Patrik D'haeseleer

• PhD
• Researcher at Lawrence Livermore National Laboratory

Mechanistic, constraint-based models of microbial isolates or communities are a staple in the metabolic analysis toolbox, but predictions about microbe-microbe and microbe-environment interactions are only as good as the accuracy of transporter annotations. A number of hurdles stand in the way of comprehensive functional assignments for membrane tr...

The polymorphic membrane proteins (Pmps) are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high qual...

Chlamydia trachomatis is the most common bacterial sexually transmitted pathogen. The number of chlamydial infections continuous to increase and there is an urgent need for a safe and efficacious vaccine. To assess the ability of the Chlamydia muridarum polymorphic membrane protein G (PmpG) and the plasmid glycoprotein 3 (Pgp3) as single antigens,...

Algal-bacterial interactions provide clues to algal physiology, but mutualistic interactions are complicated by dynamic exchange. We characterized the response of Chlamydomonas reinhardtii to the presence of a putative alga-benefitting commensal bacterium (Arthrobacter strain ‘P2b’). Co-cultivation promoted chlorophyll content, biomass, average cel...

The polymorphic membrane proteins are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, and that these repeats correspond to the coils of a large beta-helical domain in...

Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of linear co...

Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of peptide e...

For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, tak...

Introduction: For over ten years, the ModelSEED has been a primary resource for researchers endeavoring to construct draft genome-scale metabolic models based on annotated microbial or plant genomes. As described here, and now being released, the ModelSEED biochemistry database serves as the foundation of biochemical data underlying the ModelSEED a...

Antimicrobial peptides (AMPs) are regarded as attractive alternatives to conventional antibiotics, but their production in microbes remains challenging due to their inherent bactericidal nature. To address these limitations, we have developed a novel AMP fusion protein system based on an encapsulin nanocompartment protein and have demonstrated its...

Supplementary Figure S1. Overlap of annotated genes between the tools (average numbers of genes annotated per genome). Supplementary Figure S2. Average transporter annotations per genome produced by TransportDB (426.0), KEGG (203.8) and RAST (113.7) and the distributions of their substrate specificities (rank 1 is most specific, rank 5 has no subs...

Background Genome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional annotations. Annotated genomes typically contain 30–50% of genes without functional annotation, severely limiting our knowledge of the “...

EC annotations. Excel file with all EC annotations by all 4 tools for all 27 genomes. (XLS 3442 kb)

Transporter annotations. Excel file with all transporter annotations by all 3 tools for all 27 genomes. (XLS 2134 kb)

EC numbers predicted by all 4 tools. Excel file with the EC numbers predicted by all 4 tools in most genomes. (XLS 35 kb)

Substrate ranks. Excel file with all transporter substrate ranks. (XLS 74 kb)

Genome data. Zip file with the 27 reference genomes in Genbank format, cleaned to include only coding sequences and locus tags. (ZIP 68984 kb)

EC numbers predicted by all 4 tools. Excel file with the EC numbers predicted by all 4 tools in most genomes. (XLS 35 kb)

Burkholderia pseudomallei and B. mallei are the causative agents of melioidosis and glanders, respectively, and are often fatal to humans and animals. Owing to the high fatality rate, potential for spread by aerosolization, and the lack of efficacious therapeutics, B. pseudomallei and B. mallei are considered biothreat agents of concern. In this st...

STRING Interaction network between the 125 proteins differentially expressed during infection vs. monoculture. B. thailandensis proteins were mapped to the B. pseudomallei proteins in the STRING database. Colored edges indicate different types of protein-protein associations. Cyan: known interactions from curated databases. Pink: experimentally det...

Detection of residue-specific incorporation of Anl in Q2T838 (BTH_II0461, Acetoacetyl-CoA reductase). (A) Highlighted sequences depict coverage by LC-MS/MS; modified Met residues are highlighted in green indicating incorporation of Anl. (B) Representative peptide spectrum from an LC-MS/MS analysis on a precursor ion of the TDLDAM+23FNVTK peptide, o...

List of all identified proteins under monoculture and infection conditions. The list of all identified proteins and their spectral counts in three biological replicates of monoculture and infection conditions.

Complete list of all differentially expressed proteins in infection vs. monoculture conditions. Columns from left to right: Gene: Uniprot accession number; Locus: Locus tag; Identified proteins: Uniprot protein name; STRING annotation: Annotation of homologous B. pseudomallei protein in STRING; Log2fold: Log-2 fold protein overexpression infection...

The dirty little secret behind genome-wide systems biology modeling efforts is that they are invariably based on very incomplete functional annotations. Annotated genomes typically contain 30-50% of genes with little or no functional annotation [1], severely limiting our knowledge of the "parts lists" that the organisms have at their disposal. In m...

Cyanobacterial mats are laminated microbial ecosystems which occur in highly diverse environments and which may provide a possible model for early life on Earth. Their ability to produce hydrogen also makes them of interest from a biotechnological and bioenergy perspective. Samples of an intertidal microbial mat from the Elkhorn Slough estuary in M...

Here, we present the draft genome sequence of Burkholderia pseudomallei PHLS 6, a virulent clinical strain isolated from a melioidosis patient in Bangladesh in 1960. The draft genome consists of 39 contigs and is 7,322,181 bp long.

New lignocellulolytic enzymes are needed that maintain optimal activity under the harsh conditions present during industrial enzymatic deconstruction of biomass, including high temperatures, the absence of free water, and the presence of inhibitors from the biomass. Enriching lignocellulolytic microbial communities under these conditions provides a...

Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput Mass Spectrometry, and applied it to the systematic characteriza...

The development of advanced biofuels from lignocellulosic biomass will require the use of both efficient pretreatment methods and new biomass-deconstructing enzyme cocktails to generate sugars from lignocellulosic substrates. Certain ionic liquids (ILs) have emerged as a promising class of compounds for biomass pretreatment and have been demonstrat...

This year for Halloween, we decellularized a pig heart. We got a nice bleeding heart, hooked it up to some plumbing, stripped out all its cells with enzymes and detergents, and then bottled the thing in Everclear. Because every mad scientist’s den deserves to have some mad science on display.

An Amazon soil microbial community metagenomic fosmid library was functionally screened for β-glucosidase activity. Contig analysis of positive clones revealed the presence of two ORFs encoding novel β-glucosidases, AmBGL17 and AmBGL18, from the GH3 and GH1 families, respectively. Both AmBGL17 and AmBGL18 were functionally identified as β-glucosida...

High-solids incubations were performed to enrich for microbial communities and enzymes that decompose rice straw under mesophilic (35°C) and thermophilic (55°C) conditions. Thermophilic enrichments yielded a community that was 7.5 times more metabolically active on rice straw than mesophilic enrichments. Extracted xylanase and endoglucanse activiti...

Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of...

Completeness of the genome coverage within the metagenomic clusters, estimated based on presence of 54 single-copy or almost single-copy phylogenetic COGs. (XLSX)

Peptides and proteins detected in all three fractions of the proteome, normalized protein abundances, corresponding gene annotations, proteins overrepresented in the supernatant, and comparison of sugar isomerase abundance across the three fractions. (XLSX)

Lignocellulolytic enzymes identified based on dbCAN [25], blastp against a local copy of the CAZy [26] and FOLy [27] databases (E<1e−20), and bacterial laccases [28], [29]. Also includes a table of CAZy enzymes found per phylogenetic bin, and a comparison of glycoside hydrolase content in termite hindgut [72], cow rumen [12], a switchgrass adapted...

Scaffold name, IMG Object ID, read coverage, GC%, length, and phylogenetic bin assignment for all the scaffolds in the assembled metagenome. (XLSX)

Comparison of average read coverage of the metagenomic clusters versus 16S rRNA composition of the consortium, with and without correcting for average 16S rRNA copy number in sequenced reference genomes. (XLSX)

In the future, we may be faced with the need to provide treatment for an emergent biological threat against which existing vaccines and drugs have limited efficacy or availability. To prepare for this eventuality, our objective was to employ a metabolic network-based approach to rapidly identify potential drug targets and prospectively screen and v...

PBPK results. Column 1 shows the ChemNavigator structure identifier, column 2 shows the molecular SMILES code, column 3 shows a picture of the molecule, column 4 shows the volume of distribution (Vd; in l/kg), column 5 shows the clearance (CL; in ml·min−1·kg−1), column 6 shows the mean residence time (MRT; in h), column 7 shows the half-life (T½; i...

Essential metabolic genes. The F. tularensis subspecies tularensis Schu S4 nomenclature was used for the gene association. (PDF)

Growth curves for the six active compounds. (PDF)

A recent metagenomic analysis sequenced a switchgrass-adapted compost community to identify enzymes from microorganisms that were specifically adapted to switchgrass under thermophilic conditions. These enzymes are being examined as part of the pretreatment process for the production of “second-generation” biofuels. Among the enzymes discovered was...

Tropical forest soils decompose litter rapidly with frequent episodes of anoxia, making it likely that bacteria using alternate terminal electron acceptors (TEAs) such as iron play a large role in supporting decomposition under these conditions. The prevalence of many types of metabolism in litter deconstruction makes these soils useful templates f...

Metagenomics approaches provide access to environmental genetic diversity for biotechnology applications, enabling the discovery of new enzymes and pathways for numerous catalytic processes. Discovery of new glycoside hydrolases with improved biocatalytic properties for the efficient conversion of lignocellulosic material to biofuels is a critical...

Generation of biofuels from sugars in lignocellulosic biomass is a promising alternative to liquid fossil fuels, but efficient and inexpensive bioprocessing configurations must be developed to make this technology commercially viable. One of the major barriers to commercialization is the recalcitrance of plant cell wall polysaccharides to enzymatic...

Growth of an E. coli strain engineered to produce biodiesel on CTec2 hydrolysate (A) and control samples containing 2% glucose and 1% xylose (B), 2% glucose and 1% xylose with the CTec2 enzyme product (C), and 2% glucose (D). Oxygen transfer rate (OTR), cell density (OD600), and sugar concentration were monitored during the fermentation to determin...

Dose curve of the CTec2 cellulase cocktail on ionic-liquid pretreated switchgrass in M9 salts pH 5.0 at 50°C. The CTec2 dose is reported mg of enzyme product added per gram of total solids based on triplicate samples. (DOC)

Zymography of the Endoglucanase (A) and endoxylanase (B) enzymes produced by the thermophilic community. Gels were embedded with carboxymethyl cellulose or soluble birchwood xylan and enzyme reactions were run at pH 5.0 and 70°C for 30 minutes to 2 h. Substrate clearing zones created by enzymatic digestion are black. Molecular weight markers are in...

UV/Vis absorbance scans of the Hydrolysates. JTherm (from Figure 6) and CTec2 (from Figure 8) IL-pretreated switchgrass hydrolysates were diluted 20 fold and the water soluble fraction of organosolv lignin (Sigma #371033) was at 5 mg/ml. The hydrolysates and lignin have an absorbance peak at around 280 nm, and the hydrolysates have a second absorba...

To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobac...

Environmental organisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an a...

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety...

Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its ex...

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Enterobacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA,...

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety...

In microbial communities, extracellular polymeric substances (EPS), also called the extracellular matrix, provide the spatial organization and structural stability during biofilm development. One of the major components of EPS is protein, but it is not clear what specific functions these proteins contribute to the extracellular matrix or to microbi...

"Thioalkalivibrio sulfidophilus" HL-EbGr7 is an obligately chemolithoautotrophic, haloalkaliphilic sulfur-oxidizing bacterium (SOB) belonging to the Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor, removing sulfide from biogas. Here we report the complete genome sequence of strain HL-EbGr7 and its annotation. The ge...

The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous γ-Proteobacteria that are closely related to known petroleum degraders. Hydrocarbo...

Producing cellulosic biofuels from plant material has recently emerged as a key US Department of Energy goal. For this technology to be commercially viable on a large scale, it is critical to make production cost efficient by streamlining both the deconstruction of lignocellulosic biomass and fuel production. Many natural ecosystems efficiently deg...

Chromosome of a circular phage recovered from the SAC community metagenome (contig JMC02169) related to Iodobacteriophage. Genes were predicted using fgenesV (www.softberry.com). (1.12 MB EPS)

Evolutionary distance (maximum likelihood) tree of aligned representatives of glycoside hydrolase family 9 proteins showing the relative position of the two characterized GH9 proteins identified in the SAC microbiome. Bootstrap values (100 bootstraps) are given for selected nodes. (1.35 MB EPS)

Correspondence analysis of the compost bioreactor microbiome to other lignocellulosic (pentagons) and non-lignocellulosic (circles) microbiomes. The total variance extracted by the coordinate axes was 46.8% (31.1%+15.7%). Metagenome IDs given in the legend correspond to references metagenomes in MG-RAST (http://metagenomics.nmpdr.org/) used for com...

Putative full-length cellulase and hemicellulase enzyme sequences extracted from the SAC metagenome data set. The two GH9 cellulases in bold were tested for activity on CMC, pNPC and pNPG. (a) Best BLASTX hit against any sequence in CAZy with a validated EC number indicating a lignocellulolytic enzyme. (b) Number of frameshift corrections required,...

Domain structure, protein expression and activity profiles of the two full-length genes belonging to family GH9. U: uninduced negative control; I: IPTG induced sample. (0.03 MB DOC)

Development of cellulosic biofuels from non-food crops is currently an area of intense research interest. Tailoring depolymerizing enzymes to particular feedstocks and pretreatment conditions is one promising avenue of research in this area. Here we added a green-waste compost inoculum to switchgrass (Panicum virgatum) and simulated thermophilic co...

Slackia heliotrinireducens (Lanigan 1983) Wade et al. 1999 is of phylogenetic interest because of its location in a genomically yet uncharted section of the family Coriobacteriaceae, within the deep branching Actinobacteria. Strain RHS 1(T) was originally isolated from the ruminal flora of a sheep. It is a proteolytic anaerobic coccus, able to redu...

Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genom...

Sanguibacter keddieii is the type species of the genus Sanguibacter, the only genus within the family of Sanguibacteraceae. Phylogenetically, this family is located in the neighborhood of the genus Oerskovia and the family Cellulomonadaceae within the actinobacterial suborder Micrococcineae. The strain described in this report was isolated from blo...

Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified among the usually Gram-positive actinomycetes. Members of the species are frequently found in hot c...

Halogeometricum borinquense Montalvo-Rodríguez et al. 1998 is the type species of the genus, and is of phylogenetic interest because of its distinct location between the halobacterial genera Haloquadratum and Halosarcina. H. borinquense requires extremely high salt (NaCl) concentrations for growth. It can not only grow aerobically but also anaerobi...

Cryptobacterium curtum Nakazawa etal. 1999 is the type species of the genus, and is of phylogenetic interest because of its very distant and isolated position within the family Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical occurrence in the oral cavity, involved in dental and oral infections like periodont...

Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. Kytococcus sedentarius is known for the production of oligoketide antibiotics as well as...

Brachybacterium faecium Collins et al. 1988 is the type species of the genus, and is of phylogenetic interest because of its location in the Dermabacteraceae, a rather isolated family within the actinobacterial suborder Micrococcineae. B. faecium is known for its rod-coccus growth cycle and the ability to degrade uric acid. It grows aerobically or...

Microorganisms are a promising source of novel carbohydrate-active enzymes (cellulases, hemicellulases, and lignases) since they are primarily responsible for plant biomass degradation in nature. However, most carbohydrate-active enzymes used by industry come from only a few model organisms. To identify new lignocellulolytic enzymes we shotgun sequ...

Microorganisms are a promising source of novel carbohydrate-active enzymes (cellulases, hemicellulases, and lignases) since they are primarily responsible for plant biomass degradation in nature. However, most carbohydrate-active enzymes used by industry come from only a few model organisms. To identify new lignocellulolytic enzymes we shotgun sequ...

Microbial phenotypes are typically due to the concerted action of multiple gene functions, yet the presence of each gene may have only a weak correlation with the observed phenotype. Hence, it may be more appropriate to examine co-occurrence between sets of genes and a phenotype (multiple-to-one) instead of pairwise relations between a single gene...