IDBA – A Practical Iterative de Bruijn Graph De Novo Assembler

Presence and Persistence of ESKAPEE Bacteria before and after Hospital Wastewater Treatment

The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends of antibiotic-resistant bacteria. In this study, a cross-sectional collection of samples of hospital-associated raw and treated wastewater were obtained from February to March 2020. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize bacterial abundance and antimicrobial resistance gene analysis. The main bacterial phyla found in all the samples were as follows: Proteobacteria, Bacteroides, Firmicutes, and Actinobacteria. At the species level, ESKAPEE bacteria such as E. coli relative abundance decreased between raw and treated wastewater, but S. aureus, A. baumannii, and P. aeruginosa increased, as did the persistence of K. pneumoniae in both raw and treated wastewater. A total of 172 different ARGs were detected; blaOXA, blaVEB, blaKPC, blaGES, mphE, mef, erm, msrE, AAC(6'), ant(3″), aadS, lnu, PBP-2, dfrA, vanA-G, tet, and sul were found at the highest abundance and persistence. This study demonstrates the ability of ESKAPEE bacteria to survive tertiary treatment processes of hospital wastewater, as well as the persistence of clinically important antimicrobial resistance genes that are spreading in the environment.

Draft Genome Sequence and Comparative Genome Analysis Reveal Potential Functional Properties in Lacticaseibacillus paracasei ItalPN16

Nowadays, there is a great interest on rapid and effective methods for initial identification of probiotic bacteria. In this work, potential probiotic features of the lactic acid bacteria strain ItalPN16 isolated from a traditional Brazilian cheese were studied using bioinformatic tools. The complete genome sequence was obtained, and in silico analyses were carried out to identify the strain and its potential probiotic properties. The sequenced genome (3.02 Mb) presented 3126 protein-coding sequences distributed on 244 SEED subsystems, classifying the strain as nomadic lactobacilli. Phylogenetic and ANI analyses allowed to locate the ItalPN16 strain as a member of the Lacticaseibacillus paracasei group, due to the highest number of orthologous genes in common with reference L. paracasei strains (>98%). In silico analyses revealed the presence of CDSs related to microbe-host interactions, such as adhesion proteins and exopolysaccharide biosynthesis genes. The comparative analysis reveals the presence of a strain-specific glycosyl transferases, compared with other three L. paracasei strains and a high level of protein expression (92%) with the probiotic L. paracasei BL29. The results obtained here indicated interesting probiotic features of the strain L. paracasei ItalPN16 that could favor a future application in the food industry.

Space-time Trade-offs for the LCP Array of Wheeler DFAs

Recently, Conte et al. generalized the longest-common prefix (LCP) array from strings to Wheeler DFAs, and they showed that it can be used to efficiently determine matching statistics on a Wheeler DFA [DCC 2023]. However, storing the LCP array requires O n log n bits, n being the number of states, while the compact representation of Wheeler DFAs often requires much less space. In particular, the BOSS representation of a de Bruijn graph only requires a linear number of bits, if the size of alphabet is constant. In this paper, we propose a sampling technique that allows to access an entry of the LCP array in logarithmic time by only storing a linear number of bits. We use our technique to provide a space-time tradeoff to compute matching statistics on a Wheeler DFA. In addition, we show that by augmenting the BOSS representation of a k -th order de Bruijn graph with a linear number of bits we can navigate the underlying variable-order de Bruijn graph in time logarithmic in k , thus improving a previous bound by Boucher et al. which was linear in k [DCC 2015].

Hot moment of N2O emissions in seasonally frozen peatlands

Since the start of the Anthropocene, northern seasonally frozen peatlands have been warming at a rate of 0.6 °C per decade, twice that of the Earth's average rate, thereby triggering increased nitrogen mineralization with subsequent potentially large losses of nitrous oxide (N2O) to the atmosphere. Here we provide evidence that seasonally frozen peatlands are important N2O emission sources in the Northern Hemisphere and the thawing periods are the hot moment of annual N2O emissions. The flux during the hot moment of thawing in spring was 1.20 ± 0.82 mg N2O m-2 d-1, significantly higher than that during the other periods (freezing, -0.12 ± 0.02 mg N2O m-2 d-1; frozen, 0.04 ± 0.04 mg N2O m-2 d-1; thawed, 0.09 ± 0.01 mg N2O m-2 d-1) or observed for other ecosystems at the same latitude in previous studies. The observed emission flux is even higher than those of tropical forests, the World's largest natural terrestrial N2O source. Furthermore, based on soil incubation with 15N and 18O isotope tracing and differential inhibitors, heterotrophic bacterial and fungal denitrification was revealed as the main source of N2O in peatland profiles (0-200 cm). Metagenomic, metatranscriptomic, and qPCR assays further revealed that seasonally frozen peatlands have high N2O emission potential, but thawing significantly stimulates expression of genes encoding N2O-producing protein complexes (hydroxylamine dehydrogenase (hao) and nitric oxide reductase (nor)), resulting in high N2O emissions during spring. This hot moment converts seasonally frozen peatlands into an important N2O emission source when it is otherwise a sink. Extrapolation of our data to all northern peatland areas reveals that the hot moment emissions could amount to approximately 0.17 Tg of N2O yr-1. However, these N2O emissions are still not routinely included in Earth system models and global IPCC assessments.

The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes

Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to allow such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.

Bacillus velezensis strain Ag75 as a new multifunctional agent for biocontrol, phosphate solubilization and growth promotion in maize and soybean crops

Soybean and maize are some of the main drivers of Brazilian agribusiness. However, biotic and abiotic factors are of great concern, causing huge grain yield and quality losses. Phosphorus (P) deficiency is important among the abiotic factors because most Brazilian soils have a highly P-fixing nature. Thus, large amounts of phosphate fertilizers are regularly applied to overcome the rapid precipitation of P. Searching for alternatives to improve the use of P by crops is essential to reduce the demand for P input. The use of multifunctional rhizobacteria can be considered one of these alternatives. In this sense, the objective of the present work was to select and validate bacterial strains with triple action (plant growth promoter, phosphate solubilizer, and biocontrol agent) in maize and soybean, aiming to develop a multifunctional microbial inoculant for Brazilian agriculture. Bacterial strains with high indole acetic acid (IAA) production, phosphate solubilization, and antifungal activity against soil pathogenic fungi (Rhizoctonia solani, Macrophomina phaseolina, and Fusarium solani) were selected from the maize rhizosphere. Then, they were evaluated as growth promoters in maize under greenhouse conditions. Based on this study, strain 03 (Ag75) was selected due to its high potential for increasing biomass (root and shoot) and shoot P content in maize. This strain was identified through genomic sequencing as Bacillus velezensis. In field experiments, the inoculation of this bacterium increased maize and soybean yields by 17.8 and 26.5%, respectively, compared to the control (25 kg P₂O₅). In addition, the inoculation results did not differ from the control with 84 kg P₂O₅, indicating that it is possible to reduce the application of phosphate in these crops. Thus, the Ag75 strain has great potential for developing a multifunctional microbial inoculant that combines the ability to solubilize phosphate, promote plant growth, and be a biocontrol agent for several phytopathogenic fungi.

Phylogenetic relationships among Bombycinae (Lepidoptera, Bombycoidea, and Bombycidae) based on mitochondrial genomes

The subfamily Bombycinae Latreille, [1802] is an important silk-producing group, including well-known economical insects. Although there are many studies on the development of these economic insects, the relationships between genera/species of this subfamily are still unclear. Two data sets of mitochondrial genomes, 13 protein-coding genes (13PCGs) and 13PCGs-AA, were used to estimate phylogenetic relationships based on the maximum likelihood and Bayesian inference methods. The results strongly support the subfamily Bombycinae as a monophyletic group divided into two clades.

SNP4OrphanSpecies: A bioinformatics pipeline to isolate molecular markers for studying genetic diversity of orphan species

Background

For several decades, an increase in disease or pest emergences due to anthropogenic introduction or environmental changes has been recorded. This increase leads to serious threats to the genetic and species diversity of numerous ecosystems. Many of these events involve species with poor or no genomic resources (called here "orphan species"). This lack of resources is a serious limitation to our understanding of the origin of emergent populations, their ability to adapt to new environments and to predict future consequences to biodiversity. Analyses of genetic diversity are an efficient method to obtain this information rapidly, but require available polymorphic genetic markers.

New information

We developed a generic bioinformatics pipeline to rapidly isolate such markers with the goal for the pipeline to be applied in studies of invasive taxa from different taxonomic groups, with a special focus on forest fungal pathogens and insect pests. This pipeline is based on: 1) an automated de novo genome assembly obtained from shotgun whole genome sequencing using paired-end Illumina technology; 2) the isolation of single-copy genes conserved in species related to the studied emergent organisms; 3) primer development for multiplexed short sequences obtained from these conserved genes. Previous studies have shown that intronic regions of these conserved genes generally contain several single nucleotide polymorphisms within species. The pipeline's functionality was evaluated with sequenced genomes of five invasive or expanding pathogen and pest species in Europe (Armillariaostoyae (Romagn.) Herink 1973, Bursaphelenchusxylophilus Steiner & Buhrer 1934, Sphaeropsissapinea (fr.) Dicko & B. Sutton 1980, Erysiphealphitoides (Griffon & Maubl.) U. Braun & S. Takam. 2000, Thaumetopoeapityocampa Denis & Schiffermüller, 1775). We successfully isolated several pools of one hundred short gene regions for each assembled genome, which can be amplified in multiplex. The bioinformatics pipeline is user-friendly and requires little computational resources. This easy-to-set-up and run method for genetic marker identification will be useful for numerous laboratories studying biological invasions, but with limited resources and expertise in bioinformatics.

Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species

Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as "ATGATAA". Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).

RResolver: efficient short-read repeat resolution within ABySS

BACKGROUND

De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes. De novo short-read assemblers commonly use de Bruijn graphs, where nodes are sequences of equal length k, also known as k-mers. Edges in this graph are established between nodes that overlap by [Formula: see text] bases, and nodes along unambiguous walks in the graph are subsequently merged. The selection of k is influenced by multiple factors, and optimizing this value results in a trade-off between graph connectivity and sequence contiguity. Ideally, multiple k sizes should be used, so lower values can provide good connectivity in lesser covered regions and higher values can increase contiguity in well-covered regions. However, current approaches that use multiple k values do not address the scalability issues inherent to the assembly of large genomes.

RESULTS

Here we present RResolver, a scalable algorithm that takes a short-read de Bruijn graph assembly with a starting k as input and uses a k value closer to that of the read length to resolve repeats. RResolver builds a Bloom filter of sequencing reads which is used to evaluate the assembly graph path support at branching points and removes paths with insufficient support. RResolver runs efficiently, taking only 26 min on average for an ABySS human assembly with 48 threads and 60 GiB memory. Across all experiments, compared to a baseline assembly, RResolver improves scaffold contiguity (NGA50) by up to 15% and reduces misassemblies by up to 12%.

CONCLUSIONS

RResolver adds a missing component to scalable de Bruijn graph genome assembly. By improving the initial and fundamental graph traversal outcome, all downstream ABySS algorithms greatly benefit by working with a more accurate and less complex representation of the genome. The RResolver code is integrated into ABySS and is available at https://github.com/bcgsc/abyss/tree/master/RResolver .

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.

The complete sequence of a human genome

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

BACKGROUND

Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome.

FINDINGS

Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20-30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in <2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding.

CONCLUSIONS

The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity.

Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads

Although most existing genome assemblers are based on de Bruijn graphs, the construction of these graphs for large genomes and large k-mer sizes has remained elusive. This algorithmic challenge has become particularly pressing with the emergence of long, high-fidelity (HiFi) reads that have been recently used to generate a semi-manual telomere-to-telomere assembly of the human genome. To enable automated assemblies of long, HiFi reads, we present the La Jolla Assembler (LJA), a fast algorithm using the Bloom filter, sparse de Bruijn graphs and disjointig generation. LJA reduces the error rate in HiFi reads by three orders of magnitude, constructs the de Bruijn graph for large genomes and large k-mer sizes and transforms it into a multiplex de Bruijn graph with varying k-mer sizes. Compared to state-of-the-art assemblers, our algorithm not only achieves five-fold fewer misassemblies but also generates more contiguous assemblies. We demonstrate the utility of LJA via the automated assembly of a human genome that completely assembled six chromosomes.

High Prevalence and Diversity of Caliciviruses in a Community Setting Determined by a Metagenomic Approach

We recently carried out a metagenomic study to determine the fecal virome of infants during their first year of life in a semirural community in Mexico. A total of 97 stool samples from nine children were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In this work, we describe the prevalence and incidence of caliciviruses in this birth cohort. We found that 54 (56%) and 24 (25%) of the samples were positive for norovirus and sapovirus sequence reads detected by next-generation sequencing, respectively. Potential infections were arbitrarily considered when at least 20% of the complete virus genome was determined. Considering only these samples, there were 3 cases per child/year for norovirus and 0.33 cases per child/year for sapovirus. All nine children had sequence reads related to norovirus in at least 2 and up to 10 samples, and 8 children excreted sapovirus sequence reads in 1 and up to 5 samples during the study. The virus in 35 samples could be genotyped. The results showed a high diversity of both norovirus (GI.3[P13], GI.5, GII.4, GII.4[P16], GII.7[P7], and GII.17[P17]) and sapovirus (GI.1, GI.7, and GII.4) in the community. Of interest, despite the frequent detection of caliciviruses in the stools, all children remained asymptomatic during the study. Our results clearly show that metagenomic studies in stools may reveal a detailed picture of the prevalence and diversity of gastrointestinal viruses in the human gut during the first year of life.

IMPORTANCE Human caliciviruses are important etiological agents of acute gastroenteritis in children under 5 years of age. Several studies have characterized their association with childhood diarrhea and their presence in nondiarrheal stool samples. In this work, we used a next-generation sequencing approach to determine, in a longitudinal study, the fecal virome of infants during their first year of life. Using this method, we found that caliciviruses can be detected significantly more frequently than previously reported, providing a more detailed picture of the prevalence and genetic diversity of these viruses in the human gut during early life.

Draft Genome Sequence of Brevibacillus brevis LABIM17, a Biotechnologically Important Antimicrobial-Producing Bacterium

Brevibacillus brevis LABIM17 is a bacterial isolate with biotechnological potential. Its draft genome sequence contains a chromosome of 5,950,202 bp, with 5,477 coding sequences, and exhibits 12 clusters involved in the production of secondary metabolites, which are likely responsible for its antimicrobial activity against several human and plant pathogens.

Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide

Computational and statistical analysis of shotgun metagenomes can predict gene abundance and is helpful for elucidating the functional and taxonomic compositions of environmental samples. Gene products are compared against physicochemical conditions or perturbations to shed light on the functions performed by the microbial community of an environmental sample; however, this information is not always available. The present study proposes a method for inferring the metabolic potential of metagenome samples by constructing a reference based on determining the probability distribution of the counts of each enzyme annotated. To test the methodology, we used marine water samples distributed worldwide as references. Then, the references were utilized to compare the annotated enzymes of two different water samples extracted from the Gulf of Mexico (GoM) to distinguish those enzymes with atypical behavior. The enzymes whose annotation counts presented frequencies significantly different from those of the reference were used to perform metabolic reconstruction, which naturally identified pathways. We found that several of the enzymes were involved in the biodegradation of petroleum, which is consistent with the impact of human hydrocarbon extraction activity and its ubiquitous presence in the GoM. The examination of other reconstructed pathways revealed significant enzymes indicating the presence of microbial communities characterizing each ocean depth and ocean cycle, providing a fingerprint of each sampled site.

Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection

Aspergillus fumigatus is an environmental saprobe and opportunistic human fungal pathogen. Despite an estimated annual occurrence of more than 300,000 cases of invasive disease worldwide, a comprehensive survey of the genomic diversity present in A. fumigatus-including the relationship between clinical and environmental isolates and how this genetic diversity contributes to virulence and antifungal drug resistance-has been lacking. In this study we define the pan-genome of A. fumigatus using a collection of 300 globally sampled genomes (83 clinical and 217 environmental isolates). We found that 7,563 of the 10,907 unique orthogroups (69%) are core and present in all isolates and the remaining 3,344 show presence/absence of variation, representing 16-22% of the genome of each isolate. Using this large genomic dataset of environmental and clinical samples, we found an enrichment for clinical isolates in a genetic cluster whose genomes also contain more accessory genes, including genes coding for transmembrane transporters and proteins with iron-binding activity, and genes involved in both carbohydrate and amino-acid metabolism. Finally, we leverage the power of genome-wide association studies to identify genomic variation associated with clinical isolates and triazole resistance as well as characterize genetic variation in known virulence factors. This characterization of the genomic diversity of A. fumigatus allows us to move away from a single reference genome that does not necessarily represent the species as a whole and better understand its pathogenic versatility, ultimately leading to better management of these infections.

Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

Background

We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation “short-read” and third-generation “long-read” sequencing methods.

Results

We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data, and ABySS for HiSeq data from eight short-read assembly methods. Two approaches were applied to benchmark long-read and hybrid assembly strategies: long-read-first assembly followed by correction with short reads (Canu/Pilon, Flye/Pilon) and short-read-first assembly along with scaffolding based on long reads (Unicyler, SPAdes). Hybrid assembly can resolve large repetitive regions best with a “long-read first” approach.

Conclusions

Genomic structures of the Francisella pathogenicity islands frequently showed misassembly. Insertion sequences (IS) could be used to perform an evolutionary conservation analysis. A phylogenetic structure of insertion sequences and the evolution within the clades elucidated the clade structure of the highly conservative F. tularensis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08115-x.

Intestinal microbiota has important effect on severity of hand foot and mouth disease in children

Background

The incidence of hand foot and mouth disease (HFMD) has increased in recent years, making it a very common childhood illness worldwide. The relationship between different enterovirus genotypes and disease severity is not clearly understood. Given that enteroviruses are transmitted through the gastrointestinal tract, we hypothesized that variation in intestinal microorganisms of the host might play a role in the prognosis of HFMD.

Methods

We carried out a meta-transcriptomic-wide association study of fecal samples obtained from a cohort of children (254 patients, 227 tested positive for enterovirus, including 16 patients co-infectied with 2 kinds of enterovirus) with mild and severe HFMD and healthy controls.

Results

We found there was no significant difference in the amount of each virus type between the mild and severe cases. Genes of enterovirus 71 (EV71) and coxsackievirus A (CV-A) from the severe and mild cases did not show significant clustering. Clostridium sp. L2-50 and Bacteroides stercoris ATCC 43183 were enriched in the guts of children with severe HFMD and KEGG enrichment was found between mild and severe cases.

Conclusions

Intestinal microorganisms appear to interact with enterovirus to determine the progression of HFMD. Genes of Bacteroides and Clostridium may be used as predictive markers for a more efficient prognosis and intervention. The enrichment of intestinal bacteria genes with functions may facilitate the development of severe symptoms for HFMD patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06748-7.

High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils

Arsenic (As) metabolism genes are generally present in soils but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversity of ars, aioA, and arrA genes were not significantly different between low and high (∼10 vs ∼100 mg kg^-1) As soils. By comparison to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars genes abundance only when its concentration was higher than 410 mg kg^-1. In contrast, between low and high As soils, metatranscriptomics revealed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community-wide as opposed to taxon-specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil, or other environments, should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level and thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.

A New Micromonospora Strain with Antibiotic Activity Isolated from the Microbiome of a Mid-Atlantic Deep-Sea Sponge

To tackle the growing problem of antibiotic resistance, it is essential to identify new bioactive compounds that are effective against resistant microbes and safe to use. Natural products and their derivatives are, and will continue to be, an important source of these molecules. Sea sponges harbour a diverse microbiome that co-exists with the sponge, and these bacterial communities produce a rich array of bioactive metabolites for protection and resource competition. For these reasons, the sponge microbiota constitutes a potential source of clinically relevant natural products. To date, efforts in bioprospecting for these compounds have focused predominantly on sponge specimens isolated from shallow water, with much still to be learned about samples from the deep sea. Here we report the isolation of a new Micromonospora strain, designated 28ISP2-46^T, recovered from the microbiome of a mid-Atlantic deep-sea sponge. Whole-genome sequencing reveals the capacity of this bacterium to produce a diverse array of natural products, including kosinostatin and isoquinocycline B, which exhibit both antibiotic and antitumour properties. Both compounds were isolated from 28ISP2-46^T fermentation broths and were found to be effective against a plethora of multidrug-resistant clinical isolates. This study suggests that the marine production of isoquinocyclines may be more widespread than previously supposed and demonstrates the value of targeting the deep-sea sponge microbiome as a source of novel microbial life with exploitable biosynthetic potential.

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

BACKGROUND

The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability of the soil microbiome. Communities differing in phylogenetic diversity were generated by inoculating serially diluted soil suspensions into sterilized soil, and the stability of the microbiome was assessed by detecting community variations under various pH levels. The taxonomic features and potential functional traits were detected by DNA sequencing.

RESULTS

We found that bacterial communities with higher phylogenetic diversity tended to be more stable, implying that microbiomes with higher biodiversity are more resistant to perturbation. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially "nitrogen metabolism" and "phosphonate and phosphinate metabolism," as keystone functions. Further taxonomic annotation found that keystone functions are carried out by specific bacterial taxa, including Nitrospira and Gemmatimonas, among others.

CONCLUSIONS

This study provides new insights into our understanding of the relationships between soil microbiome biodiversity and ecosystem stability and highlights specialized metabolic functions embedded in keystone taxa that may be essential for soil microbiome stability. Video abstract.

Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons

Background

Efficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. Lack of complete operonic reference and functional information makes the prediction of metagenomic operons a challenging task; thus, opening new perspectives on the interpretation of the host-microbe interactions.

Results

In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). MetaRon identifies operons without any experimental or functional information. MetaRon was implemented on datasets with different levels of complexity and information. Starting from its application on whole-genome to simulated mixture of three whole-genomes (E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. MetaRon consistently achieved high operon prediction sensitivity, specificity and accuracy across E. coli whole-genome (97.8, 94.1 and 92.4%), simulated genome (93.7, 75.5 and 88.1%) and E. coli c20 (87, 91 and 88%,), respectively. Finally, we identified 1,232,407 unique operons from 145 paired-end human gut metagenome samples. We also report strong association of type 2 diabetes with Maltose phosphorylase (K00691), 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate synthase (K21279) and an uncharacterized protein (K07101).

Conclusion

With MetaRon, we were able to remove two notable limitations of existing whole-genome operon prediction methods: (1) generalizability (ability to predict operons in unrelated bacterial genomes), and (2) whole-genome and metagenomic data management. We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data and the role of secondary metabolites in the occurrence of disease condition. Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more precise data. Furthermore, the identification of metabolic pathways associated with the occurrence of type 2 diabetes (T2D) also presents another dimension of analyzing the human gut metagenome. Presumably, this study is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case type 2 diabetes. The application of MetaRon to metagenomic data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics.

Genomic Insights Into the Antifungal Activity and Plant Growth-Promoting Ability in Bacillus velezensis CMRP 4490

The main objective of this study was to evaluate Bacillus velezensis strain CMRP 4490 regarding its ability to inhibit soil-borne plant pathogens and to increase plant growth. The study included evaluation of in vitro antifungal control, sequencing the bacterial genome, mining genes responsible for the synthesis of secondary metabolites, root colonization ability, and greenhouse studies for the assessment of plant growth–promoting ability. The strain was obtained from soil samples in the north of Paraná in Brazil and was classified as a B. velezensis, which is considered a promising biological control agent. In vitro assay showed that B. velezensis CMRP 4490 presented antagonistic activity against Sclerotinia sclerotiorum, Macrophomina phaseolina, Botrytis cinerea, and Rhizoctonia solani with a mycelial growth inhibition of approximately 60%, without any significant difference among them. To well understand this strain and to validate its effect on growth-promoting rhizobacteria, it was decided to explore its genetic content through genome sequencing, in vitro, and greenhouse studies. The genome of CMRP 4490 was estimated at 3,996,396 bp with a GC content of 46.4% and presents 4,042 coding DNA sequences. Biosynthetic gene clusters related to the synthesis of molecules with antifungal activity were found in the genome. Genes linked to the regulation/formation of biofilms, motility, and important properties for rhizospheric colonization were also found in the genome. Application of CMRP 4490 as a coating film on soybean increased from 55.5 to 64% on germination rates when compared to the control; no differences were observed among treatments for the maize germination. The results indicated that B. velezensis CMRP 4490 could be a potential biocontrol agent with plant growth–promoting ability.

Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)

The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially non-synonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ.

Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization

The human-gut-DNA virome is highly diverse and individual specific, but little is known of its variation at a population level. Here, we report the fecal DNA virome of 930 healthy adult subjects from two regions in China (Hong Kong and Yunnan) spanning six ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), and including urban and rural residents for each ethnicity. Twenty host factors were found to significantly correlate with the human-gut virome variation, with geography carrying the strongest impact and ethnicity-distinct diets associating with certain viral species. Urbanization enhances interindividual dissimilarities between gut viromes, with the duration of urban residence associating with multiple bacteriophages, including Lactobacillus phage and Lactococcus phage. Overall, the gut virome presents more heterogeneity relative to the bacterial microbiome across the examined Chinese populations. This study highlights population-based variations and the importance of host and environmental factors in shaping the DNA virome in the human gut.

Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico

The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio, Alteromonas, and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes.

The effect of variant interference on de novo assembly for viral deep sequencing

BACKGROUND

Viruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored.

RESULTS

Our results from > 15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This "variant interference" (VI) is highly consistent and reproducible by ten commonly-used de novo assemblers, and occurs over a range of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective removal of minor variant reads from clinical datasets allow the "rescue" of full viral genomes from fragmented contigs.

CONCLUSIONS

These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing.

Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons

In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database were performed. The genome of B. velezensis UFLA258 consisted of a single circular chromosome of 3.95 Mb in length, with a mean GC content of 46.69%. It contained 3,949 genes encoding proteins and 27 RNA genes. Analyses based on Average Nucleotide Identity and Digital DNA–DNA Hybridization and a phylogeny with complete sequences of the rpoB gene confirmed that 19 strains deposited in the database as Bacillus amyloliquefaciens were in fact B. velezensis. In total, 115 genomes were analyzed and taxonomically classified as follows: 105 were B. velezensis, 9 were B. amyloliquefaciens, and 1 was Bacillus siamensis. Although these species are phylogenetically close, the combined analyses of several genomic characteristics, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, Average Nucleotide Identity and Digital DNA–DNA Hybridization, and other information on the strains, including isolation source, allowed their unequivocal classification. This genomic analysis expands our knowledge about the closely related species, B. velezensis, B. amyloliquefaciens, and B. siamensis, with emphasis on their taxonomical status.

Complete Genome Sequences of Seven New Chrysodeixis includens Nucleopolyhedrovirus Isolates from Minas Gerais and Mato Grosso States in Brazil

We report the complete genomic sequences of seven viral isolates from the soybean looper (Chrysodeixis includens) from midwestern and southeastern Brazil. The genomes range from 138,760 to 139,637 bp in length with a G+C content of 39.2% and 140 open reading frames (ORFs).

We report the complete genomic sequences of seven viral isolates from the soybean looper (Chrysodeixis includens) from midwestern and southeastern Brazil. The genomes range from 138,760 to 139,637 bp in length with a G+C content of 39.2% and 140 open reading frames (ORFs).

Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome

BACKGROUND

As one of the most densely populated microbial communities on Earth, the gut microbiota serves as an important reservoir of antibiotic resistance genes (ARGs), referred to as the gut resistome. Here, we investigated the association of dietary nutritional content with gut ARG diversity and composition, using publicly available shotgun metagenomic sequence data generated from canine and feline fecal samples. Also, based on network theory, we explored ARG-sharing patterns between gut bacterial genera by identifying the linkage structure between metagenomic assemblies and their functional genes obtained from the same data.

RESULTS

In both canine and feline gut microbiota, an increase in protein and a reduction in carbohydrate in the diet were associated with increased ARG diversity. ARG diversity of the canine gut microbiota also increased, but less strongly, after a reduction in protein and an increase in carbohydrate in the diet. The association between ARG and taxonomic composition suggests that diet-induced changes in the gut microbiota may be responsible for changes in ARG composition, supporting the links between protein metabolism and antibiotic resistance in gut microbes. In the analysis of the ARG-sharing patterns, 22 ARGs were shared among 46 genera in the canine gut microbiota, and 11 ARGs among 28 genera in the feline gut microbiota. Of these ARGs, the tetracycline resistance gene tet(W) was shared among the largest number of genera, predominantly among Firmicutes genera. Bifidobacterium, a genus extensively used in the fermentation of dairy products and as probiotics, shared tet(W) with a wide variety of other genera. Finally, genera from the same phylum were more likely to share ARGs than with those from different phyla.

CONCLUSIONS

Our findings show that dietary nutritional content, especially protein content, is associated with the gut resistome and suggest future research to explore the impact of dietary intervention on the development of antibiotic resistance in clinically-relevant gut microbes. Our network analysis also reveals that the genetic composition of bacteria acts as an important barrier to the horizontal transfer of ARGs. By capturing the underlying gene-sharing relationships between different bacterial taxa from metagenomes, our network approach improves our understanding of horizontal gene transfer dynamics.

First Report of Isolation and Genome Sequence of L. petauri Strain from a Rainbow Trout Lactococcosis Outbreak

Lactococcosis is a disease encountered in a wide variety of fish species causing mortalities and having great economic impact on farmed fish. In this study, we report for the first time the isolation of a strain of the recently described novel species Lactococcus petauri, from rainbow trout suffering from lactococcosis. The aim of this study was to determine the complete genome sequence of L. petauri strain LG_SAV_20 and to characterize its antimicrobial resistance and virulence. The genome of L. petauri LG_SAV_20 consists of 2,078,949 base pair (bp) with a GC content of 38.05%, 1950 predicted coding sequence (CDS), and 60 RNAs (51 tRNAs, 3 ncRNAs, and 6 rRNAs). Phylogenetic analysis revealed that L. petauri LG_SAV_20 shares most of its genome with L. garvieae strains isolated from rainbow trout. Detection of genes associated with antimicrobial resistance indicated that the isolate possesses the multidrug transporter mdt(A) gene, while using comparative analysis we identified several genes that might be related to bacterial pathogenesis. This genomic information provides new insights into the role of this novel species as an etiological agent of lactococcosis.

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

Genotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to select a priori the optimal assembler and parameter settings. To assembly the genome of Pseudomonas aeruginosa strain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate of P. aeruginosa carrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen.

Isopod holobionts as promising models for lignocellulose degradation

BACKGROUND

Isopods have colonized all environments, partly thanks to their ability to decompose the organic matter. Their enzymatic repertoire, as well as the one of their associated microbiota, has contributed to their colonization success. Together, these holobionts have evolved several interesting life history traits to degrade the plant cell walls, mainly composed of lignocellulose. It has been shown that terrestrial isopods achieve lignocellulose degradation thanks to numerous and diverse CAZymes provided by both the host and its microbiota. Nevertheless, the strategies for lignocellulose degradation seem more diversified in isopods, in particular in aquatic species which are the least studied. Isopods could be an interesting source of valuable enzymes for biotechnological industries of biomass conversion.

RESULTS

To provide new features on the lignocellulose degradation in isopod holobionts, shotgun sequencing of 36 metagenomes of digestive and non-digestive tissues was performed from several populations of four aquatic and terrestrial isopod species. Combined to the 15 metagenomes of an additional species from our previous study, as well as the host transcriptomes, this large dataset allowed us to identify the CAZymes in both the host and the associated microbial communities. Analyses revealed the dominance of Bacteroidetes and Proteobacteria in the five species, covering 36% and 56% of the total bacterial community, respectively. The identification of CAZymes and new enzymatic systems for lignocellulose degradation, such as PULs, cellulosomes and LPMOs, highlights the richness of the strategies used by the isopods and their associated microbiota.

CONCLUSIONS

Altogether, our results show that the isopod holobionts are promising models to study lignocellulose degradation. These models can provide new enzymes and relevant lignocellulose-degrading bacteria strains for the biotechnological industries of biomass conversion.

Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using Language Models

The performance of most error-correction (EC) algorithms that operate on genomics reads is dependent on the proper choice of its configuration parameters, such as the value of k in k-mer based techniques. In this work, we target the problem of finding the best values of these configuration parameters to optimize error correction and consequently improve genome assembly. We perform this in an adaptive manner, adapted to different datasets and to EC tools, due to the observation that different configuration parameters are optimal for different datasets, i.e., from different platforms and species, and vary with the EC algorithm being applied. We use language modeling techniques from the Natural Language Processing (NLP) domain in our algorithmic suite, Athena, to automatically tune the performance-sensitive configuration parameters. Through the use of N-Gram and Recurrent Neural Network (RNN) language modeling, we validate the intuition that the EC performance can be computed quantitatively and efficiently using the “perplexity” metric, repurposed from NLP. After training the language model, we show that the perplexity metric calculated from a sample of the test (or production) data has a strong negative correlation with the quality of error correction of erroneous NGS reads. Therefore, we use the perplexity metric to guide a hill climbing-based search, converging toward the best configuration parameter value. Our approach is suitable for both de novo and comparative sequencing (resequencing), eliminating the need for a reference genome to serve as the ground truth. We find that Athena can automatically find the optimal value of k with a very high accuracy for 7 real datasets and using 3 different k-mer based EC algorithms, Lighter, Blue, and Racer. The inverse relation between the perplexity metric and alignment rate exists under all our tested conditions—for real and synthetic datasets, for all kinds of sequencing errors (insertion, deletion, and substitution), and for high and low error rates. The absolute value of that correlation is at least 73%. In our experiments, the best value of k found by Athena achieves an alignment rate within 0.53% of the oracle best value of k found through brute force searching (i.e., scanning through the entire range of k values). Athena’s selected value of k lies within the top-3 best k values using N-Gram models and the top-5 best k values using RNN models With best parameter selection by Athena, the assembly quality (NG50) is improved by a Geometric Mean of 4.72X across the 7 real datasets.

Scalable Genome Assembly through Parallel de Bruijn Graph Construction for Multiple k-mers

Remarkable advancements in high-throughput gene sequencing technologies have led to an exponential growth in the number of sequenced genomes. However, unavailability of highly parallel and scalable de novo assembly algorithms have hindered biologists attempting to swiftly assemble high-quality complex genomes. Popular de Bruijn graph assemblers, such as IDBA-UD, generate high-quality assemblies by iterating over a set of k-values used in the construction of de Bruijn graphs (DBG). However, this process of sequentially iterating from small to large k-values slows down the process of assembly. In this paper, we propose ScalaDBG, which metamorphoses this sequential process, building DBGs for each distinct k-value in parallel. We develop an innovative mechanism to “patch” a higher k-valued graph with contigs generated from a lower k-valued graph. Moreover, ScalaDBG leverages multi-level parallelism, by both scaling up on all cores of a node, and scaling out to multiple nodes simultaneously. We demonstrate that ScalaDBG completes assembling the genome faster than IDBA-UD, but with similar accuracy on a variety of datasets (6.8X faster for one of the most complex genome in our dataset).

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

Shotgun metagenomics has greatly advanced our understanding of microbial communities over the last decade. Metagenomic analyses often include assembly and genome binning, computationally daunting tasks especially for big data from complex environments such as soil and sediments. In many studies, however, only a subset of genes and pathways involved in specific functions are of interest; thus, it is not necessary to attempt global assembly. In addition, methods that target genes can be computationally more efficient and produce more accurate assembly by leveraging rich databases, especially for those genes that are of broad interest such as those involved in biogeochemical cycles, biodegradation, and antibiotic resistance or used as phylogenetic markers. Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, SAT-Assembler, HMM-GRASPx, GenSeed-HMM, and MEGAN. We tested these tools using two datasets with known genomes, a synthetic community of artificial reads derived from the genomes of 17 bacteria, shotgun sequence data from a mock community with 48 bacteria and 16 archaea genomes, and a large soil shotgun metagenomic dataset. We compared assemblies of a universal single copy gene (rplB) and two N cycle genes (nifH and nirK). We measured their computational efficiency, sensitivity, specificity, and chimera rate and found Xander and MegaGTA, which both use a probabilistic graph structure to model the genes, have the best overall performance with all three datasets, although MEGAN, a reference matching assembler, had better sensitivity with synthetic and mock community members chosen from its reference collection. Also, Xander and MegaGTA are the only tools that include post-assembly scripts tuned for common molecular ecology and diversity analyses. Additionally, we provide a mathematical model for estimating the probability of assembling targeted genes in a metagenome for estimating required sequencing depth.

Independent Evolution with the Gene Flux Originating from Multiple Xanthomonas Species Explains Genomic Heterogeneity in Xanthomonas perforans

Xanthomonas perforans is the predominant pathogen responsible for bacterial leaf spot of tomato and X. euvesicatoria for that of pepper in the southeast United States. Previous studies have indicated significant changes in the X. perforans population collected from Florida tomato fields over the span of 2 decades, including a shift in race and diversification into three phylogenetic groups driven by genome-wide homologous-recombination events derived from X. euvesicatoria In our sampling of Xanthomonas strains associated with bacterial spot disease in Alabama, we were readily able to isolate X. perforans from symptomatic pepper plants grown in several Alabama counties, indicating a recent shift in the host range of the pathogen. To investigate the diversity of these pepper-pathogenic strains and their relation to populations associated with tomatoes grown in the southeast United States, we sequenced the genomes of eight X. perforans strains isolated from tomatoes and peppers grown in Alabama and compared them with previously published genome data available from GenBank. Surprisingly, reconstruction of the X. perforans core genome revealed the presence of two novel genetic groups in Alabama that each harbored a different transcription activation-like effector (TALE). While one TALE, AvrHah1, was associated with an emergent lineage pathogenic to both tomato and pepper, the other was identified as a new class within the AvrBs3 family, here designated PthXp1, and was associated with enhanced symptom development on tomato. Examination of patterns of homologous recombination across the larger X. euvesicatoria species complex revealed a dynamic pattern of gene flow, with multiple donors of Xanthomonas spp. associated with diverse hosts of isolation.IMPORTANCE Bacterial leaf spot of tomato and pepper is an endemic plant disease with a global distribution. In this study, we investigated the evolutionary processes leading to the emergence of novel X. perforans lineages identified in Alabama. While one lineage was isolated from symptomatic tomato and pepper plants, confirming the host range expansion of X. perforans, the other lineage was isolated from tomato and acquired a novel transcription activation-like effector, here designated PthXp1. Functional analysis of PthXp1 indicated that it does not induce Bs4-mediated resistance in tomato and contributes to virulence, providing an adaptive advantage to strains on tomato. Our findings also show that different phylogenetic groups of the pathogen have experienced independent recombination events originating from multiple Xanthomonas species. This suggests a continuous gene flux between related xanthomonads associated with diverse plant hosts that results in the emergence of novel pathogen lineages and associated phenotypes, including host range.

Diversity-triggered deterministic bacterial assembly constrains community functions

A growing body of evidence suggests that microbial α-diversity (local species richness) may have positive effects on ecosystem function. However, less attention has been paid to β-diversity (the variation among local microbial assemblages). Here we studied the impact of microbial α-diversity on stochastic/deterministic microbial community assembly processes, which are related to β-diversity, and the consequences for community function. Bacterial communities differing in α-diversity were generated and their structures and potential community functional traits were inferred from DNA sequencing. Phylogenetic null modeling analysis suggests that stochastic assembly processes are dominant in high-diversity communities. However, in low-diversity communities, deterministic assembly processes are dominant, associating with the reduction of specialized functions that are correlated with specific bacterial taxa. Overall, we suggest that the low-diversity-induced deterministic community assembly processes may constrain community functions, highlighting the potential roles of specialized functions in community assembly and in generating and sustaining the function of soil ecosystems.

The role of microbial β-diversity in soil ecosystem function is not well-studied. Here, the authors use genetic data to show that microbial α-diversity levels may have impacts on stochastic/deterministic assembly processes and functions of soil microbiome.

Metagenomic characterization of antibiotic resistance genes in Antarctic soils

Antibiotic resistance genes (ARGs) are considered environmental pollutants. Comprehensive characterization of the ARGs in pristine environments is essential towards understanding the evolution of antibiotic resistance. Here, we analyzed ARGs in soil samples collected from relatively pristine Antarctica using metagenomic approaches. We identified 79 subtypes related to 12 antibiotic classes in Antarctic soils, in which ARGs related to multidrug and polypeptide were dominant. The characteristics of ARGs in Antarctic soils were significantly different from those in active sludge, chicken feces and swine feces, in terms of composition, abundance and potential transferability. ARG subtypes (e.g., bacA, ceoB, dfrE, mdtB, amrB, and acrB) were more abundant than others in Antarctic soils. Approximately 60% of the ARGs conferred antibiotic resistance via an efflux mechanism, and a low fraction of ARGs (∼16%) might be present on plasmids. Culturable bacterial consortiums isolated from Antarctic soils were consistently susceptible to most of the tested antibiotics frequently used in clinical therapies. The amrB and ceoB carried by culturable species did not express the resistance to aminoglycoside and fluoroquinolone at the levels of clinical concern. Our results suggest that the wide use of antibiotics may have contributed to developing higher antibiotic resistance and mobility.

BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach

Motivation

It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the second generation sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the single-molecule real-time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity and variability of coverage. However, current assemblers of SGS data do not sufficiently take advantage of the OLC approach.

Results

Aiming at minimizing uncertainty, the proposed method BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can (i) perform reference-assisted assembly based on the genome of a close species (ii) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. The tests on two eukaryote genomes, a wild rice Oryza longistaminata and a parrot Melopsittacus undulatus, show that BAUM achieved substantial improvement on genome size and continuity. Besides, BAUM reconstructed a considerable amount of repetitive regions that failed to be assembled by existing short read assemblers. We also propose statistical approaches to control the uncertainty in different steps of BAUM.

Availability and implementation

http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum.

Supplementary information

Supplementary data are available at Bioinformatics online.

Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

BACKGROUND

Isopods constitute a particular group of crustaceans that has successfully colonized all environments including marine, freshwater and terrestrial habitats. Their ability to use various food sources, especially plant biomass, might be one of the reasons of their successful spread. All isopods, which feed on plants and their by-products, must be capable of lignocellulose degradation. This complex composite is the main component of plants and is therefore an important nutrient source for many living organisms. Its degradation requires a large repertoire of highly specialized Carbohydrate-Active enZymes (called CAZymes) which are produced by the organism itself and in some cases, by its associated microbiota. The acquisition of highly diversified CAZymes could have helped isopods to adapt to their diet and to their environment, especially during land colonization.

RESULTS

To test this hypothesis, isopod host CAZomes (i.e. the entire CAZyme repertoire) were characterized in marine, freshwater and terrestrial species through a transcriptomic approach. Many CAZymes were identified in 64 isopod transcriptomes, comprising 27 de novo datasets. Our results show that marine, freshwater and terrestrial isopods exhibit different CAZomes, illustrating different strategies for lignocellulose degradation. The analysis of variations of the size of CAZy families shows these are expanded in terrestrial isopods while they are contracted in aquatic isopods; this pattern is probably resulting from the evolution of the host CAZomes during the terrestrial adaptation of isopods. We show that CAZyme gene duplications and horizontal transfers can be involved in adaptive divergence between isopod CAZomes.

CONCLUSIONS

Our characterization of the CAZomes in 64 isopods species provides new insights into the evolutionary processes that enabled isopods to conquer various environments, especially terrestrial ones.

Illumina error correction near highly repetitive DNA regions improves de novo genome assembly

Background

Several standalone error correction tools have been proposed to correct sequencing errors in Illumina data in order to facilitate de novo genome assembly. However, in a recent survey, we showed that state-of-the-art assemblers often did not benefit from this pre-correction step. We found that many error correction tools introduce new errors in reads that overlap highly repetitive DNA regions such as low-complexity patterns or short homopolymers, ultimately leading to a more fragmented assembly.

Results

We propose BrownieCorrector, an error correction tool for Illumina sequencing data that focuses on the correction of only those reads that overlap short DNA patterns that are highly repetitive in the genome. BrownieCorrector extracts all reads that contain such a pattern and clusters them into different groups using a community detection algorithm that takes into account both the sequence similarity between overlapping reads and their respective paired-end reads. Each cluster holds reads that originate from the same genomic region and hence each cluster can be corrected individually, thus providing a consistent correction for all reads within that cluster.

Conclusions

BrownieCorrector is benchmarked using six real Illumina datasets for different eukaryotic genomes. The prior use of BrownieCorrector improves assembly results over the use of uncorrected reads in all cases. In comparison with other error correction tools, BrownieCorrector leads to the best assembly results in most cases even though less than 2% of the reads within a dataset are corrected. Additionally, we investigate the impact of error correction on hybrid assembly where the corrected Illumina reads are supplemented with PacBio data. Our results confirm that BrownieCorrector improves the quality of hybrid genome assembly as well. BrownieCorrector is written in standard C++11 and released under GPL license. BrownieCorrector relies on multithreading to take advantage of multi-core/multi-CPU systems. The source code is available at https://github.com/biointec/browniecorrector.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2906-2) contains supplementary material, which is available to authorized users.

Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community

Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.

Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1

Bacteriophages are highly abundant in human microbiota where they coevolve with resident bacteria. Phage predation can drive the evolution of bacterial resistance, which can then drive reciprocal evolution in the phage to overcome that resistance. Such coevolutionary dynamics have not been extensively studied in human gut bacteria, and are of particular interest for both understanding and eventually manipulating the human gut microbiome. We performed experimental evolution of an Enterococcus faecium isolate from healthy human stool in the absence and presence of a single infecting Myoviridae bacteriophage, EfV12-phi1. Four replicates of E. faecium and phage were grown with twice daily serial transfers for 8 days. Genome sequencing revealed that E. faecium evolved resistance to phage through mutations in the yqwD2 gene involved in exopolysaccharide biogenesis and export, and the rpoC gene which encodes the RNA polymerase β’ subunit. In response to bacterial resistance, phage EfV12-phi1 evolved varying numbers of 1.8 kb tandem duplications within a putative tail fiber gene. Host range assays indicated that coevolution of this phage-host pair resulted in arms race dynamics in which bacterial resistance and phage infectivity increased over time. Tracking mutations from population sequencing of experimental coevolution can quickly illuminate phage entry points along with resistance strategies in both phage and host – critical information for using phage to manipulate microbial communities.

Draft Genome Sequence of Lactobacillus reuteri Strain LR CGMCC 11154, Isolated from the Feces of Healthy Weaned Piglets

Lactobacillus reuteri strain LR CGMCC 11154, which was isolated from the feces of healthy weaned piglets, was experimentally proven to be a probiotic bacterium. The whole genome was sequenced on the Illumina Miseq platform to obtain the draft genome, which consists of 120 contigs totaling 1.9 Mbp encoding 1,854 genes.

Lactobacillus reuteri strain LR CGMCC 11154, which was isolated from the feces of healthy weaned piglets, was experimentally proven to be a probiotic bacterium. The whole genome was sequenced on the Illumina Miseq platform to obtain the draft genome, which consists of 120 contigs totaling 1.9 Mbp encoding 1,854 genes.

A new mitochondrial gene order in the banded cusk-eel Raneya brasiliensis (Actinopterygii, Ophidiiformes)

The complete mitochondrial genome of the banded cusk-eel, Raneya brasilensis (Kaup, 1856), was obtained using next-generation sequencing approaches. The genome sequence was 16,881 bp and exhibited a novel gene order for a vertebrate. Specifically, the WANCY and the nd6 – D-loop regions were re-ordered, supporting the hypothesis that these two regions are hotspots for gene rearrangements in Actinopterygii. Phylogenetic reconstructions confirmed that R. brasiliensis is nested within Ophidiiformes. Mitochondrial genomes are required from additional ophidiins to determine whether the gene rearrangements that we observed are specific to the genus Raneya or to the subfamily Ophidiinae.