CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

Characterization and evaluation of actinomycete from the Protaetia brevitarsis Larva Frass

Protaetia brevitarsis larvae (PBL) are soil insects important for the soil organic carbon cycle, and PBL frass not only contains a large amount of humic acid but also affects the diversity, novelty, and potential functions of actinomycetes. Here, we characterized and assessed the actinomycete. The operational taxonomic unit (OTU) data showed that 90% of the actinomycetes cannot be annotated to species, and pure culture and genome analysis showed that 35% of the strains had the potential to be new species, indicating the novelty of PBL frass actinomycetes. Additionally, genome annotation showed that many gene clusters related to antifungal, antibacterial and insecticidal compound synthesis were identified, and confrontation culture confirmed the antifungal activities of the actinomycetes against soil-borne plant pathogenic fungi. The incubation experiment results showed that all isolates were able to thrive on media composed of straw powder and alkaline lignin. These results indicated that PBL hindgut-enriched actinomycetes could survive in soil by using the residual lignocellulose organic matter from plant residues, and the antibiotics produced not only give them a competitive advantage among soil microflora but also have a certain inhibitory effect on plant diseases and pests. This study suggests that the application of PBL frass can not only supplement soil humic acid but also potentially affect the soil microbiota of cultivated land, which is beneficial for the healthy growth of crops.

Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces

Brachybacterium species have been identified in various ecological niches and belong to the family Dermabacteriaceae within the phylum Actinobacteria. In this study, we isolated a novel Brachybacterium equifaecis JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other Brachybacterium strains. Moreover, comparative genomic analysis using publicly available Brachybacterium genomes was performed to determine the properties involved in their ecological adaptation and metabolic potential. Novel species delineation was determined phylogenetically through 16S rRNA gene similarity (up to 97.9%), average nucleotide identity (79.5-82.5%), average amino acid identity (66.7-75.8%), and in silico DNA-DNA hybridization (23.7-27.9) using closely related strains. This study also presents the first report of the kinetic properties of Brachybacterium species. Most of the Brachybacterium strains displayed high oxygen (K m(app) =1.6-24.2 µM) and glucose (K m(app) =0.73-1.22 µM) affinities, which may manifest niche adaptations. Various carbohydrate metabolisms under aerobic and anaerobic conditions, antibiotic resistance, mobile genetic elements, carbohydrate-active enzymes, lactic acid production, and the clustered regularly interspaced short palindromic repeats-Cas and bacteriophage exclusion systems were observed in the genotypic and/or phenotypic properties of Brachybacterium species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of Brachybacterium species, including the novel JHP9 strain, which advocates for their tolerant and thriving nature in various environments, leading to their ecological adaptation. IMPORTANCE Basic physiological and genomic properties of most of the Brachybacterium isolates have been studied; however, the ability of this bacterium to adapt to diverse environments, which may demonstrate its role in niche differentiation, is to be identified yet. Therefore, here, we explored cellular kinetics, metabolic diversity, and ecological adaptation/defensive properties of the novel Brachybacterium strain through physiological and comparative genomic analysis. In addition, we presented the first report examining Brachybacterium kinetics, indicating that all strains of Brachybacterium, including the novel one, have high oxygen and glucose affinity. Furthermore, the comparative genomic analysis also revealed that the novel bacterium contains versatile genomic properties, which provide the novel bacterium with significant competitive advantages. Thus, in-depth genotypic and phenotypic analysis with kinetic properties at the species level of this genus is beneficial in clarifying its differential characteristics, conferring the ability to inhabit diverse ecological niches.

KINN: An alignment-free accurate phylogeny reconstruction method based on inner distance distributions of k-mer pairs in biological sequences

Alignment-based methods have faced disadvantages in sequence comparison and phylogeny reconstruction due to their high computational complexity. Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Here, we explore an alignment-free approach that uses inner distance distributions of k-mer pairs in biological sequences for phylogeny inference. For every sequence in a dataset, our method transforms the sequence into a numeric feature vector consisting of features each representing a specific k-mer pair's contribution to the characterization of the sequentiality uniqueness of the sequence. This newly defined k-mer pair's contribution is an integration of the reverse Kullback-Leibler divergence, pseudo mode and the classic entropy of an inner distance distribution of the k-mer pair in the sequence. Our method has been tested on datasets of complete genome sequences, complete protein sequences, and gene sequences of rRNA of various lengths. Our method achieves the best performance in comparison with state-of-the-art alignment-free methods as measured by the Robinson-Foulds distance between the reference and the constructed phylogeny trees.

Phylogenies from unaligned proteomes using sequence environments of amino acid residues

Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Several algorithms have been implemented in diverse software packages. Despite the great number of existing methods, most of them are based on word statistics. Although they propose different filtering and weighting strategies and explore different metrics, their performance may be limited by the phylogenetic signal preserved in these words. Herein, we present a different approach based on the species-specific amino acid neighborhood preferences. These differential preferences can be assessed in the context of vector spaces. In this way, a distance-based method to build phylogenies has been developed and implemented into an easy-to-use R package. Tests run on real-world datasets show that this method can reconstruct phylogenetic relationships with high accuracy, and often outperforms other alignment-free approaches. Furthermore, we present evidence that the new method can perform reliably on datasets formed by non-orthologous protein sequences, that is, the method not only does not require the identification of orthologous proteins, but also does not require their presence in the analyzed dataset. These results suggest that the neighborhood preference of amino acids conveys a phylogenetic signal that may be of great utility in phylogenomics.

Characterization of Microorganisms from Protaetia brevitarsis Larva Frass

Decomposers play an important role in the biogeochemical cycle. Protaetia brevitarsis larvae (PBLs) can transform wastes into frass rich in humic acid (HA) and microorganisms, which may increase the disease resistance of plants and promote plant growth. Beyond HA, the microorganisms may also contribute to the biostimulant activity. To address this hypothesis, we investigated the potential microbial community in the PBL frass samples and elucidated their functions of disease resistance and plant growth promotion. High-throughput sequencing analysis of four PBL-relevant samples showed that their frass can influence the microbial community of the surrounding environment. Further analysis showed that there were many microorganisms beneficial to agriculture, such as Bacillus. Therefore, culturable Bacillus microbes were isolated from frass, and 16S rDNA gene analysis showed that Bacillus subtilis was the dominant species. In addition, some Bacillus microorganisms isolated from the PBL frass had antibacterial activities against pathogenic fungi. The plant growth promotion pot experiment also proved that some strains promote plant growth. In conclusion, this study demonstrated that the microorganisms in the PBL frass are conducive to colonizing the surrounding organic matrix, which will help beneficial microbes to increase the disease resistance of plants and promote plant growth.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

The Second Chromosome Promotes the Adaptation of the Genus Flammeovirga to Complex Environments

Approximately 10% of bacterial strains contain more than one chromosome; however, in contrast to the primary chromosomes, the mechanisms underlying the formation of the second chromosomes and the significance of their existence remain unclear. Species of the genus Flammeovirga are typical polysaccharide-degrading bacteria, and herein, we report complete genome maps of this genus. These genomes all had multireplicons and second chromosomes. The second chromosome, much larger than plasmids and even megaplasmids, had rRNA and a disparity of 1% relative to the main chromosome in guanine-cytosine (GC) content. The largest chromosomes carried core genes for cellular processes, while the second chromosomes were enriched with genes involved in the transport and metabolism of inorganic ions and carbohydrates, particularly genes encoding glycoside hydrolases and polysaccharide lyases, which constituted the genetic basis for the strains’ excellent capabilities to utilize polysaccharides. The second chromosomal evolution had a higher mutation rate than the primary chromosomes. Furthermore, the second chromosomes were also enriched in horizontal transfer genes and duplicated genes. The primary chromosomes were more evolutionarily conserved, while the second chromosomes were more plastic, which might be related to their different roles in the bacterial survival process. This study can be used as an example to explain possible formation mechanisms and functions of the second chromosomes, providing a reference for peer research on the second chromosomes. In particular, the second chromosomes were enriched in polysaccharide-degrading enzymes, which will provide theoretical support for using genomic data to mine tool-type carbohydrase resources.

IMPORTANCE For decades, the typical bacterial genome has been thought to contain a single chromosome and a few small plasmids carrying nonessential genes. However, an increasing number of secondary chromosomes have been identified in various bacteria (e.g., plant symbiotic bacteria and human pathogens). This study reported three complete genomes of the polysaccharide-degrading marine bacterial genus Flammeovirga, revealed that they harbor two chromosomes, and further identified that the presence of a multireplicon system is a characteristic of complete Flammeovirga genomes. These sequences will add to our knowledge on secondary chromosomes, especially within Bacteroidetes. This study indicated that the second chromosomes of the genus Flammeovirga initially originated from an ancestral plasmid and subsequently expanded by gene duplication or by obtaining heterologous genes with functions, thus promoting host strains to adapt to complex living environments (e.g., to degrade more diverse polysaccharides from marine environments). These findings will promote the understanding of the evolution and function of bacteria with multireplicon systems.

Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum

DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria.

IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.

Relationship of the Pine Growth Promoting Pantoea eucalypti FBS135 with Type Strains P. eucalypti LMG 24197T and P. vagans 24199T

Endophytes in woody plants are much less understood. Pantoea strain FBS135 is an endophytic bacterium isolated from Pinus massoniana with the ability to promote pine growth significantly. In this study, we demonstrated that FBS135 has the astonishing ability of low nitrogen tolerance but no ability of nitrogen fixation. To exactly determine the phylogenetic status of FBS135, we sequenced the whole genomes of P. eucalypti LMG 24197^T and P. vagans 24199^T, type strains of two Pantoea species, which are evolutionarily closest to FBS135. P. eucalypti LMG 24197^T contained a single chromosome of 4,035,995 bp (C+G, 54.6%) plus three circular plasmids while LMG 24199^T comprises a single circular chromosome of 4,050,173 bp (C+G, 55.6%) and two circular plasmids. With the genomic information, FBS135 was finally identified as a P. eucalypti strain, although it showed some different physiological traits from the two type strains. Comparative genomic analyses were performed for the three strains, revealing their common molecular basis associated with plant lifecycle as well as the differences in their gene arrangements relating to nitrogen utilization.

CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool based on Composition Vectors of Genomes

CVTree is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It had been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplasts, mitochondria, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16S rRNA sequences, we showed that CVTree software is an efficient and effective tool for the studying of phylogeny and taxonomy based on genome sequences. Code availability: https://github.com/ghzuo/cvtree.

The Gut Microbiota in Prediabetes and Diabetes: A Population-Based Cross-Sectional Study

The link between the gut microbiota and type 2 diabetes (T2D) warrants further investigation because of known confounding effects from antidiabetic treatment. Here, we profiled the gut microbiota in a discovery (n = 1,011) and validation (n = 484) cohort comprising Swedish subjects naive for diabetes treatment and grouped by glycemic status. We observed that overall gut microbiota composition was altered in groups with impaired glucose tolerance, combined glucose intolerance and T2D, but not in those with impaired fasting glucose. In addition, the abundance of several butyrate producers and functional potential for butyrate production were decreased both in prediabetes and T2D groups. Multivariate analyses and machine learning microbiome models indicated that insulin resistance was strongly associated with microbial variations. Therefore, our study indicates that the gut microbiota represents an important modifiable factor to consider when developing precision medicine approaches for the prevention and/or delay of T2D.

Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by Recombination

Many bacterial species contain DNA methyltransferases that have random on/off switching of expression. These systems, called phasevarions (phase-variable regulons), control the expression of multiple genes by global methylation changes. In every previously characterized phasevarion, genes involved in pathobiology, antibiotic resistance, and potential vaccine candidates are randomly varied in their expression, commensurate with methyltransferase switching. Our systematic study to determine the extent of phasevarions controlled by invertible Type I R-M systems will provide valuable information for understanding how bacteria regulate genes and is key to the study of physiology, virulence, and vaccine development; therefore, it is critical to identify and characterize phase-variable methyltransferases controlling phasevarions.

N⁶-Adenine DNA methyltransferases associated with some Type I and Type III restriction-modification (R-M) systems are able to undergo phase variation, randomly switching expression ON or OFF by varying the length of locus-encoded simple sequence repeats (SSRs). This variation of methyltransferase expression results in genome-wide methylation differences and global changes in gene expression. These epigenetic regulatory systems are called phasevarions, phase-variable regulons, and are widespread in bacteria. A distinct switching system has also been described in Type I R-M systems, based on recombination-driven changes in hsdS genes, which dictate the DNA target site. In order to determine the prevalence of recombination-driven phasevarions, we generated a program called RecombinationRepeatSearch to interrogate REBASE and identify the presence and number of inverted repeats of hsdS downstream of Type I R-M loci. We report that 3.9% of Type I R-M systems have duplicated variable hsdS genes containing inverted repeats capable of phase variation. We report the presence of these systems in the major pathogens Enterococcus faecalis and Listeria monocytogenes, which could have important implications for pathogenesis and vaccine development. These data suggest that in addition to SSR-driven phasevarions, many bacteria have independently evolved phase-variable Type I R-M systems via recombination between multiple, variable hsdS genes.

IMPORTANCE Many bacterial species contain DNA methyltransferases that have random on/off switching of expression. These systems, called phasevarions (phase-variable regulons), control the expression of multiple genes by global methylation changes. In every previously characterized phasevarion, genes involved in pathobiology, antibiotic resistance, and potential vaccine candidates are randomly varied in their expression, commensurate with methyltransferase switching. Our systematic study to determine the extent of phasevarions controlled by invertible Type I R-M systems will provide valuable information for understanding how bacteria regulate genes and is key to the study of physiology, virulence, and vaccine development; therefore, it is critical to identify and characterize phase-variable methyltransferases controlling phasevarions.

Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera

Members of the genus Metallosphaera are widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequenced Metallosphaera tengchongensis Ric-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with other Metallosphaera genomes. The genome of M. tengchongensis had an average nucleotide identity (ANI) of approximately 70% to that of Metallosphaera cuprina. Genes sqr, tth, sir, tqo, hdr, tst, soe, and sdo associated with sulfur oxidation, and gene clusters fox and cbs involved in iron oxidation existed in all Metallosphaera genomes. However, the adenosine-5'-phosphosulfate (APS) pathway was only detected in Metallosphaera sedula and Metallosphaera yellowstonensis, and several subunits of fox cluster were lost in M. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in all Metallosphaera genomes. A large number of gene family gain events occurred in M. yellowstonensis and M. sedula, whereas gene family loss events occurred frequently in M. cuprina. Pervasive strong purifying selection was found acting on the gene families of Metallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits of Metallosphaera species and sheds light on their evolution.

Comparative Genomics of Acinetobacter baumannii Clinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes

Acinetobacter baumannii is an opportunistic bacterial pathogen infecting immunocompromised patients and has gained attention worldwide due to its increased antimicrobial resistance. Here, we report a comparative whole-genome sequencing and analysis coupled with an assessment of antibiotic resistance of 46 Acinetobacter strains (45 A. baumannii plus one Acinetobacter nosocomialis) originated from five hospitals from the city of Recife, Brazil, between 2010 and 2014. An average of 3,809 genes were identified per genome, although only 2,006 genes were single copy orthologs or core genes conserved across all sequenced strains, with an average of 42 new genes found per strain. We evaluated genetic distance through a phylogenetic analysis and MLST as well as the presence of antibiotic resistance genes, virulence markers and mobile genetic elements (MGE). The phylogenetic analysis recovered distinct monophyletic A. baumannii groups corresponding to five known (ST1, ST15, ST25, ST79, and ST113) and one novel ST (ST881, related to ST1). A large number of ST specific genes were found, with the ST79 strains having the largest number of genes in common that were missing from the other STs. Multiple genes associated with resistance to β-lactams, aminoglycosides and other antibiotics were found. Some of those were clearly mapped to defined MGEs and an analysis of those revealed known elements as well as a novel Tn7-Tn3 transposon with a clear ST specific distribution. An association of selected resistance/virulence markers with specific STs was indeed observed, as well as the recent spread of the OXA-253 carbapenemase encoding gene. Virulence genes associated with the synthesis of the capsular antigens were noticeably more variable in the ST113 and ST79 strains. Indeed, several resistance and virulence genes were common to the ST79 and ST113 strains only, despite a greater genetic distance between them, suggesting common means of genetic exchange. Our comparative analysis reveals the spread of multiple STs and the genomic plasticity of A. baumannii from different hospitals in a single metropolitan area. It also highlights differences in the spread of resistance markers and other MGEs between the investigated STs, impacting on the monitoring and treatment of Acinetobacter in the ongoing and future outbreaks.

Shifts in the Bacterial Population and Ecosystem Functions in Response to Vegetation in the Yellow River Delta Wetlands

Vegetation represents probably the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift along with vegetation. In this study, we found that the richness and diversity of soil bacteria increased with vegetation levels and that the community composition was distinctly shifted from bare to vegetative places. The bare land displayed an extremely high abundance of Cyanobacteria as a monospecies genus, while a Gemmatimonadetes genus was predominant as multiple species in all the vegetative wetlands, suggesting their important ecosystem functions and potential mechanisms. Expression of the genes related to photosynthesis was enriched exclusively in bare land. Genes involved in biological organic carbon metabolism and the cycling of main elements (C, N, S, and P) were highly expressed in vegetative wetlands and were mostly included in the metagenome-assembled genome (MAG) of Gemmatimonadetes Some compounds identified from soil metabolomic results also corresponded to pathways involving these key active genes. Cyanobacteria is thus responsible for the carbon sink in early infertile wetlands, and Gemmatimonadetes plays a crucial role in ecosystem functions in vegetative wetlands. Our results highlight that the soil microbial populations execute ecosystem functions for wetlands and that vegetation is the determinant for the population and functional shifts in the coastal estuarine wetland of the Yellow River Delta.IMPORTANCE Vegetation probably represents the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift in pace with the colonization and succession of vegetation. In this study, we found that a Cyanobacteria monospecies genus and a Gemmatimonadetes multispecies genus are fastidiously predominant in the bare and vegetative wetlands of the Yellow River Delta, respectively. Consistently, photosynthesis genes were enriched exclusively in bare land, while genes involved in biological organic carbon metabolism and the cycling of main elements were highly expressed in vegetative wetlands, were mostly included in the MAG of Gemmatimonadetes, and were consistent with soil metabolomic results. Our results provide insight into the adaptive succession of predominant bacterial species and their ecosystem functions in response to the presence of vegetation.

Positional Correlation Natural Vector: A Novel Method for Genome Comparison

Advances in sequencing technology have made large amounts of biological data available. Evolutionary analysis of data such as DNA sequences is highly important in biological studies. As alignment methods are ineffective for analyzing large-scale data due to their inherently high costs, alignment-free methods have recently attracted attention in the field of bioinformatics. In this paper, we introduce a new positional correlation natural vector (PCNV) method that involves converting a DNA sequence into an 18-dimensional numerical feature vector. Using frequency and position correlation to represent the nucleotide distribution, it is possible to obtain a PCNV for a DNA sequence. This new numerical vector design uses six suitable features to characterize the correlation among nucleotide positions in sequences. PCNV is also very easy to compute and can be used for rapid genome comparison. To test our novel method, we performed phylogenetic analysis with several viral and bacterial genome datasets with PCNV. For comparison, an alignment-based method, Bayesian inference, and two alignment-free methods, feature frequency profile and natural vector, were performed using the same datasets. We found that the PCNV technique is fast and accurate when used for phylogenetic analysis and classification of viruses and bacteria.

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota

The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.

Resolution of deep divergence of club fungi (phylum Basidiomycota)

A long-standing question about the early evolution of club fungi (phylum Basidiomycota) is the relationship between the three major groups, Pucciniomycotina, Ustilaginomycotina and Agaricomycotina. It is unresolved whether Agaricomycotina are more closely related to Ustilaginomycotina or to Pucciniomycotina. Here we reconstructed the branching order of the three subphyla through two sources of phylogenetic signals, i.e. standard phylogenomic analysis and alignment-free phylogenetic approach. Overall, beyond congruency within the frame of standard phylogenomic analysis, our results consistently and robustly supported the early divergence of Ustilaginomycotina and a closer relationship between Agaricomycotina and Pucciniomycotina.

Comprehensive genomic analysis of an indigenous Pseudomonas pseudoalcaligenes degrading phenolic compounds

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.

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.

Prevalence and characterization of Staphylococcus aureus in wastewater treatment plants by whole genomic sequencing

Infections with Staphylococcus aureus are being spread through contact with the community environment, but the role of wastewater treatment plants in the transmission routes is not defined. This study investigated the prevalence, types, genetic elements, and potential for transmission of S. aureus by these engineered systems. Synchronized sampling events at two wastewater treatment plants were conducted with isolates of S. aureus obtained by a selective enrichment method using acriflavine that suppressed Staphylococcus epidermidis growth. DNA was extracted from a subset of the S. aureus isolates, checked by PCR to assure the absence of S. epidermidis, and sequenced to determine the multilocus sequence type, spa type, and carriage of the methicillin resistance and Panton-Valentine leukocidin genetic elements. Sequences were analyzed for single nucleotide polymorphism differences in pairwise comparison of isolates. There were two dominant S. aureus clonal complexes identified in the isolates, one commonly identified as hospital-related (CC5) and one community-related (CC8). Both types of isolates were found at both treatment facilities, even though only one facility had significant hospital sewage inputs. The presence of S. aureus persisted through treatment, with some isolates recovered from the final processes showing genetic diversity. The presence of the Panton-Valentine leukocidin genetic element was greater than the 1-5% expected from global reports. Our results suggest that treatment provides an opportunity for genetic shift, while the persistence and release of evolved strains of S. aureus may provide an environmentally relevant pathway to new hosts in the environment.

A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

This paper describes a novel alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences using publicly available bioinformatics tools. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution. These pairwise evolutionary distances are then used to infer a phylogenetic tree and assess a confidence support for each internal branch. Analyses of both simulated and real genome datasets show that this bioinformatics procedure allows accurate phylogenetic trees to be reconstructed with fast running times, especially when launched on multiple threads. Implemented in a publicly available script, named JolyTree, this procedure is a useful approach for quickly inferring species trees without the burden and potential biases of multiple sequence alignments.

Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.

Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders

Phylogenetic studies based on a definite set of marker genes usually reconstruct evolutionary relationships among the prokaryotic species. Based on specific target sequences, such studies represent variations and allow identification of similarities or dissimilarities in organisms. With the advent of completely sequenced genomes and accumulation of information on whole prokaryotic genomes, phylogenetic reconstructions should be considered more reliable if they are ideally based on entire genomes to resolve phylogenetic interest. We applied phylogenomics approaches taking into account completely sequenced cyanobacterial genomes to reconstruct underlying species that represented major taxonomic classes and belonged to distinctly different habitats (freshwater, marine, soils, and rocks). We did not rely on describing phylogeny of all representative class of cyanobacterial species on the basis of only ribosomal gene, 16S rDNA gene. In contrast, we analyzed combined molecular marker and phylogenomics approaches (genome alignment, gene content and gene order, composition vector and protein domain content) for accurately inferring phylogenetic relationship of species. We have shown that this approach reflects the impact of evolution on the organisms and considers connects with the ecological adaptation in cyanobacteria in different habitats. Analysis revealed that the members from marine habitat occupy different profile than those from freshwater. Impact of GC content and genomic repetitiveness over the diversification of cyanobacterial species and their possible role in adaptation was also reflected. Members occupying similar habitats cover more evolutionary distance together and also evolve various strategies for adaptation and survival either through genomic repetitiveness or preferences for genes of particular functions or modified GC content. Genomes undergo different changes for their adaptation in diverse habitats.

Role of the acquisition of a type 3 secretion system in the emergence of novel pathogenic strains of Xanthomonas

Cases of emergence of novel plant-pathogenic strains are regularly reported that reduce the yields of crops and trees. However, the molecular mechanisms underlying such emergence are still poorly understood. The acquisition by environmental non-pathogenic strains of novel virulence genes by horizontal gene transfer has been suggested as a driver for the emergence of novel pathogenic strains. In this study, we tested such an hypothesis by transferring a plasmid encoding the type 3 secretion system (T3SS) and four associated type 3 secreted proteins (T3SPs) to the non-pathogenic strains of Xanthomonas CFBP 7698 and CFBP 7700, which lack genes encoding T3SS and any previously known T3SPs. The resulting strains were phenotyped on Nicotiana benthamiana using chlorophyll fluorescence imaging and image analysis. Wild-type, non-pathogenic strains induced a hypersensitive response (HR)-like necrosis, whereas strains complemented with T3SS and T3SPs suppressed this response. Such suppression depends on a functional T3SS. Amongst the T3SPs encoded on the plasmid, Hpa2, Hpa1 and, to a lesser extent, XopF1 collectively participate in suppression. Monitoring of the population sizes in planta showed that the sole acquisition of a functional T3SS by non-pathogenic strains impairs growth inside leaf tissues. These results provide functional evidence that the acquisition via horizontal gene transfer of a T3SS and four T3SPs by environmental non-pathogenic strains is not sufficient to make strains pathogenic. In the absence of a canonical effector, the sole acquisition of a T3SS seems to be counter-selective, and further acquisition of type 3 effectors is probably needed to allow the emergence of novel pathogenic strains.

Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.

Dissemination of Genetic Acquisition/Loss Provides a Variety of Quorum Sensing Regulatory Properties in Pseudoalteromonas

A bstract: Quorum sensing (QS) enables single-celled bacteria to communicate with chemical signals in order to synchronize group-level bacterial behavior. Pseudoalteromonas are marine bacteria found in versatile environments, of which QS regulation for their habitat adaptation is extremely fragmentary. To distinguish genes required for QS regulation in Pseudoalteromonas, comparative genomics was deployed to define the pan-genomics for twelve isolates and previously-sequenced genomes, of which acyl-homoserine lactone (AHL)-based QS traits were characterized. Additionally, transposon mutagenesis was used to identify the essential QS regulatory genes in the selected Pseudoalteromonas isolate. A remarkable feature showed that AHL-based colorization intensity of biosensors induced by Pseudoalteromonas most likely correlates with QS regulators genetic heterogeneity within the genus. This is supported by the relative expression levels of two of the main QS regulatory genes (luxO and rpoN) analyzed in representative Pseudoalteromonas isolates. Notably, comprehensive QS regulatory schema and the working model proposed in Pseudoalteromonas seem to phylogenetically include the network architectures derived from Escherichia coli, Pseudomonas, and Vibrio. Several associated genes were mapped by transposon mutagenesis. Among them, a right origin-binding protein-encoding gene (robp) was functionally identified as a positive QS regulatory gene. This gene lies on a genomic instable region and exists in the aforementioned bioinformatically recruited QS regulatory schema. The obtained data emphasize that the distinctly- and hierarchically-organized mechanisms probably target QS association in Pseudoalteromonas dynamic genomes, thus leading to bacterial ability to accommodate their adaption fitness and survival advantages.

Metabolic Interactions of a Chain Elongation Microbiome

Carbon chain elongation (CCE), a reaction within the carboxylate platform that elongates short-chain to medium-chain carboxylates by mixed culture, has attracted worldwide interest. The present study provides insights into the microbial diversity and predictive microbial metabolic pathways of a mixed-culture CCE microbiome on the basis of a comparative analysis of the metagenome and metatranscriptome. We found that the microbial structure of an acclimated chain elongation microbiome was a highly similar to that of the original inoculating biogas reactor culture; however, the metabolic activities were completely different, demonstrating the high stability of the microbial structure and flexibility of its functions. Additionally, the fatty acid biosynthesis (FAB) pathway, rather than the well-known reverse β-oxidation (RBO) pathway for CCE, was more active and pivotal, though the FAB pathway had more steps and consumed more ATP, a phenomenon that has rarely been observed in previous CCE studies. A total of 91 draft genomes were reconstructed from the metagenomic reads, of which three were near completion (completeness, >97%) and were assigned to unknown strains of Methanolinea tarda, Bordetella avium, and Planctomycetaceae The last two strains are likely new-found active participators of CCE in the mixed culture. Finally, a conceptual framework of CCE, including both pathways and the potential participators, was proposed.IMPORTANCE Carbon chain elongation means the conversion of short-chain volatile fatty acids to medium-chain carboxylates, such as n-caproate and n-caprylate with electron donors under anaerobic condition. This bio-reaction can both expand the resource of valuable biochemicals and broaden the utilization of low-grade organic residues in a sustainable biorefinery context. Clostridium kluyveri is conventionally considered model microbe for carbon chain elongation which uses the reverse β-oxidation pathway. However, little is known about the detailed microbial structure and function of other abundant microorganism in a mixed culture (or open culture) of chain elongation. We conducted the comparative metagenomic and metatranscriptomic analysis of a chain elongation microbiome to throw light on the underlying functional microbes and alternative pathways.

Genome mining of Streptomyces xinghaiensis NRRL B-24674T for the discovery of the gene cluster involved in anticomplement activities and detection of novel xiamycin analogs

Marine actinobacterium Streptomyces xinghaiensis NRRL B-24674^T has been characterized as a novel species, but thus far, its biosynthetic potential remains unexplored. In this study, the high-quality genome sequence of S. xinghaiensis NRRL B-24674^T was obtained, and the production of anticomplement agents, xiamycin analogs, and siderophores was investigated by genome mining. Anticomplement compounds are valuable for combating numerous diseases caused by the abnormal activation of the human complement system. The biosynthetic gene cluster (BGC) nrps1 resembles that of complestatins, which are potent microbial-derived anticomplement agents. The identification of the nrps1 BGC revealed a core peptide that differed from that in complestatin; thus, we studied the anticomplement activity of this strain. The culture broth of S. xinghaiensis NRRL B-24674^T displayed good anticomplement activity. Subsequently, the disruption of the genes in the nrps1 BGC resulted in the loss of anticomplement activity, confirming the involvement of this BGC in the biosynthesis of anticomplement agents. In addition, the mining of the BGC tep5, which resembles that of the antiviral pentacyclic indolosesquiterpene xiamycin, resulted in the discovery of nine xiamycin analogs, including three novel compounds. In addition to the BGCs responsible for desferrioxamine B, neomycin, ectoine, and carotenoid, 18 BGCs present in the genome are predicted to be novel. The results of this study unveil the potential of S. xinghaiensis as a producer of novel anticomplement agents and provide a basis for further exploration of the biosynthetic potential of S. xinghaiensis NRRL B-24674^T for the discovery of novel bioactive compounds by genome mining.

Imputing missing distances in molecular phylogenetics

Missing data are frequently encountered in molecular phylogenetics, but there has been no accurate distance imputation method available for distance-based phylogenetic reconstruction. The general framework for distance imputation is to explore tree space and distance values to find an optimal combination of output tree and imputed distances. Here I develop a least-square method coupled with multivariate optimization to impute multiple missing distance in a distance matrix or from a set of aligned sequences with missing genes so that some sequences share no homologous sites (whose distances therefore need to be imputed). I show that phylogenetic trees can be inferred from distance matrices with about 10% of distances missing, and the accuracy of the resulting phylogenetic tree is almost as good as the tree from full information. The new method has the advantage over a recently published one in that it does not assume a molecular clock and is more accurate (comparable to maximum likelihood method based on simulated sequences). I have implemented the function in DAMBE software, which is freely available at http://dambe.bio.uottawa.ca.

Bioinformatics and Translation Elongation

Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.

Genome Sequencing and analyses of Two Marine Fungi from the North Sea Unraveled a Plethora of Novel Biosynthetic Gene Clusters

Marine Fungi are potent secondary metabolite producers. However, limited genetic information are available their biosynthetic gene clusters (BGCs) and their biotechnological applications. To overcome this lack of information, herein, we used next-generation sequencing methods for genome sequencing of two marine fungi, isolated from the German Wadden Sea, namely Calcarisporium sp. KF525 and Pestalotiopsis sp. KF079. The assembled genome size of the marine isolate Calcarisporium sp. KF525 is about 36.8 Mb with 60 BGCs, while Pestalotiopsis sp. KF079 has a genome size of 47.5 Mb harboring 67 BGCs. Of all BGCs, 98% and 97% are novel clusters of Calcarisporium sp. and Pestalotiopsis sp., respectively. Only few of the BGCs were found to be expressed under laboratory conditions by RNA-seq analysis. The vast majority of all BGCs were found to be novel and unique for these two marine fungi. Along with a description of the identified gene clusters, we furthermore present important genomic features and life-style properties of these two fungi. The two novel fungal genomes provide a plethora of new BGCs, which may have biotechnological applications in the future, for example as novel drugs. The genomic characterizations will provide assistance in future genetics and genomic analyses of marine fungi.

Genome Mining of the Marine Actinomycete Streptomyces sp. DUT11 and Discovery of Tunicamycins as Anti-complement Agents

Marine actinobacteria are potential producers of various secondary metabolites with diverse bioactivities. Among various bioactive compounds, anti-complement agents have received great interest for drug discovery to treat numerous diseases caused by inappropriate activation of the human complement system. However, marine streptomycetes producing anti-complement agents are still poorly explored. In this study, a marine-derived strain Streptomyces sp. DUT11 showing superior anti-complement activity was focused, and its genome sequence was analyzed. Gene clusters showing high similarities to that of tunicamycin and nonactin were identified, and their corresponding metabolites were also detected. Subsequently, tunicamycin I, V, and VII were isolated from Streptomyces sp. DUT11. Anti-complement assay showed that tunicamycin I, V, VII inhibited complement activation through the classic pathway, whereas no anti-complement activity of nonactin was detected. This is the first time that tunicamycins are reported to have such activity. In addition, genome analysis indicates that Streptomyces sp. DUT11 has the potential to produce novel lassopeptides and lantibiotics. These results suggest that marine Streptomyces are rich sources of anti-complement agents for drug discovery.

Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

The gut microbiota benefits humans via short-chain fatty acid (SCFA) production from carbohydrate fermentation, and deficiency in SCFA production is associated with type 2 diabetes mellitus (T2DM). We conducted a randomized clinical study of specifically designed isoenergetic diets, together with fecal shotgun metagenomics, to show that a select group of SCFA-producing strains was promoted by dietary fibers and that most other potential producers were either diminished or unchanged in patients with T2DM. When the fiber-promoted SCFA producers were present in greater diversity and abundance, participants had better improvement in hemoglobin A1c levels, partly via increased glucagon-like peptide-1 production. Promotion of these positive responders diminished producers of metabolically detrimental compounds such as indole and hydrogen sulfide. Targeted restoration of these SCFA producers may present a novel ecological approach for managing T2DM.

A Large-Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom-Forming Microcystis-Epibiont Communities

Cyanobacterial blooms are worldwide issues of societal concern and scientific interest. Lake Taihu and Lake Dianchi, two of the largest lakes in China, have been suffering from annual Microcystis-based blooms over the past two decades. These two eutrophic lakes differ in both nutrient load and environmental parameters, where Microcystis microbiota consisting of different Microcystis morphospecies and associated bacteria (epibionts) have dominated. We conducted a comprehensive metagenomic study that analyzed species diversity, community structure, functional components, metabolic pathways and networks to investigate functional interactions among the members of six Microcystis-epibiont communities in these two lakes. Our integrated metagenomic pipeline consisted of efficient assembly, binning, annotation, and quality assurance methods that ensured high-quality genome reconstruction. This study provides a total of 68 reconstructed genomes including six complete Microcystis genomes and 28 high quality bacterial genomes of epibionts belonging to 14 distinct taxa. This metagenomic dataset constitutes the largest reference genome catalog available for genome-centric studies of the Microcystis microbiome. Epibiont community composition appears to be dynamic rather than fixed, and the functional profiles of communities were related to the environment of origin. This study demonstrates mutualistic interactions between Microcystis and epibionts at genetic and metabolic levels. Metabolic pathway reconstruction provided evidence for functional complementation in nitrogen and sulfur cycles, fatty acid catabolism, vitamin synthesis, and aromatic compound degradation among community members. Thus, bacterial social interactions within Microcystis-epibiont communities not only shape species composition, but also stabilize the communities functional profiles. These interactions appear to play an important role in environmental adaptation of Microcystis colonies.

Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus denitrificans Strain ISTOD1, Isolated from Wastewater

We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb, isolated from wastewater. It has been identified as a heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis revealed genes related to nitrogen and phosphorus removal, showing that the strain holds potential for bioremediation and biorefinery uses.

Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights

Clostridium species (particularly Clostridium difficile, Clostridium botulinum, Clostridium tetani and Clostridium perfringens) are associated with a range of human and animal diseases. Several other species including Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum have also been linked with sporadic human infections, however there is very limited, or in some cases, no genomic information publicly available. Thus, we isolated one C. tertium strain, one C. cadaveris strain and three C. paraputrificum strains from preterm infants residing within neonatal intensive care units and performed Whole Genome Sequencing (WGS) using Illumina HiSeq. In this report, we announce the open availability of the draft genomes: C. tertium LH009, C. cadaveris LH052, C. paraputrificum LH025, C. paraputrificum LH058, and C. paraputrificum LH141. These genomes were checked for contamination in silico to ensure purity, and we confirmed species identity and phylogeny using both 16S rRNA gene sequences (from PCR and in silico) and WGS-based approaches. Average Nucleotide Identity (ANI) was used to differentiate genomes from their closest relatives to further confirm speciation boundaries. We also analysed the genomes for virulence-related factors and antimicrobial resistance genes, and detected presence of tetracycline and methicillin resistance, and potentially harmful enzymes, including multiple phospholipases and toxins. The availability of genomic data in open databases, in tandem with our initial insights into the genomic content and virulence traits of these pathogenic Clostridium species, should enable the scientific community to further investigate the disease-causing mechanisms of these bacteria with a view to enhancing clinical diagnosis and treatment.

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

Draft Genome Sequence of Zhihengliuella sp. Strain ISTPL4, a Psychrotolerant and Halotolerant Bacterium Isolated from Pangong Lake, India

Zhihengliuella sp. strain ISTPL4, a psychrotolerant bacterium, was isolated from brackish water of the high-altitude Pangong Lake in India. In this study, we report its draft genome sequence, which contains 3,529,629 bp with a G+C content of 69.84%. The genome is enriched in genes associated with cold adaptation and plant growth promotion.

A Potential New Human Pathogen Belonging to Helicobacter Genus, Identified in a Bloodstream Infection

We isolated from aerobic and anaerobic blood culture bottles from a febrile patient, a Helicobacter-like Gram negative, rod-shaped bacterium that MALDI-TOF MS failed to identify. Blood agar cultures incubated in a microaerobic atmosphere revealed a motile Gram negative rod, which was oxidase, catalase, nitrate reductase, esterase, and alkaline phosphatase positive. It grew at 42°C with no detectable urease activity. Antimicrobial susceptibility testing showed that the organism was susceptible to beta-lactams, gentamicin, erythromycin, and tetracycline but resistant to ciprofloxacin. Electronic microscopy analysis revealed a 3 × 0.5 μm curved rod bacterium harboring two sheathed amphitrichous flagella. Whole genome sequencing revealed a genome 1,708,265 base-pairs long with a GC content of 37.80% and a total of 1,697 coding sequences. The genomic analyses using the nucleotide sequences of the 16S rRNA gene, hsp60 and gyrB genes, as well as the GyrA protein sequence, and the results of Average Nucleotide Identity and in silico DNA-DNA hybridization suggest evidence for a novel Helicobacter species close to Helicobacter equorum and belonging to the group of enterohepatic Helicobacter species. As soon as the particular peptide mass fingerprint of this pathogen is added to the spectral databases, MALDI-TOF MS technology will improve its identification from clinical specimens, especially in case of “sterile infection”. We propose to associate the present strain with the Latin name of the place of isolation; Caesarodunum (Tours, France) and suggest “Helicobacter caesarodunensis” for further description of this new bacterium.

Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties

Genomic islands are genomic fragments of alien origin in bacterial and archaeal genomes, usually involved in symbiosis or pathogenesis. In this work, we described Zisland Explorer, a novel tool to predict genomic islands based on the segmental cumulative GC profile. Zisland Explorer was designed with a novel strategy, as well as a combination of the homogeneity and heterogeneity of genomic sequences. While the sequence homogeneity reflects the composition consistence within each island, the heterogeneity measures the composition bias between an island and the core genome. The performance of Zisland Explorer was evaluated on the data sets of 11 different organisms. Our results suggested that the true-positive rate (TPR) of Zisland Explorer was at least 10.3% higher than that of four other widely used tools. On the other hand, the new tool did not lose overall accuracy with the improvement in the TPR and showed better equilibrium among various evaluation indexes. Also, Zisland Explorer showed better accuracy in the prediction of experimental island data. Overall, the tool provides an alternative solution over other tools, which expands the field of island prediction and offers a supplement to increase the performance of the distinct predicting strategy. We have provided a web service as well as a graphical user interface and open-source code across multiple platforms for Zisland Explorer, which is available at http://cefg.uestc.edu.cn/Zisland_Explorer/ or http://tubic.tju.edu.cn/Zisland_Explorer/.

Global landscape of cell envelope protein complexes in Escherichia coli

Bacterial cell envelope protein (CEP) complexes mediate a range of processes, including membrane assembly, antibiotic resistance and metabolic coordination. However, only limited characterization of relevant macromolecules has been reported to date. Here we present a proteomic survey of 1,347 CEPs encompassing 90% inner- and outer-membrane and periplasmic proteins of Escherichia coli. After extraction with non-denaturing detergents, we affinity-purified 785 endogenously tagged CEPs and identified stably associated polypeptides by precision mass spectrometry. The resulting high-quality physical interaction network, comprising 77% of targeted CEPs, revealed many previously uncharacterized heteromeric complexes. We found that the secretion of autotransporters requires translocation and the assembly module TamB to nucleate proper folding from periplasm to cell surface through a cooperative mechanism involving the β-barrel assembly machinery. We also establish that an ABC transporter of unknown function, YadH, together with the Mla system preserves outer membrane lipid asymmetry. This E. coli CEP 'interactome' provides insights into the functional landscape governing CE systems essential to bacterial growth, metabolism and drug resistance.

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference.

Sequence-based information-theoretic features for gene essentiality prediction

Background

Identification of essential genes is not only useful for our understanding of the minimal gene set required for cellular life but also aids the identification of novel drug targets in pathogens. In this work, we present a simple and effective gene essentiality prediction method using information-theoretic features that are derived exclusively from the gene sequences.

Results

We developed a Random Forest classifier and performed an extensive model performance evaluation among and within 15 selected bacteria. In intra-organism predictions, where training and testing sets are taken from the same organism, AUC (Area Under the Curve) scores ranging from 0.73 to 0.90, 0.84 on average, were obtained. Cross-organism predictions using 5-fold cross-validation, pairwise, leave-one-species-out, leave-one-taxon-out, and cross-taxon yielded average AUC scores of 0.88, 0.75, 0.80, 0.82, and 0.78, respectively. To further show the applicability of our method in other domains of life, we predicted the essential genes of the yeast Schizosaccharomyces pombe and obtained a similar accuracy (AUC 0.84).

Conclusions

The proposed method enables a simple and reliable identification of essential genes without searching in databases for orthologs and demanding further experimental data such as network topology and gene-expression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1884-5) contains supplementary material, which is available to authorized users.

Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism of Pseudomonas sp. JY-Q

Microbial degradation of nicotine is an important process to control nicotine residues in the aqueous environment. In this study, a high active nicotine degradation strain named Pseudomonas sp. JY-Q was isolated from tobacco waste extract (TWE). This strain could completely degrade 5.0 g l⁻¹ nicotine in 24 h under optimal culture conditions, and it showed some tolerance even at higher concentrations (10.0 g l⁻¹) of nicotine. The complete genome of JY-Q was sequenced to understand the mechanism by which JY-Q could degrade nicotine and tolerate such high nicotine concentrations. Comparative genomic analysis indicated that JY-Q degrades nicotine through putative novel mechanisms. Two candidate gene cluster duplications located separately at distant loci were predicted to be responsible for nicotine degradation. These two nicotine (Nic) degradation-related loci (AA098_21325—AA098_21340, AA098_03885—AA098_03900) exhibit nearly completely consistent gene organization and component synteny. The nicotinic acid (NA) degradation gene cluster (AA098_17770–AA098_17790) and Nic-like clusters were both predicted to be flanked by mobile genetic elements (MGE). Furthermore, we analyzed the regions of genomic plasticity (RGP) in the JY-Q strain and found a dynamic genome carrying a type VI secretion system (T6SS) that promotes nicotine metabolism and tolerance based on transcriptomics and used in silico methods to identify the T6SS effector protein. Thus, a novel nicotine degradation mechanism was elucidated for Pseudomonas sp. JY-Q, suggesting its potential application in the bioremediation of nicotine-contaminated environments, such as TWEs.

Alignment-free sequence comparison: benefits, applications, and tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.

A novel fast vector method for genetic sequence comparison

With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for sequence analysis. Among these methods, many sorts of feature vector methods are established and applied to reconstruction of species phylogeny. The vectors basically consist of some typical numerical features for certain biological problems. The features may come from the primary sequences, secondary or three dimensional structures of macromolecules. In this study, we propose a novel numerical vector based on only primary sequences of organism to build their phylogeny. Three chemical and physical properties of primary sequences: purine, pyrimidine and keto are also incorporated to the vector. Using each property, we convert the nucleotide sequence into a new sequence consisting of only two kinds of letters. Therefore, three sequences are constructed according to the three properties. For each letter of each sequence we calculate the number of the letter, the average position of the letter and the variation of the position of the letter appearing in the sequence. Tested on several datasets related to mammals, viruses and bacteria, this new tool is fast in speed and accurate for inferring the phylogeny of organisms.

Prevalence and comparative analysis of the type IV secretion system in Aggregatibacter actinomycetemcomitan

BACKGROUD/PURPOSE

Aggregatibacter actinomycetemcomitans has emerged as one of the aetiological agents in periodontal disease. Although Type IV secretion systems (T4SSs) are widely distributed in many bacteria, the genetic features and distribution of T4SSs in A. actinomycetemcomitans remain unclear. In this study, we investigated the prevalence of A. actinomycetemcomitans serotypes and their T4SSs in a Taiwanese population.

METHODS

A comparative analysis of 20 A. actinomycetemcomitans genomes and their T4SSs deposited in GenBank was performed. One hundred subjects, including 20 periodontitis and 80 normal subjects, were enrolled and PCR identification of A. actinomycetemcomitans serotypes and T4SS genes were performed.

RESULTS

Of 100 subjects, serotypes C (22%) and E (11%) were most common. In addition, T4SSs were distributed in all of the serotypes. The prevalence of T4SSs and their location in plasmids in periodontitis subjects were 1.28-2 fold higher but not significantly different compared to normal subjects. Of 20 A. actinomycetemcomitans genomes, only ten with complete T4SS modules could be detected, which was highly correlated with localized aggressive periodontitis (p < 0.1). Nine of ten T4SS modules were from periodontitis subjects. Phylogenetic analysis of 10 T4SSs in A. actinomycetemcomitans showed that they were clustered into two groups, T4SS_AaI and T4SS_AaII, with only T4SS_AaI appearing in the Taiwanese subjects.

CONCLUSION

A. actinomycetemcomitans strains with different serotypes carrying T4SS_AaI are widely distributed in a Taiwanese population. This is the first report to show the distribution and detailed comparative genomics of T4SSs in A. actinomycetemcomitans.