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The isolation of novel microbes from environmental samples continues to be a key strategy for the discovery of new metabolic capacities for the degradation and transformation of lignocellulose. We report the draft genome sequence of a new strain of Brevibacillus borstelensis isolated from a sorghum-adapted microbial community derived from a compost sample.
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4 . The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas , land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.
The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.
The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.
The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center maintains cleanrooms to archive extraterrestrial materials returned from space exploration missions. Compared to typical built environments, oligotrophic conditions make these facilities inhospitable to microbes. Despite these controls, bacteria and fungi are regularly cultured from these cleanrooms. In particular, Bacillus sp. are frequently isolated during routine microbial monitoring. Endospores associated with this genus can survive extreme environments, such as cleanrooms. This microbial contamination may affect the integrity of astromaterials.
No abstract provided
Lachancea sp. yHQL494, whole genome shotgun sequencing project
Aureobasidium pullulans strain CRUB 1823, whole genome shotgun sequencing project.
Wastewater SARS-CoV-2 surveillance has been deployed since the beginning of the COVID-19 pandemic to monitor the dynamics in virus burden in local communities. Genomic surveillance of SARS-CoV-2 in wastewater, particularly efforts aimed at whole genome sequencing for variant tracking and identification, are still challenging due to low target concentration, complex microbial and chemical background, and lack of robust nucleic acid recovery experimental procedures. The intrinsic sample limitations are inherent to wastewater and are thus unavoidable. Here, we use a statistical approach that couples correlation analyses to a random forest-based machine learning algorithm to evaluate potentially important factors associated with wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes, with a specific focus on the breadth of genome coverage. We collected 182 composite and grab wastewater samples from the Chicago area between November 2020 to October 2021. Samples were processed using a mixture of processing methods reflecting different homogenization intensities (HA + Zymo beads, HA + glass beads, and Nanotrap), and were sequenced using one of the two library preparation kits (the Illumina COVIDseq kit and the QIAseq DIRECT kit). Technical factors evaluated using statistical and machine learning approaches include sample types, certain sample intrinsic features, and processing and sequencing methods. The results suggested that sample processing methods could be a predominant factor affecting sequencing outcomes, and library preparation kits was considered a minor factor. Finally, a synthetic SARS-CoV-2 RNA spike-in experiment was performed to validate the impact from processing methods and suggested that the intensity of the processing methods could lead to different RNA fragmentation
An organism tree of life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms. Such a tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the organisms. Since the whole-genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a whole-genome sequence-based ToL can be an empirically derivable surrogate for the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. We have constructed three types of ToLs for diversely sampled organisms using the sequences of whole genome, of whole transcriptome, and of whole proteome. Of the three, whole-proteome sequence-based ToL (whole-proteome ToL), constructed by applying information theory-based feature frequency profile method, an “alignment-free” method, gave the most topologically stable ToL. Here, we describe the main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels. The ToL reveals 1) all extant organisms of this study can be grouped into 2 “Supergroups,” 6 “Major Groups,” or 35+ “Groups”; 2) the order of emergence of the “founders” of all of the groups may be assigned on an evolutionary progression scale; 3) all of the founders of the groups have emerged in a “deep burst” at the very beginning period near the root of the ToL—an explosive birth of life’s diversity.
A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.
We have isolated a new strain of Acidovorax temperans strain LMJ (hereafter called strain LMJ) from a contaminated Tris-Acetate-Phosphate (TAP) medium plate of a green micro-alga Chlamydomonas reinhardtii strain LMJ.SG0182 (a Chlamydomonas Library project (CLiP) strain). We sequenced the whole genome of the strain LMJ using the PacBio Sequel II technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. We present the whole genome sequence of this strain that offer insights into its coding and non-coding genes and its nearest taxonomic neighbors.
We have isolated a new species of Microbacterium, an Actinobacterium. We have temporarily named this bacterium as Microbacterium sp. strain Clip185 (hereafter called strain Clip185) from a contaminated Tris-Acetate-Phosphate (TAP) medium culture plate of a green micro-alga Chlamydomonas reinhardtii strain LMJ.RY0402.185141 (a Chlamydomonas Library project CLiP strain). We sequenced the whole genome of strain Clip185 using the PacBio Sequel II Continuous Long Read technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. Additionally, we have submitted the PacBio methylome to REBASE, Ref#35996. We present the whole genome sequence of this new Microbacterium species that offers insights into its coding and non-coding genes and its nearest taxonomic neighbors.
We have isolated a new strain of Sphingobium yanoikuyae , which belongs to the class Alphaproteobacteria, order Sphingomonadales, and family Sphingomonadaceae. This carotenoid-producing strain is capable of degrading xenobiotics and is tolerant to toxic levels of six heavy metals. We have designated the newly isolated strain of S. yanoikuyae as S. yanoikuyae strain CC4533 (hereafter called strain CC4533) because it was isolated from a contaminated Tris-Acetate-Phosphate (TAP) medium culture plate of a green micro-alga Chlamydomonas reinhardtii wild type strain CC4533. We sequenced the whole genome of strain CC4533 using the PacBio Sequel II Continuous Long Read technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. Additionally, we have submitted the PacBio methylome to REBASE, Ref#35996. We present the whole genome sequence of S. yanoikuyae strain CC4533 that offers insights into its coding and non-coding genes and its nearest taxonomic neighbors.
This software builds on PHAME developed at LANL to generate phylogenetic trees of bacterial whole genome sequences. Where PHAME uses whole genome alignments to generate informative sites to base tress on, PHAME-OuS annotates bacterial genes, identifies orthologous sequences, aligns related proteins, uses those alignments to inform transcript alignments, then builds trees with several methods. The first is a conventional gene concatenation and ML tree estemation method. The second attempts to reconcile gene tree with a unified species tree using quartets (ASTRAL). Both methods allow filtering of gene lists on number of species represented, length, and gappiness in order to tune noise-to-signal for tree estimation
The drivers of critical coronavirus disease 2019 (COVID-19) remain unknown. Given major confounding factors such as age and comorbidities, true mediators of this condition have remained elusive. We used a multi-omics analysis combined with artificial intelligence in a young patient cohort where major comorbidities were excluded at the onset. The cohort included 47 “critical” (in the intensive care unit under mechanical ventilation) and 25 “non-critical” (in a non-critical care ward) patients with COVID-19 and 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cell proteomics, cytokine profiling, and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing, and structural causal modeling were used. Patients with critical COVID-19 were characterized by exacerbated inflammation, perturbed lymphoid and myeloid compartments, increased coagulation, and viral cell biology. Among differentially expressed genes, we observed up-regulation of the metalloprotease ADAM9. This gene signature was validated in a second independent cohort of 81 critical and 73 recovered patients with COVID-19 and was further confirmed at the transcriptional and protein level and by proteolytic activity. Ex vivo ADAM9 inhibition decreased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, cohort of individuals with COVID-19, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. We further identified ADAM9 as a driver of disease severity and a candidate therapeutic target.
Members of the family Trichomeriaceae, belonging to the Chaetothyriales order and the Ascomycota phylum, are known for their capability to inhabit hostile environments characterized by extreme temperatures, oligotrophic conditions, drought, or presence of toxic compounds. The genus Knufia encompasses many polyextremophilic species. In this report, the genomic and morphological features of the strain FJI-L2-BK-P2 presented, which was isolated from the Mars 2020 mission spacecraft assembly facility located at the Jet Propulsion Laboratory in Pasadena, California. The identification is based on sequence alignment for marker genes, multi-locus sequence analysis, and whole genome sequence phylogeny. The morphological features were studied using a diverse range of microscopic techniques (bright field, phase contrast, differential interference contrast and scanning electron microscopy). The phylogenetic marker genes of the strain FJI-L2-BK-P2 exhibited highest similarities with type strain of Knufia obscura (CBS 148926 T ) that was isolated from the gas tank of a car in Italy. To validate the species identity, whole genomes of both strains (FJI-L2-BK-P2 and CBS 148926 T ) were sequenced, annotated, and strain FJI-L2-BK-P2 was confirmed as K. obscura. The morphological analysis and description of the genomic characteristics of K. obscura FJI-L2-BK-P2 may contribute to refining the taxonomy of Knufia species. Key morphological features are reported in this K. obscura strain, resembling microsclerotia and chlamydospore-like propagules. These features known to be characteristic features in black fungi which could potentially facilitate their adaptation to harsh environments.