental microbiology [Epub ahead of print].

Members of the SAR11 clade, despite their high abundance, are often poorly represented by MAGs. This fact has hampered our knowledge about their ecology and genetic diversity. Here we examined 175 SAR11 genomes, including 47 new single-amplified genomes (SAGs). The presence of the first genomes associated with subclade IV suggests that, in the same way as subclade V, they might be outside the proposed Pelagibacterales order. An expanded phylogenomic classification together with patterns of metagenomic recruitment at a global scale have allowed us to define new ecogenomic units of classification (genomospecies), appearing at different, and sometimes restricted, metagenomic datasets. We detected greater microdiversity across the water column at a single location than in samples collected from similar depth across the global ocean, suggesting little influence of biogeography. In addition, pangenome analysis revealed that the flexible genome was essential to shape genomospecies distribution. In one genomospecies preferentially found within the Mediterranean, a set of genes involved in phosphonate utilisation was detected. While another, with a more cosmopolitan distribution, was unique in having an aerobic purine degradation pathway. Together, these results provide a glimpse of the enormous genomic diversity within this clade at a finer resolution than the currently defined clades. This article is protected by copyright. All rights reserved.

RevDate: 2019-12-15

Choi JY, Kim SC, PC Lee (2019)

Comparative genome analysis of Psychrobacillus strain PB01, isolated from an iceberg.

Journal of microbiology and biotechnology pii:10.4014/jmb.1909.09008 [Epub ahead of print].

A novel psychrotolerant Psychrobacillus strain PB01, isolated from an Antarctic iceberg, was comparatively analyzed with five related strains. The complete genome of strain PB01 consists of a single circular chromosome (4.3 Mbp) and a plasmid (19 Kbp). As potential low temperature adaption strategies strain PB01 has four genes encoding cold-shock proteins, two genes encoding DEAD-box RNA helicases, and eight genes encoding transporters for glycine betaine, which can serve as a cryoprotectant, on the genome. The pan-genome structure of the six Psychrobacillus strains suggest that strain PB01 might evolve to adapt to extreme environments by changing genome content such as high capacity for DNA repair, translation, and membrane transporter. Notably, strain PB01 possess a complete TCA cycle consisting of eight enzymes as well as additional Helicobacter pylori type three enzymes: ferredoxin-dependent 2-oxoglutarate synthase, succinyl-CoA/acetoacetyl-CoA transferase, and malate/quinone oxidoreductase. The co-existence of the genes for TCA cycle enzymes are also identified in the other five Psychrobacillus strains.

RevDate: 2019-12-11

Lee BH, Cole S, Badel-Berchoux S, et al (2019)

Biofilm Formation of Listeria monocytogenes Strains Under Food Processing Environments and Pan-Genome-Wide Association Study.

Frontiers in microbiology, 10:2698.

Concerns about food contamination by Listeria monocytogenes are on the rise with increasing consumption of ready-to-eat foods. Biofilm production of L. monocytogenes is presumed to be one of the ways that confer its increased resistance and persistence in the food chain. In this study, a collection of isolates from foods and food processing environments (FPEs) representing persistent, prevalent, and rarely detected genotypes was evaluated for biofilm forming capacities including adhesion and sessile biomass production under diverse environmental conditions. The quantity of sessile biomass varied according to growth conditions, lineage, serotype as well as genotype but association of clonal complex (CC) 26 genotype with biofilm production was evidenced under cold temperature. In general, relative biofilm productivity of each strain varied inconsistently across growth conditions. Under our experimental conditions, there were no clear associations between biofilm formation efficiency and persistent or prevalent genotypes. Distinct extrinsic factors affected specific steps of biofilm formation. Sudden nutrient deprivation enhanced cellular adhesion while a prolonged nutrient deficiency impeded biofilm maturation. Salt addition increased biofilm production, moreover, nutrient limitation supplemented by salt significantly stimulated biofilm formation. Pan-genome-wide association study (Pan-GWAS) assessed genetic composition with regard to biofilm phenotypes for the first time. The number of reported genes differed depending on the growth conditions and the number of common genes was low. However, a broad overview of the ontology contents revealed similar patterns regardless of the conditions. Functional analysis showed that functions related to transformation/competence and surface proteins including Internalins were highly enriched.

RevDate: 2019-12-09

Jandrasits C, Kröger S, Haas W, et al (2019)

Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.

PLoS computational biology, 15(12):e1007527 pii:PCOMPBIOL-D-19-00340 [Epub ahead of print].

Next-generation sequencing based base-by-base distance measures have become an integral complement to epidemiological investigation of infectious disease outbreaks. This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differences between cases, even when located in regions of lineage specific reference genomes. We show that our approach is superior to previously published methods in several datasets and across different Mycobacterium tuberculosis lineages, as its characteristics allow the comparison of a high number of diverse samples in one analysis-a scenario that becomes more and more likely with the increased usage of whole-genome sequencing in transmission surveillance.

RevDate: 2019-12-05

Emery A, Marpaux N, Naegelen C, et al (2019)

Genotypic study of Citrobacter koseri, an emergent platelet contaminant since 2012 in France.

Transfusion [Epub ahead of print].

BACKGROUND: Transfusion-transmitted bacterial infection is a rare occurrence but the most feared complication in transfusion practices. Between 2012 and 2017, five cases of platelet concentrates (PCs) contaminated with the bacterial pathogen Citrobacter koseri (PC-Ck) have been reported in France, with two leading to the death of the recipients. We tested the possibilities of the emergence of a PC-specific clone of C. koseri (Ck) and of specific bacterial genes associated with PC contamination.

STUDY DESIGN AND METHODS: The phylogenetic network, based on a homemade Ck core genome scheme, inferred from the genomes of 20 worldwide Ck isolates unrelated to PC contamination taken as controls (U-Ck) and the genomes of the five PC-Ck, explored the clonal relationship between the genomes and evaluated the distribution of PC-Ck throughout the species. Along with this core genome multilocus sequence typing approach, a Ck pan genome has been used to seek genes specific to PC-Ck isolates.

RESULTS: Our genomic approach suggested that the population of C. koseri is nonclonal, although it also identified a cluster containing three PC-Ck and eight U-Ck. Indeed, the PC-Ck did not share any specific genes.

CONCLUSION: The elevated incidence of PCs contaminated by C. koseri in France between 2012 and 2017 was not due to the dissemination of a clone. The determinants of the recent outbreaks of PC contamination with C. koseri are still unknown.

RevDate: 2019-12-09

Li R, Fu W, Su R, et al (2019)

Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome.

Frontiers in genetics, 10:1169.

It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock. However, the rich diversity of worldwide goat breeds indicates that a genome from one individual would be insufficient to represent the whole genomic contents of goats. By comparing nine de novo assemblies from seven sibling species of domestic goat with ARS1 and using resequencing and transcriptome data from goats for verification, we identified a total of 38.3 Mb sequences that were absent in ARS1. The pan-sequences contain genic fractions with considerable expression. Using the pan-genome (ARS1 together with the pan-sequences) as a reference genome, variation calling efficacy can be appreciably improved. A total of 56,657 spurious SNPs per individual were repressed and 24,414 novel SNPs per individual on average were recovered as a result of better reads mapping quality. The transcriptomic mapping rate was also increased by ∼1.15%. Our study demonstrated that comparing de novo assemblies from closely related species is an efficient and reliable strategy for finding missing sequences from the reference genome and could be applicable to other species. Pan-genome can serve as an improved reference genome in animals for a better exploration of the underlying genomic variations and could increase the probability of finding genotype-phenotype associations assessed by a comprehensive variation database containing much more differences between individuals. We have constructed a goat pan-genome web interface for data visualization (http://animal.nwsuaf.edu.cn/panGoat).

RevDate: 2019-12-04

Sutton D, Livingstone PG, Furness E, et al (2019)

Genome-Wide Identification of Myxobacterial Predation Genes and Demonstration of Formaldehyde Secretion as a Potentially Predation-Resistant Trait of Pseudomonas aeruginosa.

Frontiers in microbiology, 10:2650.

Despite widespread use in human biology, genome-wide association studies (GWAS) of bacteria are few and have, to date, focused primarily on pathogens. Myxobacteria are predatory microbes with large patchwork genomes, with individual strains secreting unique cocktails of predatory proteins and metabolites. We investigated whether a GWAS strategy could be applied to myxobacteria to identify genes associated with predation. Deduced proteomes from 29 myxobacterial genomes (including eight Myxococcus genomes sequenced for this study), were clustered into orthologous groups, and the presence/absence of orthologues assessed in superior and inferior predators of ten prey organisms. 139 'predation genes' were identified as being associated significantly with predation, including some whose annotation suggested a testable predatory mechanism. Formaldehyde dismutase (fdm) was associated with superior predation of Pseudomonas aeruginosa, and predatory activity of a strain lacking fdm could be increased by the exogenous addition of a formaldehyde detoxifying enzyme, suggesting that production of formaldehyde by P. aeruginosa acts as an anti-predation behaviour. This study establishes the utility of bacterial GWAS to investigate microbial processes beyond pathogenesis, giving plausible and verifiable associations between gene presence/absence and predatory phenotype. We propose that the slow growth rate of myxobacteria, coupled with their predatory mechanism of constitutive secretion, has rendered them relatively resistant to genome streamlining. The resultant genome expansion made possible their observed accumulation of prey-specific predatory genes, without requiring them to be selected for by frequent or recent predation on diverse prey, potentially explaining both the large pan-genome and broad prey range of myxobacteria.

RevDate: 2019-12-13

Yuan J, Li YY, Xu Y, et al (2019)

Molecular Signatures Related to the Virulence of Bacillus cereus Sensu Lato, a Leading Cause of Devastating Endophthalmitis.

mSystems, 4(6): pii:4/6/e00745-19.

Bacillus endophthalmitis is a devastating eye infection that causes rapid blindness through extracellular tissue-destructive exotoxins. Despite its importance, knowledge of the phylogenetic relationships and population structure of intraocular Bacillus spp. is lacking. In this study, we sequenced the whole genomes of eight Bacillus intraocular pathogens independently isolated from 8/52 patients with posttraumatic Bacillus endophthalmitis infections in the Eye Hospital of Wenzhou Medical University between January 2010 and December 2018. Phylogenetic analysis revealed that the pathogenic intraocular isolates belonged to Bacillus cereus, Bacillus thuringiensis and Bacillus toyonensis To determine the virulence of the ocular isolates, three representative strains were injected into mouse models, and severe endophthalmitis leading to blindness was observed. Through incorporating publicly available genomes for Bacillus spp., we found that the intraocular pathogens could be isolated independently but displayed a similar genetic context. In addition, our data provide genome-wide support for intraocular and gastrointestinal sources of Bacillus spp. belonging to different lineages. Importantly, we identified five molecular signatures of virulence and motility genes associated with intraocular infection, namely, plcA-2, InhA-3, InhA-4, hblA-5, and fliD using pangenome-wide association studies. The characterization of overrepresented genes in the intraocular isolates holds value to predict bacterial evolution and for the design of future intervention strategies in patients with endophthalmitis.IMPORTANCE In this study, we provided a detailed and comprehensive clinicopathological and pathogenic report of Bacillus endophthalmitis over the 8 years of the study period. We first reported the whole-genome sequence of Bacillus spp. causing devastating endophthalmitis and found that Bacillus toyonensis is able to cause endophthalmitis. Finally, we revealed significant endophthalmitis-associated virulence genes involved in hemolysis, immunity inhibition, and pathogenesis. Overall, as more sequencing data sets become available, these data will facilitate comparative research and will reveal the emergence of pathogenic "ocular bacteria."

RevDate: 2019-12-02

Khan AW, Garg V, Roorkiwal M, et al (2019)

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement.

Trends in plant science pii:S1360-1385(19)30281-X [Epub ahead of print].

The pangenome provides genomic variations in the cultivated gene pool for a given species. However, as the crop's gene pool comprises many species, especially wild relatives with diverse genetic stock, here we suggest using accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which we refer to as a super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement. This opinion article focuses on recent developments in crop pangenomics, the need for a super-pangenome that should include wild species, and its application for crop improvement.

RevDate: 2019-12-06

Chaudhry V, PB Patil (2019)

Evolutionary insights into adaptation of Staphylococcus haemolyticus to human and non-human niches.

Genomics pii:S0888-7543(19)30804-3 [Epub ahead of print].

Staphylococcus haemolyticus is a well-known member of human skin microbiome and an emerging opportunistic human pathogen. Presently, evolutionary studies are limited to human isolates even though it is reported from plants with beneficial properties and in environmental settings. In the present study, we report isolation of novel S. haemolyticus strains from surface sterilized rice seeds and compare their genome to other isolates from diverse niches available in public domain. The study showed expanding nature of pan-genome and revealed set of genes with putative functions related to its adaptability. This is seen by presence of type II lanthipeptide cluster in rice isolates, metal homeostasis genes in an isolate from copper coin and gene encoding methicillin resistance in human isolates. The present study on differential genome dynamics and role of horizontal gene transfers has provided novel insights into capability for ecological diversification of a bacterium of significance to human health.

RevDate: 2019-12-01

Peeters C, De Canck E, Cnockaert M, et al (2019)

Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism.

Frontiers in microbiology, 10:2556.

Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The gyrB, recA, and gltB phylogenetic trees were used to select 27 strains for whole-genome sequence analysis and for a comparative genomics study that also included 41 publicly available Pandoraea genome sequences. The phylogenomic analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise digital DNA-DNA hybridization values and their confidence intervals, average nucleotide identity analyses using the OrthoANIu algorithm, and a whole-genome phylogeny reconstruction based on 107 single-copy core genes using bcgTree. These analyses, along with subsequent chemotaxonomic and traditional phenotypic analyses, revealed the presence of 17 novel Pandoraea species among the strains analyzed, and allowed the identification of several unclassified Pandoraea strains reported in the literature. The genus Pandoraea has an open pan genome that includes many orthogroups in the 'Xenobiotics biodegradation and metabolism' KEGG pathway, which likely explains the enrichment of these species in polluted soils and participation in the biodegradation of complex organic substances. We propose to formally classify the 17 novel Pandoraea species as P. anapnoica sp. nov. (type strain LMG 31117T = CCUG 73385T), P. anhela sp. nov. (type strain LMG 31108T = CCUG 73386T), P. aquatica sp. nov. (type strain LMG 31011T = CCUG 73384T), P. bronchicola sp. nov. (type strain LMG 20603T = ATCC BAA-110T), P. capi sp. nov. (type strain LMG 20602T = ATCC BAA-109T), P. captiosa sp. nov. (type strain LMG 31118T = CCUG 73387T), P. cepalis sp. nov. (type strain LMG 31106T = CCUG 39680T), P. commovens sp. nov. (type strain LMG 31010T = CCUG 73378T), P. communis sp. nov. (type strain LMG 31110T = CCUG 73383T), P. eparura sp. nov. (type strain LMG 31012T = CCUG 73380T), P. horticolens sp. nov. (type strain LMG 31112T = CCUG 73379T), P. iniqua sp. nov. (type strain LMG 31009T = CCUG 73377T), P. morbifera sp. nov. (type strain LMG 31116T = CCUG 73389T), P. nosoerga sp. nov. (type strain LMG 31109T = CCUG 73390T), P. pneumonica sp. nov. (type strain LMG 31114T = CCUG 73388T), P. soli sp. nov. (type strain LMG 31014T = CCUG 73382T), and P. terrigena sp. nov. (type strain LMG 31013T = CCUG 73381T).

RevDate: 2019-11-28

Lupolova N, Lycett SJ, DL Gally (2019)

A guide to machine learning for bacterial host attribution using genome sequence data.

Microbial genomics [Epub ahead of print].

With the ever-expanding number of available sequences from bacterial genomes, and the expectation that this data type will be the primary one generated from both diagnostic and research laboratories for the foreseeable future, then there is both an opportunity and a need to evaluate how effectively computational approaches can be used within bacterial genomics to predict and understand complex phenotypes, such as pathogenic potential and host source. This article applied various quantitative methods such as diversity indexes, pangenome-wide association studies (GWAS) and dimensionality reduction techniques to better understand the data and then compared how well unsupervised and supervised machine learning (ML) methods could predict the source host of the isolates. The study uses the example of the pangenomes of 1203 Salmonella enterica serovar Typhimurium isolates in order to predict 'host of isolation' using these different methods. The article is aimed as a review of recent applications of ML in infection biology, but also, by working through this specific dataset, it allows discussion of the advantages and drawbacks of the different techniques. As with all such sub-population studies, the biological relevance will be dependent on the quality and diversity of the input data. Given this major caveat, we show that supervised ML has the potential to add real value to interpretation of bacterial genomic data, as it can provide probabilistic outcomes for important phenotypes, something that is very difficult to achieve with the other methods.

RevDate: 2019-12-13

Eggertsson HP, Kristmundsdottir S, Beyter D, et al (2019)

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs.

Nature communications, 10(1):5402.

Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.

RevDate: 2019-12-13

Chernysheva N, Bystritskaya E, Stenkova A, et al (2019)

Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T.

Marine drugs, 17(12): pii:md17120661.

We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.

RevDate: 2019-11-28

Cabrera-Contreras R, Santamaría RI, Bustos P, et al (2019)

Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children's Hospital in México City in an eight-years survey.

PeerJ, 7:e8068.

Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children's health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.

RevDate: 2019-11-28

Sujitha S, Vishnu US, Karthikeyan R, et al (2019)

Genome Investigation of a Cariogenic Pathogen with Implications in Cardiovascular Diseases.

Indian journal of microbiology, 59(4):451-459.

The proportion of people suffering from cardiovascular diseases has risen by 34% in the last 15 years in India. Cardiomyopathy is among the many forms of CVD s present. Infection of heart muscles is the suspected etiological agent for the same. Oral pathogens gaining entry into the bloodstream are responsible for such infections. Streptococcus mutans is an oral pathogen with implications in cardiovascular diseases. Previous studies have shown certain strains of S. mutans are found predominantly within atherosclerotic plaques and extirpated valves. To decipher the genetic differences responsible for endothelial cell invasion, we have sequenced the genome of Streptococcus mutans B14. Pan-genome analysis, search for adhesion proteins through a special algorithm, and protein-protein interactions search through HPIDB have been done. Pan-genome analysis of 187 whole genomes, assemblies revealed 6965 genes in total and 918 genes forming the core gene cluster. Adhesion to the endothelial cell is a critical virulence factor distinguishing virulent and non-virulent strains. Overall, 4% of the total proteins in S. mutans B14 were categorized as adhesion proteins. Protein-protein interaction between putative adhesion proteins and Human extracellular matrix components was predicted, revealing novel interactions. A conserved gene catalyzing the synthesis of branched-chain amino acids in S. mutans B14 shows possible interaction with isoforms of cathepsin protein of the ECM. This genome sequence analysis indicates towards other proteins in the S. mutans genome, which might have a specific role to play in host cell interaction.

RevDate: 2019-12-13

Decano AG, T Downing (2019)

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates.

Scientific reports, 9(1):17394.

Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131's origin, adaptation and spread is essential. E. coli ST131's ESBL genes are typically embedded in mobile genetic elements (MGEs) that aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene screening to resolve ST131's population structure across three genetically distinct Clades (A, B, C) and abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were located at distinct locations across the chromosomes and plasmids between isolates. Within the three C subclades, the core and accessory genome diversity levels were not correlated due to plasmid and MGE activity, unlike patterns between the three main clades, A, B and C. This population genomic study highlights the dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically variable outbreaks with broader antibiotic resistance levels. Our findings emphasise the potential of evolutionary pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover accessory genome changes linked to novel subtypes.

RevDate: 2019-11-21

de Fátima Rauber Würfel S, Jorge S, de Oliveira NR, et al (2019)

Campylobacter jejuni isolated from poultry meat in Brazil: in silico analysis and genomic features of two strains with different phenotypes of antimicrobial susceptibility.

Molecular biology reports pii:10.1007/s11033-019-05174-y [Epub ahead of print].

Campylobacter jejuni is the most common bacterial cause of foodborne diarrheal disease worldwide and is among the antimicrobial resistant "priority pathogens" that pose greatest threat to public health. The genomes of two C. jejuni isolated from poultry meat sold on the retail market in Southern Brazil phenotypically characterized as multidrug-resistant (CJ100) and susceptible (CJ104) were sequenced and analyzed by bioinformatic tools. The isolates CJ100 and CJ104 showed distinct multilocus sequence types (MLST). Comparative genomic analysis revealed a large number of single nucleotide polymorphisms, rearrangements, and inversions in both genomes, in addition to virulence factors, genomic islands, prophage sequences, and insertion sequences. A circular 103-kilobase megaplasmid carrying virulence factors was identified in the genome of CJ100, in addition to resistance mechanisms to aminoglycosides, beta-lactams, macrolides, quinolones, and tetracyclines. The molecular characterization of distinct phenotypes of foodborne C. jejuni and the discovery of a novel virulence megaplasmid provide useful data for pan-genome and large-scale studies to monitor the virulent C. jejuni in poultry meat is warranted.

RevDate: 2019-12-13

Chapeton-Montes D, Plourde L, Bouchier C, et al (2019)

Author Correction: The population structure of Clostridium tetani deduced from its pan-genome.

Scientific reports, 9(1):17409 pii:10.1038/s41598-019-53688-z.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

RevDate: 2019-11-19

Lawson MAE, O'Neill IJ, Kujawska M, et al (2019)

Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem.

The ISME journal pii:10.1038/s41396-019-0553-2 [Epub ahead of print].

Diet-microbe interactions play an important role in modulating the early-life microbiota, with Bifidobacterium strains and species dominating the gut of breast-fed infants. Here, we sought to explore how infant diet drives distinct bifidobacterial community composition and dynamics within individual infant ecosystems. Genomic characterisation of 19 strains isolated from breast-fed infants revealed a diverse genomic architecture enriched in carbohydrate metabolism genes, which was distinct to each strain, but collectively formed a pangenome across infants. Presence of gene clusters implicated in digestion of human milk oligosaccharides (HMOs) varied between species, with growth studies indicating that within single infants there were differences in the ability to utilise 2'FL and LNnT HMOs between strains. Cross-feeding experiments were performed with HMO degraders and non-HMO users (using spent or 'conditioned' media and direct co-culture). Further 1H-NMR analysis identified fucose, galactose, acetate, and N-acetylglucosamine as key by-products of HMO metabolism; as demonstrated by modest growth of non-HMO users on spend media from HMO metabolism. These experiments indicate how HMO metabolism permits the sharing of resources to maximise nutrient consumption from the diet and highlights the cooperative nature of bifidobacterial strains and their role as 'foundation' species in the infant ecosystem. The intra- and inter-infant bifidobacterial community behaviour may contribute to the diversity and dominance of Bifidobacterium in early life and suggests avenues for future development of new diet and microbiota-based therapies to promote infant health.

RevDate: 2019-12-09

Robertson J, Lin J, Wren-Hedgus A, et al (2019)

Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella.

PloS one, 14(11):e0218638.

Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salmonella Typhi, was found to encode a flagellar operon that can mediate phase variation, which results in the rare z66 flagella phenotype. The identification and tracking of homologs of pBSSB1 is limited because it falls outside the normal replicon typing schemes for plasmids. Here we report the generation of nine new pBSSB1-family sequences using Illumina and Nanopore sequence data. Homologs of pBSSB1 were identified in 154 genomes representing 25 distinct serotypes from 67,758 Salmonella public genomes. Pangenome analysis of pBSSB1-family contigs was performed using roary and we identified three core genes amenable to a minimal pMLST scheme. Population structure analysis based on the newly developed pMLST scheme identified three major lineages representing 35 sequence types, and the distribution of these sequence types was found to span multiple serovars across the globe. This in silico pMLST scheme has shown utility in tracking and subtyping pBSSB1-family plasmids and it has been incorporated into the plasmid MLST database under the name "pBSSB1-family".

RevDate: 2019-11-21

Suresh G, Lodha TD, Indu B, et al (2019)

Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.

Frontiers in microbiology, 10:2480.

The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.

RevDate: 2019-12-13

Ghosh S, Sarangi AN, Mukherjee M, et al (2019)

Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position.

Microorganisms, 7(11): pii:microorganisms7110487.

Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism.

RevDate: 2019-11-15

Seribelli AA, Gonzales JC, de Almeida F, et al (2019)

Phylogenetic analysis revealed that Salmonella Typhimurium ST313 isolated from humans and food in Brazil presented a high genomic similarity.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] pii:10.1007/s42770-019-00155-6 [Epub ahead of print].

Salmonella Typhimurium sequence type 313 (S. Typhimurium ST313) has caused invasive disease mainly in sub-Saharan Africa. In Brazil, ST313 strains have been recently described, and there is a lack of studies that assessed by whole genome sequencing (WGS)-the relationship of these strains. The aims of this work were to study the phylogenetic relationship of 70 S. Typhimurium genomes comparing strains of ST313 (n = 9) isolated from humans and food in Brazil among themselves, with other STs isolated in this country (n = 31) and in other parts of the globe (n = 30) by 16S rRNA sequences, the Gegenees software, whole genome multilocus sequence typing (wgMLST), and average nucleotide identity (ANI) for the genomes of ST313. Additionally, pangenome analysis was performed to verify the heterogeneity of these genomes. The phylogenetic analyses showed that the ST313 genomes were very similar among themselves. However, the ST313 genomes were usually clustered more distantly to other STs of strains isolated in Brazil and in other parts of the world. By pangenome calculation, the core genome was 2,880 CDSs and 4,171 CDSs singletons for all the 70 S. Typhimurium genomes studied. Considering the 10 ST313 genomes analyzed the core genome was 4,112 CDSs and 76 CDSs singletons. In conclusion, the ST313 genomes from Brazil showed a high similarity among them which information might eventually help in the development of vaccines and antibiotics. The pangenome analysis showed that the S. Typhimurium genomes studied presented an open pangenome, but specifically tending to become close for the ST313 strains.

RevDate: 2019-11-13

Chhotaray C, Wang S, Tan Y, et al (2019)

Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain.

G3 (Bethesda, Md.) pii:g3.119.400737 [Epub ahead of print].

Mycobacterium abscessus is a fast growing mycobacterium species mainly causing skin and respiratory infections in human. M. abscessus is resistant to numerous drugs, which is a major challenge for the treatment. In this study, we have sequenced the genomes of two clinical M. abscessus strains having rough and smooth morphology, using the single molecule real-time and Illumina HiSeq sequencing technology. In addition, we reported the first comparative methylome profiles of a rough and a smooth M. abscessus clinical strains. The number of N4-methylcytosine (4mC) and N6-methyladenine (6mA) modified bases obtained from smooth phenotype were 2-fold and 1.6-fold respectively higher than that of rough phenotype. We have also identified 4 distinct novel motifs in two clinical strains and genes encoding antibiotic-modifying/targeting enzymes and genes associated with intracellular survivability having different methylation patterns. To our knowledge, this is the first report about genome-wide methylation profiles of M. abscessus strains and identification of a natural linear plasmid (15 kb) in this critical pathogen harboring methylated bases. The pan-genome analysis of 25 M. abscessus strains including two clinical strains revealed an open pan genome comprises of 7596 gene clusters. Likewise, structural variation analysis revealed that the genome of rough phenotype strain contains more insertions and deletions than the smooth phenotype and that of the reference strain. A total of 391 single nucleotide variations responsible for the non-synonymous mutations were detected in clinical strains compared to the reference genome. The comparative genomic analysis elucidates the genome plasticity in this emerging pathogen. Furthermore, the detection of genome-wide methylation profiles of M. abscessus clinical strains may provide insight into the significant role of DNA methylation in pathogenicity and drug resistance in this opportunistic pathogen.

RevDate: 2019-11-09

Kim KH, Chun BH, Baek JH, et al (2020)

Genomic and metabolic features of Lactobacillus sakei as revealed by its pan-genome and the metatranscriptome of kimchi fermentation.

Food microbiology, 86:103341.

The genomic and metabolic features of Lactobacillus sakei were investigated using its pan-genome and by analyzing the metatranscriptome of kimchi fermentation. In the genome-based relatedness analysis, the strains were divided into the Lb. sakei ssp. sakei and Lb. sakei ssp. carnosus lineage groups. Genomic and metabolic pathway analysis revealed that all Lb. sakei strains have the capability of producing d/l-lactate, ethanol, acetate, CO2, formate, l-malate, diacetyl, acetoin, and 2,3-butanediol from d-glucose, d-fructose, d-galactose, sucrose, d-lactose, l-arabinose, cellobiose, d-mannose, d-gluconate, and d-ribose through homolactic and heterolactic fermentation, whereas their capability of d-maltose, d-xylose, l-xylulose, d-galacturonate, and d-glucuronate metabolism is strain-specific. All strains carry genes for the biosynthesis of folate and thiamine, whereas genes for biogenic amine and toxin production, hemolysis, and antibiotic resistance were not identified. The metatranscriptomic analysis showed that the expression of Lb. sakei transcripts involved in carbohydrate metabolism increased as kimchi fermentation progressed, suggesting that Lb. sakei is more competitive during late fermentation stage. Homolactic fermentation pathway was highly expressed and generally constant during kimchi fermentation, whereas expression of heterolactic fermentation pathway increased gradually as fermentation progressed. l-Lactate dehydrogenase was more highly expressed than d-lactate dehydrogenase, suggesting that l-lactate is the major lactate metabolized by Lb. sakei.

RevDate: 2019-11-15

Bernheim A, R Sorek (2019)

The pan-immune system of bacteria: antiviral defence as a community resource.

Nature reviews. Microbiology pii:10.1038/s41579-019-0278-2 [Epub ahead of print].

Viruses and their hosts are engaged in a constant arms race leading to the evolution of antiviral defence mechanisms. Recent studies have revealed that the immune arsenal of bacteria against bacteriophages is much more diverse than previously envisioned. These discoveries have led to seemingly contradictory observations: on one hand, individual microorganisms often encode multiple distinct defence systems, some of which are acquired by horizontal gene transfer, alluding to their fitness benefit. On the other hand, defence systems are frequently lost from prokaryotic genomes on short evolutionary time scales, suggesting that they impose a fitness cost. In this Perspective article, we present the 'pan-immune system' model in which we suggest that, although a single strain cannot carry all possible defence systems owing to their burden on fitness, it can employ horizontal gene transfer to access immune defence mechanisms encoded by closely related strains. Thus, the 'effective' immune system is not the one encoded by the genome of a single microorganism but rather by its pan-genome, comprising the sum of all immune systems available for a microorganism to horizontally acquire and use.

RevDate: 2019-12-13

Vila Nova M, Durimel K, La K, et al (2019)

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale.

BMC genomics, 20(1):814.

BACKGROUND: Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).

RESULTS: Based on a genome dataset including Salmonella serovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively.

CONCLUSIONS: Our results suggest that the genetic and metabolic determinants of Salmonella adaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.

RevDate: 2019-12-13

Aguirre de Cárcer D (2019)

A conceptual framework for the phylogenetically constrained assembly of microbial communities.

Microbiome, 7(1):142.

Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs' identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.

RevDate: 2019-12-13

Alonge M, Soyk S, Ramakrishnan S, et al (2019)

RaGOO: fast and accurate reference-guided scaffolding of draft genomes.

Genome biology, 20(1):224.

We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps. We show that RaGOO accurately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open source at https://github.com/malonge/RaGOO .

RevDate: 2019-11-01

Oh YJ, Kim JY, Park HK, et al (2019)

Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi.

Journal of microbiology (Seoul, Korea), 57(11):997-1002.

A Gram-stain-positive, rod-shaped, alkalitolerant, and halophilic bacterium-designated as strain NKC3-5T-was isolated from kimchi that was collected from the Geumsan area in the Republic of Korea. Cells of isolated strain NKC3-5T were 0.5-0.7 μm wide and 1.4-2.8 μm long. The strain NKC3-5T could grow at up to 20.0% (w/v) NaCl (optimum 10%), pH 6.5-10.0 (optimum pH 9.0), and 25-40°C (optimum 35°C). The cells were able to reduce nitrate under aerobic conditions, which is the first report in the genus Salicibibacter. The genome size and genomic G + C content of strain NKC3-5T were 3,754,174 bp and 45.9 mol%, respectively; it contained 3,630 coding sequences, 16S rRNA genes (six 16S, five 5S, and five 23S), and 59 tRNA genes. Phylogenetic analysis based on 16S rRNA showed that strain NKC3-5T clustered with bacterium Salicibibacter kimchii NKC1-1T, with a similarity of 96.2-97.6%, but formed a distinct branch with other published species of the family Bacillaceae. In addition, OrthoANI value between strain NKC3-5T and Salicibibacter kimchii NKC1-1T was far lower than the species demarcation threshold. Using functional genome annotation, the result found that carbohydrate, amino acid, and vitamin metabolism related genes were highly distributed in the genome of strain NKC3-5T. Comparative genomic analysis revealed that strain NKC3-5T had 716 pan-genome orthologous groups (POGs), dominated with carbohydrate metabolism. Phylogenomic analysis based on the concatenated core POGs revealed that strain NKC3-5T was closely related to Salicibibacter kimchii. The predominant polar lipids were phosphatidylglycerol and two unidentified lipids. Anteiso-C15:0, iso-C17:0, anteiso-C17:0, and iso-C15:0 were the major cellular fatty acids, and menaquinone-7 was the major isoprenoid quinone present in strain NKC3-5T. Cell wall peptidoglycan analysis of strain NKC3-5T showed that meso-diaminopimelic acid was the diagnostic diamino acid. The phephenotypic, genomic, phylogenetic, and chemotaxonomic properties reveal that the strain represents a novel species of the genus Salicibibacter, for which the name Salicibibacter halophilus sp. nov. is proposed, with the type strain NKC3-5T (= KACC 21230T = JCM 33437T).

RevDate: 2019-10-26

Zhu D, Yang Z, Xu J, et al (2019)

Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands.

Functional & integrative genomics pii:10.1007/s10142-019-00715-x [Epub ahead of print].

Riemerella anatipestifer is a gram-negative bacterium that leads to severe contagious septicemia in ducks, turkeys, chickens, and wild waterfowl. Here, a pan-genome with 32 R. anatipestifer genomes is re-established, and the mathematical model is calculated to evaluate the expansion of R. anatipestifer genomes, which were determined to be open. Average nucleotide identity (ANI) and phylogenetic analysis preliminarily clarify intraspecies variation and distance. Comparative genomic analysis of R. anatipestifer found that horizontal gene transfer events, which provide an expressway for the recruitment of novel functionalities and facilitate genetic diversity in microbial genomes, play a key role in the process of acquiring and transmitting antibiotic-resistance genes in R. anatipestifer. Furthermore, a new antibiotic-resistance gene cluster was identified in the same loci in 14 genomes. The uneven distribution of virulence factors was also confirmed by our results. Our study suggests that the ability to acquire foreign genes (such as antibiotic-resistance genes) increases the adaptability of R. anatipestifer, and the virulence genes with little mobility are highly conserved in R. anatipestifer.

RevDate: 2019-10-24

Vallenet D, Calteau A, Dubois M, et al (2019)

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.

Nucleic acids research pii:5606622 [Epub ahead of print].

Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Here we present new improvements of the MicroScope user interface for genome selection, navigation and expert gene annotation. Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions. We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. To date, MicroScope contains data for >11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (>4500 personal accounts in September 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.

RevDate: 2019-10-24

Mende DR, Letunic I, Maistrenko OM, et al (2019)

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.

Nucleic acids research pii:5606617 [Epub ahead of print].

Microbiology depends on the availability of annotated microbial genomes for many applications. Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. In addition, newer concepts such as the pan-genome concept are still being implemented to help answer biological questions. Hence, we present proGenomes2, which provides 87 920 high-quality genomes in a user-friendly and interactive manner. Genome sequences and annotations can be retrieved individually or by taxonomic clade. Every genome in the database has been assigned to a species cluster and most genomes could be accurately assigned to one or multiple habitats. In addition, general functional annotations and specific annotations of antibiotic resistance genes and single nucleotide variants are provided. In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database. The database is available at http://progenomes.embl.de/.

RevDate: 2019-12-13
CmpDate: 2019-10-28

Yin Z, Yuan C, Du Y, et al (2019)

Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity.

BMC genomics, 20(1):768.

BACKGROUND: The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.

RESULTS: One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei.

CONCLUSIONS: Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

RevDate: 2019-10-23

Lu F, Wei Z, Luo Y, et al (2019)

SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm.

Nucleic acids research pii:5603220 [Epub ahead of print].

SilkDB is an open-accessibility database and powerful platform that provides comprehensive information on the silkworm (Bombyx mori) genome. Since SilkDB 2.0 was released 10 years ago, vast quantities of data about multiple aspects of the silkworm have been generated, including genome, transcriptome, Hi-C and pangenome. To visualize data at these different biological levels, we present SilkDB 3.0 (https://silkdb.bioinfotoolkits.net), a visual analytic tool for exploring silkworm data through an interactive user interface. The database contains a high-quality chromosome-level assembly of the silkworm genome, and its coding sequences and gene sets are more accurate than those in the previous version. SilkDB 3.0 provides a view of the information for each gene at the levels of sequence, protein structure, gene family, orthology, synteny, genome organization and gives access to gene expression information, genetic variation and genome interaction map. A set of visualization tools are available to display the abundant information in the above datasets. With an improved interactive user interface for the integration of large data sets, the updated SilkDB 3.0 database will be a valuable resource for the silkworm and insect research community.

RevDate: 2019-12-02

Nanayakkara BS, O'Brien CL, DM Gordon (2019)

Phenotypic characteristics contributing to the enhanced growth of Escherichia coli bloom strains.

Environmental microbiology reports, 11(6):817-824.

During bloom events, Escherichia coli cell counts increase to between 10,000 and 100,000 cfu/100 ml of water. The strains responsible for bloom events belong to E. coli phylogenetic groups A and B1, and all have acquired a capsule from Klebsiella. A pan-genome comparison of phylogroup A E. coli revealed that the ferric citrate uptake system (fecIRABCDE) was overrepresented in phylogroup A bloom strains compared with non-bloom E. coli. A series of experiments were carried out to investigate if the capsule together with ferric citrate uptake system could confer a growth rate advantage on E. coli. Capsulated strains had a growth rate advantage regardless of the media composition and the presence/absence of the fec operon, and they had a shorter lag phase compared with capsule-negative strains. The results suggest that the Klebsiella capsule may facilitate nutrient uptake or utilization by a strain. This, together with the protective roles played by the capsule and the shorter lag phase of capsule-positive strains, may explain why it is only capsule-positive strains that produce elevated counts in response to nutrient influx.

RevDate: 2019-12-13

Zhong C, Han M, Yang P, et al (2019)

Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities.

mSystems, 4(5):.

The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections.IMPORTANCEAeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.

RevDate: 2019-12-13

Brockhurst MA, Harrison E, Hall JPJ, et al (2019)

The Ecology and Evolution of Pangenomes.

Current biology : CB, 29(20):R1094-R1103.

Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content can occur among genomes belonging to the same prokaryotic species, with only a fraction of genes being universal to all genomes. These insights gave rise to the pangenome concept. The pangenome is defined as the set of all the genes present in a given species and can be subdivided into the accessory genome, present in only some of the genomes, and the core genome, present in all the genomes. Pangenomes arise due to gene gain by genomes from other species through horizontal gene transfer and differential gene loss among genomes, and have been described in both prokaryotes and eukaryotes. Our current view of pangenome variation is phenomenological and incomplete. In this review, we outline the mechanistic, ecological and evolutionary drivers of and barriers to horizontal gene transfer that are likely to structure pangenomes. We highlight the key role of conflict between the host chromosome(s) and the mobile genetic elements that mediate gene exchange. We identify shortcomings in our current models of pangenome evolution and suggest directions for future research to allow a more complete understanding of how and why pangenomes evolve.

RevDate: 2019-10-20

Zhao S, Ci J, Xue J, et al (2019)

Cutibacterium acnes Type II strains are associated with acne in Chinese patients.

Antonie van Leeuwenhoek pii:10.1007/s10482-019-01344-x [Epub ahead of print].

Acne is a common inflammatory skin disease, especially in adolescents. Certain Cutibacterium acnes subtypes are associated with acne, although more than one subtype of C. acnes strains may simultaneously reside on the surface of the skin of an individual. To better understand the relationship between the genomic characteristics of C. acnes subtypes and acnes, we collected 50 C. acnes strains from the facial skin of 10 people (5 healthy individuals, 5 patients with acne) in Liaoning, China and performed whole genome sequencing of all strains. We demonstrated that the six potential pathogenic C. acnes strains were all Type II subtype, and discovered 90 unique genes of the six strains related to acne using pan-genome analysis. The distribution of 2 of the 90 genes was identified by PCR in bacterial cultures collected from the facial skin of 171 individuals (55 healthy individuals, 52 patients with mild acne and 64 patients with moderate to severe acne). Both the genes were significantly associated with acne (Chi square test, P < 0.01). We conclude that Type II strains are associated with acne in Chinese patients.

RevDate: 2019-12-13

Mangas EL, Rubio A, Álvarez-Marín R, et al (2019)

Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation.

Microbial genomics, 5(11):.

Acinetobacter baumannii is an opportunistic bacterium that causes hospital-acquired infections with a high mortality and morbidity, since there are strains resistant to virtually any kind of antibiotic. The chase to find novel strategies to fight against this microbe can be favoured by knowledge of the complete catalogue of genes of the species, and their relationship with the specific characteristics of different isolates. In this work, we performed a genomics analysis of almost 2500 strains. Two different groups of genomes were found based on the number of shared genes. One of these groups rarely has plasmids, and bears clustered regularly interspaced short palindromic repeat (CRISPR) sequences, in addition to CRISPR-associated genes (cas genes) or restriction-modification system genes. This fact strongly supports the lack of plasmids. Furthermore, the scarce plasmids in this group also bear CRISPR sequences, and specifically contain genes involved in prokaryotic toxin-antitoxin systems that could either act as the still little known CRISPR type IV system or be the precursors of other novel CRISPR/Cas systems. In addition, a limited set of strains present a new cas9-like gene, which may complement the other cas genes in inhibiting the entrance of new plasmids into the bacteria. Finally, this group has exclusive genes involved in biofilm formation, which would connect CRISPR systems to the biogenesis of these bacterial resistance structures.

RevDate: 2019-12-13

Wan X (2019)

Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1T.

International journal of molecular sciences, 20(19):.

The genus Flavobacterium contains a large group of commensal bacteria identified in diverse terrestrial and aquatic habitats. We compared the genome of a new species Flavobacterium akiainvivens IK-1T to public available genomes of Flavobacterium species to reveal the genomic traits and ecological roles of IK-1T. Principle component analysis (PCA) of carbohydrate-active enzyme classes suggests that IK-1T belongs to a terrestrial clade of Flavobacterium. In addition, type 2 and type 9 secretion systems involved in bacteria-environment interactions were identified in the IK-1T genome. The IK-1T genome encodes eukaryotic-like domain containing proteins including ankyrin repeats, von Willebrand factor type A domain, and major royal jelly proteins, suggesting that IK-1T may alter plant host physiology by secreting eukaryotic-like proteins that mimic host proteins. A novel two-component system FaRpfC-FaYpdB was identified in the IK-1T genome, which may mediate quorum sensing to regulate global gene expressions. Our findings suggest that comparative genome analyses of Flavobacterium spp. reveal that IK-1T has adapted to a terrestrial niche. Further functional characterizations of IK-1T secreted proteins and their regulation systems will shed light on molecular basis of bacteria-plant interactions in environments.

RevDate: 2019-10-17

Zhang Y, Zhang Z, Zhang H, et al (2019)

PADS Arsenal: a database of prokaryotic defense systems related genes.

Nucleic acids research pii:5588688 [Epub ahead of print].

Defense systems are vital weapons for prokaryotes to resist heterologous DNA and survive from the constant invasion of viruses, and they are widely used in biochemistry investigation and antimicrobial drug research. So far, numerous types of defense systems have been discovered, but there is no comprehensive defense systems database to organize prokaryotic defense gene datasets. To fill this gap, we unveil the prokaryotic antiviral defense system (PADS) Arsenal (https://bigd.big.ac.cn/padsarsenal), a public database dedicated to gathering, storing, analyzing and visualizing prokaryotic defense gene datasets. The initial version of PADS Arsenal integrates 18 distinctive categories of defense system with the annotation of 6 600 264 genes retrieved from 63,701 genomes across 33 390 species of archaea and bacteria. PADS Arsenal provides various ways to retrieve defense systems related genes information and visualize them with multifarious function modes. Moreover, an online analysis pipeline is integrated into PADS Arsenal to facilitate annotation and evolutionary analysis of defense genes. PADS Arsenal can also visualize the dynamic variation information of defense genes from pan-genome analysis. Overall, PADS Arsenal is a state-of-the-art open comprehensive resource to accelerate the research of prokaryotic defense systems.

RevDate: 2019-12-13

Li R, Tian X, Yang P, et al (2019)

Recovery of non-reference sequences missing from the human reference genome.

BMC genomics, 20(1):746.

BACKGROUND: The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of structure variations with NRS exist.

RESULTS: Here, we compared 31 human de novo assemblies with the current reference genome to identify the NRS and their location. We resolved the precise location of 6113 NRS adding up to 12.8 Mb. Besides 1571 insertions, we detected 3041 alternate alleles, which were defined as having less than 90% (or none) identity with the reference alleles. These alternate alleles overlapped with 1143 protein-coding genes including a putative novel MHC haplotype. Further, we demonstrated that the alternate alleles and their flanking regions had high content of tandem repeats, indicating that their origin was associated with tandem repeats.

CONCLUSIONS: Our study detected a large number of NRS including many alternate alleles which are previously uncharacterized. We suggested that the origin of alternate alleles was associated with tandem repeats. Our results enriched the spectrum of genetic variations in human genome.

RevDate: 2019-12-13

Hoarfrost A, Nayfach S, Ladau J, et al (2020)

Global ecotypes in the ubiquitous marine clade SAR86.

The ISME journal, 14(1):178-188.

SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world's oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.

RevDate: 2019-12-13

Tralamazza SM, Rocha LO, Oggenfuss U, et al (2019)

Complex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex.

Genome biology and evolution, 11(11):3106-3122.

Fungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss, and neofunctionalization are largely unknown. We analyzed the Fusarium graminearum species complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. We de novo assembled genomes of previously uncharacterized FGSC members (two strains of F. austroamericanum, F. cortaderiae, and F. meridionale). Our analyses of 8 species of the FGSC in addition to 15 other Fusarium species identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and the Fusarium genus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.

RevDate: 2019-11-22

Tett A, Huang KD, Asnicar F, et al (2019)

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.

Cell host & microbe, 26(5):666-679.e7.

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.

RevDate: 2019-10-23

Chen S, Soehnlen M, Blom J, et al (2019)

Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains.

PloS one, 14(10):e0222648.

Three human clinical isolates of bacteria (designated strains Em1, Em2 and Em3) had high average nucleotide identity (ANI) to Elizabethkingia meningoseptica. Their genome sizes (3.89, 4.04 and 4.04 Mb) were comparable to those of other Elizabethkingia species and strains, and exhibited open pan-genome characteristics, with two strains being nearly identical and the third divergent. These strains were susceptible only to trimethoprim/sulfamethoxazole and ciprofloxacin amongst 16 antibiotics in minimum inhibitory tests. The resistome exhibited a high diversity of resistance genes, including 5 different lactamase- and 18 efflux protein- encoding genes. Forty-four genes encoding virulence factors were conserved among the strains. Sialic acid transporters and curli synthesis genes were well conserved in E. meningoseptica but absent in E. anophelis and E. miricola. E. meningoseptica carried several genes contributing to biofilm formation. 58 glycoside hydrolases (GH) and 25 putative polysaccharide utilization loci (PULs) were found. The strains carried numerous genes encoding two-component system proteins (56), transcription factor proteins (187~191), and DNA-binding proteins (6~7). Several prophages and CRISPR/Cas elements were uniquely present in the genomes.

RevDate: 2019-11-15

Bayliss SC, Thorpe HA, Coyle NM, et al (2019)

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.

GigaScience, 8(10):.

BACKGROUND: Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets.

RESULTS: Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation, and estimates sequence divergence for each gene family.

CONCLUSIONS: We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.

RevDate: 2019-12-13

John J, George S, Nori SRC, et al (2019)

Phylogenomic Analysis Reveals the Evolutionary Route of Resistant Genes in Staphylococcus aureus.

Genome biology and evolution, 11(10):2917-2926.

Multidrug-resistant Staphylococcus aureus is a leading concern worldwide. Coagulase-Negative Staphylococci are claimed to be the reservoir and source of important resistant elements in S. aureus. However, the origin and evolutionary route of resistant genes in S. aureus are still remaining unknown. Here, we performed a detailed phylogenomic analysis of 152 completely sequenced S. aureus strains in comparison with 7,529 non-Staphylococcus aureus reference bacterial genomes. Our results reveal that S. aureus has a large open pan-genome where 97 (55%) of its known resistant-related genes belonging to its accessory genome. Among these genes, 47 (27%) were located within the Staphylococcal Cassette Chromosome mec (SCCmec), a transposable element responsible for resistance against major classes of antibiotics including beta-lactams, macrolides, and aminoglycosides. However, the physically linked mec-box genes (MecA-MecR-MecI) that are responsible for the maintenance of SCCmec elements is not unique to S. aureus, instead it is widely distributed within Staphylococcaceae family. The phyletic patterns of SCCmec-encoded resistant genes in Staphylococcus species are significantly different from that of its core genes indicating frequent exchange of these genes between Staphylococcus species. Our in-depth analysis of SCCmec-resistant gene phylogenies reveals that genes such as blaZ, ble, kmA, and tetK that are responsible for beta-lactam, bleomycin, kanamycin, and tetracycline resistance in S. aureus were laterally transferred from non-Staphylococcus sources. In addition, at least 11 non-SCCmec-encoded resistant genes in S. aureus, were laterally acquired from distantly related species. Our study evidently shows that gene transfers played a crucial role in shaping the evolution of antibiotic resistance in S. aureus.

RevDate: 2019-12-13

Li G, Ji B, J Nielsen (2019)

The pan-genome of Saccharomyces cerevisiae.

FEMS yeast research, 19(7):.

Understanding genotype-phenotype relationship is fundamental in biology. With the benefit from next-generation sequencing and high-throughput phenotyping methodologies, there have been generated much genome and phenome data for Saccharomyces cerevisiae. This makes it an excellent model system to understand the genotype-phenotype relationship. In this paper, we presented the reconstruction and application of the yeast pan-genome in resolving genotype-phenotype relationship by a machine learning-assisted approach.

RevDate: 2019-10-04

Ferrés I, Fresia P, G Iraola (2019)

simurg: simulate bacterial pangenomes in R.

Bioinformatics (Oxford, England) pii:5581402 [Epub ahead of print].

MOTIVATION: The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models.

RESULTS: We developed simurg, an R package that allows to simulate bacterial pangenomes using different combinations of evolutionary constraints such as gene gain, gene loss and mutation rates. Our tool allows the straightforward and reproducible simulation of bacterial pangenomes using real sequence data, providing a valuable tool for benchmarking of pangenome softwares or comparing evolutionary hypotheses.

AVAILABILITY: The simurg package is released under the GPL-3 license, and is freely available for download from GitHub (https://github.com/iferres/simurg).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2019-10-23

Sabbagh CRR, Carrere S, Lonjon F, et al (2019)

Pangenomic type III effector database of the plant pathogenic Ralstonia spp.

PeerJ, 7:e7346.

Background: The bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a "species complex" gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. Type III-secreted effectors (T3Es) are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology).

Methods: Expert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors.

Results: We curated the T3E repertoires of 12 plant pathogenic Ralstonia strains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.

RevDate: 2019-11-15

Song B, Song Y, Fu Y, et al (2019)

Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome.

GigaScience, 8(10):.

BACKGROUND: The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops.

RESULTS: We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both "Gilo" and "Shum" groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome.

CONCLUSIONS: The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

RevDate: 2019-10-23

Wang D, F Gao (2019)

Comprehensive Analysis of Replication Origins in Saccharomyces cerevisiae Genomes.

Frontiers in microbiology, 10:2122.

DNA replication initiates from multiple replication origins (ORIs) in eukaryotes. Discovery and characterization of replication origins are essential for a better understanding of the molecular mechanism of DNA replication. In this study, the features of autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae have been comprehensively analyzed as follows. Firstly, we carried out the analysis of the ARSs available in S. cerevisiae S288C. By evaluating the sequence similarity of experimentally established ARSs, we found that 94.32% of ARSs are unique across the whole genome of S. cerevisiae S288C and those with high sequence similarity are prone to locate in subtelomeres. Subsequently, we built a non-redundant dataset with a total of 520 ARSs, which are based on ARSs annotation of S. cerevisiae S288C from SGD and then supplemented with those from OriDB and DeOri databases. We conducted a large-scale comparison of ORIs among the diverse budding yeast strains from a population genomics perspective. We found that 82.7% of ARSs are not only conserved in genomic sequence but also relatively conserved in chromosomal position. The non-conserved ARSs tend to distribute in the subtelomeric regions. We also conducted a pan-genome analysis of ARSs among the S. cerevisiae strains, and a total of 183 core ARSs existing in all yeast strains were determined. We extracted the genes adjacent to replication origins among the 104 yeast strains to examine whether there are differences in their gene functions. The result showed that the genes involved in the initiation of DNA replication, such as orc3, mcm2, mcm4, mcm6, and cdc45, are conservatively located adjacent to the replication origins. Furthermore, we found the genes adjacent to conserved ARSs are significantly enriched in DNA binding, enzyme activity, transportation, and energy, whereas for the genes adjacent to non-conserved ARSs are significantly enriched in response to environmental stress, metabolites biosynthetic process and biosynthesis of antibiotics. In general, we characterized the replication origins from the genome-wide and population genomics perspectives, which would provide new insights into the replication mechanism of S. cerevisiae and facilitate the design of algorithms to identify genome-wide replication origins in yeast.

RevDate: 2019-10-11

Dolatabadian A, Bayer PE, Tirnaz S, et al (2019)

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation.

Plant biotechnology journal [Epub ahead of print].

Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.

RevDate: 2019-09-27

Zhang W, Wang J, Zhang D, et al (2019)

Complete Genome Sequencing and Comparative Genome Characterization of Lactobacillus johnsonii ZLJ010, a Potential Probiotic With Health-Promoting Properties.

Frontiers in genetics, 10:812.

Lactobacillus johnsonii ZLJ010 is a probiotic strain isolated from the feces of a healthy sow and has putative health-promoting properties. To determine the molecular basis underlying the probiotic potential of ZLJ010 and the genes involved in the same, complete genome sequencing and comparative genome analysis with L. johnsonii ZLJ010 were performed. The ZLJ010 genome was found to contain a single circular chromosome of 1,999,879 bp with a guanine-cytosine (GC) content of 34.91% and encoded 18 ribosomal RNA (rRNA) genes and 77 transfer RNA (tRNA) genes. From among the 1,959 protein coding sequences (CDSs), genes known to confer probiotic properties were identified, including genes related to stress adaptation, biosynthesis, metabolism, transport of amino acid, secretion, and the defense machinery. ZLJ010 lacked complete or partial biosynthetic pathways for amino acids but was predicted to compensate for this with an enhanced transport system and some unique amino acid permeases and peptidases that allow it to acquire amino acids and other precursors exogenously. The comparative genomic analysis of L. johnsonii ZLP001 and seven other available L. johnsonii strains, including L. johnsonii NCC533, FI9785, DPC6026, N6.2, BS15, UMNLJ22, and PF01, revealed 2,732 pan-genome orthologous gene clusters and 1,324 core-genome orthologous gene clusters. Phylogenomic analysis based on 1,288 single copy genes showed that ZLJ010 had a closer relationship with the BS15 from yogurt and DPC6026 from the porcine intestinal tract but was located on a relatively standalone branch. The number of clusters of unique, strain-specific genes ranged from 42 to 185. A total of 219 unique genes present in the genome of L. johnsonii ZLJ010 primarily encoded proteins that are putatively involved in replication, recombination and repair, defense mechanisms, transcription, amino acid transport and metabolism, and carbohydrate transport and metabolism. Two unique prophages were predicted in the ZLJ010 genome. The present study helps us understand the ability of L. johnsonii ZLJ010 to better adapt to the gut environment and also its probiotic functionalities.

RevDate: 2019-09-27

Pain M, Hjerde E, Klingenberg C, et al (2019)

Comparative Genomic Analysis of Staphylococcus haemolyticus Reveals Key to Hospital Adaptation and Pathogenicity.

Frontiers in microbiology, 10:2096.

Staphylococcus haemolyticus is a skin commensal gaining increased attention as an emerging pathogen of nosocomial infections. However, knowledge about the transition from a commensal to an invasive lifestyle remains sparse and there is a paucity of studies comparing pathogenicity traits between commensal and clinical isolates. In this study, we used a pan-genomic approach to identify factors important for infection and hospital adaptation by exploring the genomic variability of 123 clinical isolates and 46 commensal S. haemolyticus isolates. Phylogenetic reconstruction grouped the 169 isolates into six clades with a distinct distribution of clinical and commensal isolates in the different clades. Phenotypically, multi-drug antibiotic resistance was detected in 108/123 (88%) of the clinical isolates and 5/46 (11%) of the commensal isolates (p < 0.05). In the clinical isolates, we commonly identified a homolog of the serine-rich repeat glycoproteins sraP. Additionally, three novel capsular polysaccharide operons were detected, with a potential role in S. haemolyticus virulence. Clinical S. haemolyticus isolates showed specific signatures associated with successful hospital adaption. Biofilm forming S. haemolyticus isolates that are resistant to oxacillin (mecA) and aminoglycosides (aacA-aphD) are most likely invasive isolates whereas absence of these traits strongly indicates a commensal isolate. We conclude that our data show a clear segregation of isolates of commensal origin, and specific genetic signatures distinguishing the clinical isolates from the commensal isolates. The widespread use of antimicrobial agents has probably promoted the development of successful hospital adapted clones of S. haemolyticus clones through acquisition of mobile genetic elements or beneficial point mutations and rearrangements in surface associated genes.

RevDate: 2019-12-13

Heo S, Lee J, Lee JH, et al (2019)

Genomic Insight into the Salt Tolerance of Enterococcus faecium, Enterococcus faecalis and Tetragenococcus halophilus.

Journal of microbiology and biotechnology, 29(10):1591-1602.

To shed light on the genetic basis of salt tolerance in Enterococcus faecium, Enterococcus faecalis, and Tetragenococcus halophilus, we performed comparative genome analysis of 10 E. faecalis, 11 E. faecium, and three T. halophilus strains. Factors involved in salt tolerance that could be used to distinguish the species were identified. Overall, T. halophilus contained a greater number of potassium transport and osmoprotectant synthesis genes compared with the other two species. In particular, our findings suggested that T. halophilus may be the only one among the three species capable of synthesizing glycine betaine from choline, cardiolipin from glycerol and proline from citrate. These molecules are well-known osmoprotectants; thus, we propose that these genes confer the salt-tolerance of T. halophilus.

RevDate: 2019-10-28

Hatje K, Mühlhausen S, Simm D, et al (2019)

The Protein-Coding Human Genome: Annotating High-Hanging Fruits.

BioEssays : news and reviews in molecular, cellular and developmental biology, 41(11):e1900066.

The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.

RevDate: 2019-09-18

Erwin DH (2019)

Tempos and modes of collectivity in the history of life.

Theory in biosciences = Theorie in den Biowissenschaften pii:10.1007/s12064-019-00303-4 [Epub ahead of print].

Collective integration and processing of information have increased through the history of life, through both the formation of aggregates in which the entities may have very different properties and which jointly coarse-grained environmental variables (ranging from widely varying metabolism in microbial consortia to the ecological diversity of species on reefs) and through collectives of similar entities (such as cells within an organism or social groups). Such increases have been implicated in significant transitions in the history of life, including aspects of the origin of life, the generation of pangenomes among microbes and microbial communities such as stromatolites, multicellularity and social insects. This contribution provides a preliminary overview of the dominant modes of collective information processing in the history of life, their phylogenetic distribution and extent of convergence, and the effects of new modes for integrating and acting upon information on the tempo of evolutionary change.

RevDate: 2019-09-17

Sigalova OM, Chaplin AV, Bochkareva OO, et al (2019)

Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.

BMC genomics, 20(1):710 pii:10.1186/s12864-019-6059-5.

BACKGROUND: Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.

RESULTS: We report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.

CONCLUSIONS: This combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.

RevDate: 2019-09-15

Ghaffaari A, T Marschall (2019)

Fully-sensitive seed finding in sequence graphs using a hybrid index.

Bioinformatics (Oxford, England), 35(14):i81-i89.

MOTIVATION: Sequence graphs are versatile data structures that are, for instance, able to represent the genetic variation found in a population and to facilitate genome assembly. Read mapping to sequence graphs constitutes an important step for many applications and is usually done by first finding exact seed matches, which are then extended by alignment. Existing methods for finding seed hits prune the graph in complex regions, leading to a loss of information especially in highly polymorphic regions of the genome. While such complex graph structures can indeed lead to a combinatorial explosion of possible alleles, the query set of reads from a diploid individual realizes only two alleles per locus-a property that is not exploited by extant methods.

RESULTS: We present the Pan-genome Seed Index (PSI), a fully-sensitive hybrid method for seed finding, which takes full advantage of this property by combining an index over selected paths in the graph with an index over the query reads. This enables PSI to find all seeds while eliminating the need to prune the graph. We demonstrate its performance with different parameter settings on both simulated data and on a whole human genome graph constructed from variants in the 1000 Genome Project dataset. On this graph, PSI outperforms GCSA2 in terms of index size, query time and sensitivity.

The C++ implementation is publicly available at: https://github.com/cartoonist/psi.

RevDate: 2019-09-13

Espadinha D, Sobral RG, Mendes CI, et al (2019)

Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages.

Frontiers in microbiology, 10:1971.

Background:Staphylococcus epidermidis is a common skin commensal that has emerged as a pathogen in hospitals, mainly related to medical devices-associated infections. Noteworthy, infection rates by S. epidermidis have the tendency to rise steeply in next decades together with medical devices use and immunocompromized population growth. Staphylococcus epidermidis population structure includes two major clonal lineages (A/C and B) that present contrasting pathogenic potentials. To address this distinction and explore the basis of increased pathogenicity of A/C lineage, we performed a detailed comparative analysis using phylogenetic and integrated pangenome-wide-association study (panGWAS) approaches and compared the lineages's phenotypes in in vitro conditions mimicking carriage and infection. Results: Each S. epidermidis lineage had distinct phenotypic signatures in skin and infection conditions and differed in genomic content. Combination of phenotypic and genotypic data revealed that both lineages were well adapted to skin environmental cues. However, they appear to occupy different skin niches, perform distinct biological functions in the skin and use different mechanisms to complete the same function: lineage B strains showed evidence of specialization to survival in microaerobic and lipid rich environment, characteristic of hair follicle and sebaceous glands; lineage A/C strains showed evidence for adaption to diverse osmotic and pH conditions, potentially allowing them to occupy a broader and more superficial skin niche. In infection conditions, A/C strains had an advantage, having the potential to bind blood-associated host matrix proteins, form biofilms at blood pH, resist antibiotics and macrophage acidity and to produce proteases. These features were observed to be rare in the lineage B strains. PanGWAS analysis produced a catalog of putative S. epidermidis virulence factors and identified an epidemiological molecular marker for the more pathogenic lineage. Conclusion: The prevalence of A/C lineage in infection is probably related to a higher metabolic and genomic versatility that allows rapid adaptation during transition from a commensal to a pathogenic lifestyle. The putative virulence and phenotypic factors associated to A/C lineage constitute a reliable framework for future studies on S. epidermidis pathogenesis and the finding of an epidemiological marker for the more pathogenic lineage is an asset for the management of S. epidermidis infections.

RevDate: 2019-09-22

Fariq A, Blazier JC, Yasmin A, et al (2019)

Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C.

Scientific reports, 9(1):13049 pii:10.1038/s41598-019-49213-x.

Acidithiobacillus ferrooxidans, a chemolithoautotrophic bacterium, is well known for its mineral oxidizing properties. The current study combines experimental and whole genome sequencing approaches to investigate an iron oxidizing, extreme acidophilic bacterium, A. ferrooxidans isolate (IO-2C) from an acid seep area near Carlos, TX, USA. Strain IO-2C was capable of oxidizing iron i.e. iron sulphate and iron ammonium sulphate yielding shwertmannite and jarosite minerals. Further, the bacterium's genome was sequenced, assembled and annotated to study its general features, structure and functions. To determine genetic heterogeneity, it was compared with the genomes of other published A. ferrooxidans strains. Pan-genome analysis displayed low gene conservation and significant genetic diversity in A. ferrooxidans species comprising of 6926 protein coding sequences with 23.04% (1596) core genes, 46.13% (3195) unique and 30.82% (2135) accessory genes. Variant analysis showed >75,000 variants, 287 of them with a predicted high impact, in A. ferrooxidans IO-2C genome compared to the reference strain, resulting in abandonment of some important functional key genes. The genome contains numerous functional genes for iron and sulphur metabolism, nitrogen fixation, secondary metabolites, degradation of aromatic compounds, and multidrug and heavy metal resistance. This study demonstrated the bio-oxidation of iron by newly isolated A. ferrooxidans IO-2C under acidic conditions, which was further supported by genomic analysis. Genomic analysis of this strain provided valuable information about the complement of genes responsible for the utilization of iron and tolerance of other metals.

RevDate: 2019-11-01

Kaminski MA, Sobczak A, Dziembowski A, et al (2019)

Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis.

Genes, 10(9):.

Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxislindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.

RevDate: 2019-09-20

Safari M, Yakhchali B, V Shariati J (2019)

Comprehensive genomic analysis of an indigenous Pseudomonas pseudoalcaligenes degrading phenolic compounds.

Scientific reports, 9(1):12736 pii:10.1038/s41598-019-49048-6.

Environmental contamination with aromatic compounds is a universal challenge. Aromatic-degrading microorganisms isolated from the same or similar polluted environments seem to be more suitable for bioremediation. Moreover, microorganisms adapted to contaminated environments are able to use toxic compounds as the sole sources of carbon and energy. An indigenous strain of Pseudomonas, isolated from the Mahshahr Petrochemical plant in the Khuzestan province, southwest of Iran, was studied genetically. It was characterized as a novel Gram-negative, aerobic, halotolerant, rod-shaped bacterium designated Pseudomonas YKJ, which was resistant to chloramphenicol and ampicillin. Genome of the strain was completely sequenced using Illumina technology to identify its genetic characteristics. MLST analysis revealed that the YKJ strain belongs to the genus Pseudomonas indicating the highest sequence similarity with Pseudomonas pseudoalcaligenes strain CECT 5344 (99% identity). Core- and pan-genome analysis indicated that P. pseudoalcaligenes contains 1,671 core and 3,935 unique genes for coding DNA sequences. The metabolic and degradation pathways for aromatic pollutants were investigated using the NCBI and KEGG databases. Genomic and experimental analyses showed that the YKJ strain is able to degrade certain aromatic compounds including bisphenol A, phenol, benzoate, styrene, xylene, benzene and chlorobenzene. Moreover, antibiotic resistance and chemotaxis properties of the YKJ strain were found to be controlled by two-component regulatory systems.

RevDate: 2019-09-12

Tidjani AR, Lorenzi JN, Toussaint M, et al (2019)

Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics.

mBio, 10(5): pii:mBio.01533-19.

In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.IMPORTANCE Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.

RevDate: 2019-09-22

Fernie AR, A Aharoni (2019)

Pan-Genomic Illumination of Tomato Identifies Novel Gene-Trait Interactions.

Trends in plant science, 24(10):882-884.

A recent study by Gao et al., (Nat. Genet., 2019) presents a tomato pan-genome that was constructed using genome sequences of 725 phylogenetically and geographically representative accessions. The study revealed 4873 genes that are absent from the reference genome, including important genes associated with both disease resistance and flavor, thereby providing an important breeding resource.

RevDate: 2019-11-10

Zeng C, Gilcrease EB, Hendrix RW, et al (2019)

DNA Packaging and Genomics of the Salmonella 9NA-Like Phages.

Journal of virology, 93(22):.

We present the genome sequences of Salmonella enterica tailed phages Sasha, Sergei, and Solent. These phages, along with Salmonella phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly related Proteus phage PmiS-Isfahan, have similarly sized genomes of between 52 and 57 kbp in length that are largely syntenic. Their genomes also show substantial genome mosaicism relative to one another, which is common within tailed phage clusters. Their gene content ranges from 80 to 99 predicted genes, of which 40 are common to all seven and form the core genome, which includes all identifiable virion assembly and DNA replication genes. The total number of gene types (pangenome) in the seven phages is 176, and 59 of these are unique to individual phages. Their core genomes are much more closely related to one another than to the genome of any other known phage, and they comprise a well-defined cluster within the family Siphoviridae To begin to characterize this group of phages in more experimental detail, we identified the genes that encode the major virion proteins and examined the DNA packaging of the prototypic member, phage 9NA. We show that it uses a pac site-directed headful packaging mechanism that results in virion chromosomes that are circularly permuted and about 13% terminally redundant. We also show that its packaging series initiates with double-stranded DNA cleavages that are scattered across a 170-bp region and that its headful measuring device has a precision of ±1.8%.IMPORTANCE The 9NA-like phages are clearly highly related to each other but are not closely related to any other known phage type. This work describes the genomes of three new 9NA-like phages and the results of experimental analysis of the proteome of the 9NA virion and DNA packaging into the 9NA phage head. There is increasing interest in the biology of phages because of their potential for use as antibacterial agents and for their ecological roles in bacterial communities. 9NA-like phages that infect two bacterial genera have been identified to date, and related phages infecting additional Gram-negative bacterial hosts are likely to be found in the future. This work provides a foundation for the study of these phages, which will facilitate their study and potential use.

RevDate: 2019-09-02

Lee K, Kim MS, Lee JS, et al (2019)

Chromosomal features revealed by comparison of genetic maps of Glycine max and Glycine soja.

Genomics pii:S0888-7543(19)30394-5 [Epub ahead of print].

Recombination is a crucial component of evolution and breeding. New combinations of variation on chromosomes are shaped by recombination. Recombination is also involved in chromosomal rearrangements. However, recombination rates vary tremendously among chromosome segments. Genome-wide genetic maps are one of the best tools to study variation of recombination. Here, we describe high density genetic maps of Glycine max and Glycine soja constructed from four segregating populations. The maps were used to identify chromosomal rearrangements and find the highly predictable pattern of cross-overs on the broad scale in soybean. Markers on these genetic maps were used to evaluate assembly quality of the current soybean reference genome sequence. We find a strong inversion candidate larger than 3 Mb based on patterns of cross-overs. We also identify quantitative trait loci (QTL) that control number of cross-overs. This study provides fundamental insights relevant to practical strategy for breeding programs and for pan-genome researches.

RevDate: 2019-12-08

Seif Y, Monk JM, Machado H, et al (2019)

Systems Biology and Pangenome of Salmonella O-Antigens.

mBio, 10(4): pii:mBio.01247-19.

O-antigens are glycopolymers in lipopolysaccharides expressed on the cell surface of Gram-negative bacteria. Variability in the O-antigen structure constitutes the basis for the establishment of the serotyping schema. We pursued a two-pronged approach to define the basis for O-antigen structural diversity. First, we developed a bottom-up systems biology approach to O-antigen metabolism by building a reconstruction of Salmonella O-antigen biosynthesis and used it to (i) update 410 existing Salmonella strain-specific metabolic models, (ii) predict a strain's serogroup and its O-antigen glycan synthesis capability (yielding 98% agreement with experimental data), and (iii) extend our workflow to more than 1,400 Gram-negative strains. Second, we used a top-down pangenome analysis to elucidate the genetic basis for intraserogroup O-antigen structural variations. We assembled a database of O-antigen gene islands from over 11,000 sequenced Salmonella strains, revealing (i) that gene duplication, pseudogene formation, gene deletion, and bacteriophage insertion elements occur ubiquitously across serogroups; (ii) novel serotypes in the group O:4 B2 variant, as well as an additional genotype variant for group O:4, and (iii) two novel O-antigen gene islands in understudied subspecies. We thus comprehensively defined the genetic basis for O-antigen diversity.IMPORTANCE Lipopolysaccharides are a major component of the outer membrane in Gram-negative bacteria. They are composed of a conserved lipid structure that is embedded in the outer leaflet of the outer membrane and a polysaccharide known as the O-antigen. O-antigens are highly variable in structure across strains of a species and are crucial to a bacterium's interactions with its environment. They constitute the first line of defense against both the immune system and bacteriophage infections and have been shown to mediate antimicrobial resistance. The significance of our research is in identifying the metabolic and genetic differences within and across O-antigen groups in Salmonella strains. Our effort constitutes a first step toward characterizing the O-antigen metabolic network across Gram-negative organisms and a comprehensive overview of genetic variations in Salmonella.

RevDate: 2019-10-23

Dar HA, Zaheer T, Shehroz M, et al (2019)

Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae.

Vaccines, 7(3):.

Klebsiella pneumoniae is an opportunistic gram-negative bacterium that causes nosocomial infection in healthcare settings. Despite the high morbidity and mortality rate associated with these bacterial infections, no effective vaccine is available to counter the pathogen. In this study, the pangenome of a total of 222 available complete genomes of K. pneumoniae was explored to obtain the core proteome. A reverse vaccinology strategy was applied to the core proteins to identify four antigenic proteins. These proteins were then subjected to epitope mapping and prioritization steps to shortlist nine B-cell derived T-cell epitopes which were linked together using GPGPG linkers. An adjuvant (Cholera Toxin B) was also added at the N-terminal of the vaccine construct to improve its immunogenicity and a stabilized multi-epitope protein structure was obtained using molecular dynamics simulation. The designed vaccine exhibited sustainable and strong bonding interactions with Toll-like receptor 2 and Toll-like receptor 4. In silico reverse translation and codon optimization also confirmed its high expression in E. coli K12 strain. The computer-aided analyses performed in this study imply that the designed multi-epitope vaccine can elicit specific immune responses against K. pneumoniae. However, wet lab validation is necessary to further verify the effectiveness of this proposed vaccine candidate.

RevDate: 2019-11-25

Xing J, Li X, Sun Y, et al (2019)

Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species.

Genes & genomics, 41(11):1253-1264.

BACKGROUND: Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health.

OBJECTIVE: In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied.

METHODS: Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to-Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRUCTURE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands.

RESULTS: The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila PytT.

CONCLUSION: Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future.

RevDate: 2019-10-23

Khan AMAM, Mendoza C, Hauk VJ, et al (2019)

Genomic and physiological analyses reveal that extremely thermophilic Caldicellulosiruptor changbaiensis deploys uncommon cellulose attachment mechanisms.

Journal of industrial microbiology & biotechnology, 46(9-10):1251-1263.

The genus Caldicellulosiruptor is comprised of extremely thermophilic, heterotrophic anaerobes that degrade plant biomass using modular, multifunctional enzymes. Prior pangenome analyses determined that this genus is genetically diverse, with the current pangenome remaining open, meaning that new genes are expected with each additional genome sequence added. Given the high biodiversity observed among the genus Caldicellulosiruptor, we have sequenced and added a 14th species, Caldicellulosiruptor changbaiensis, to the pangenome. The pangenome now includes 3791 ortholog clusters, 120 of which are unique to C. changbaiensis and may be involved in plant biomass degradation. Comparisons between C. changbaiensis and Caldicellulosiruptor bescii on the basis of growth kinetics, cellulose solubilization and cell attachment to polysaccharides highlighted physiological differences between the two species which are supported by their respective gene inventories. Most significantly, these comparisons indicated that C. changbaiensis possesses uncommon cellulose attachment mechanisms not observed among the other strongly cellulolytic members of the genus Caldicellulosiruptor.

RevDate: 2019-11-21

Chapeton-Montes D, Plourde L, Bouchier C, et al (2019)

The population structure of Clostridium tetani deduced from its pan-genome.

Scientific reports, 9(1):11220.

Clostridium tetani produces a potent neurotoxin, the tetanus neurotoxin (TeNT) that is responsible for the worldwide neurological disease tetanus, but which can be efficiently prevented by vaccination with tetanus toxoid. Until now only one type of TeNT has been characterized and very little information exists about the heterogeneity among C. tetani strains. We report here the genome sequences of 26 C. tetani strains, isolated between 1949 and 2017 and obtained from different locations. Genome analyses revealed that the C. tetani population is distributed in two phylogenetic clades, a major and a minor one, with no evidence for clade separation based on geographical origin or time of isolation. The chromosome of C. tetani is highly conserved; in contrast, the TeNT-encoding plasmid shows substantial heterogeneity. TeNT itself is highly conserved among all strains; the most relevant difference is an insertion of four amino acids in the C-terminal receptor-binding domain in four strains that might impact on receptor-binding properties. Other putative virulence factors, including tetanolysin and collagenase, are encoded in all genomes. This study highlights the population structure of C. tetani and suggests that tetanus-causing strains did not undergo extensive evolutionary diversification, as judged from the high conservation of its main virulence factors.

RevDate: 2019-08-08

Saad J, Phelippeau M, Khoder M, et al (2019)

"Mycobacterium mephinesia", a Mycobacterium terrae complex species of clinical interest isolated in French Polynesia.

Scientific reports, 9(1):11169 pii:10.1038/s41598-019-47674-8.

A 59-year-old tobacco smoker male with chronic bronchitis living in Taravao, French Polynesia, Pacific, presented with a two-year growing nodule in the middle lobe of the right lung. A guided bronchoalveolar lavage inoculated onto Löwenstein-Jensen medium yielded colonies of a rapidly-growing non-chromogenic mycobacterium designed as isolate P7213. The isolate could not be identified using routine matrix-assisted laser desorption ionization-time of flight-mass spectrometry and phenotypic and probe-hybridization techniques and yielded 100% and 97% sequence similarity with the respective 16S rRNA and rpoB gene sequences of Mycobacterium virginiense in the Mycobacterium terrae complex. Electron microscopy showed a 1.15 µm long and 0.38 µm large bacillus which was in vitro susceptible to rifampicin, rifabutin, ethambutol, isoniazid, doxycycline and kanamycin. Its 4,511,948-bp draft genome exhibited a 67.6% G + C content with 4,153 coding-protein genes and 87 predicted RNA genes. Genome sequence-derived DNA-DNA hybridization, OrthoANI and pangenome analysis confirmed isolate P7213 was representative of a new species in the M. terrae complex. We named this species "Mycobacterium mephinesia".

RevDate: 2019-10-29

O'Connor E, McGowan J, McCarthy CGP, et al (2019)

Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23.

G3 (Bethesda, Md.), 9(10):3057-3066.

Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as 'Heirloom'. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A. bisporus is quite diverse with between 60-70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.

RevDate: 2019-10-25
CmpDate: 2019-10-25

Duan Z, Qiao Y, Lu J, et al (2019)

HUPAN: a pan-genome analysis pipeline for human genomes.

Genome biology, 20(1):149 pii:10.1186/s13059-019-1751-y.

The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPAN) system to build the human pan-genome. We applied it to 185 deep sequencing and 90 assembled Han Chinese genomes and detected 29.5 Mb novel genomic sequences and at least 188 novel protein-coding genes missing in the human reference genome (GRCh38). It can be an important resource for the human genome-related biomedical studies, such as cancer genome analysis. HUPAN is freely available at http://cgm.sjtu.edu.cn/hupan/ and https://github.com/SJTU-CGM/HUPAN .


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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