Publications by authors named "Karsten Zengler"

101 Publications

The Ubiquitous Human Skin Commensal Staphylococcus hominis Protects against Opportunistic Pathogens.

mBio 2022 May 24:e0093022. Epub 2022 May 24.

Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA.

Staphylococcus hominis is frequently isolated from human skin, and we hypothesize that it may protect the cutaneous barrier from opportunistic pathogens. We determined that S. hominis makes six unique autoinducing peptide (AIP) signals that inhibit the major virulence factor accessory gene regulator () quorum sensing system of Staphylococcus aureus. We solved and confirmed the structures of three novel AIP signals in conditioned medium by mass spectrometry and then validated synthetic AIP activity against all S. aureus classes. Synthetic AIPs also inhibited the conserved system in a related species, Staphylococcus epidermidis. We determined the distribution of S. hominis types on healthy human skin and found S. hominis -I and -II were highly represented across subjects. Further, synthetic AIP-II was protective against S. aureus-associated dermonecrotic or epicutaneous injury. Together, these findings demonstrate that a ubiquitous colonizer of human skin has a fundamentally protective role against opportunistic damage. Human skin is home to a variety of commensal bacteria, including many species of coagulase-negative staphylococci (CoNS). While it is well established that the microbiota as a whole maintains skin homeostasis and excludes pathogens (i.e., colonization resistance), relatively little is known about the unique contributions of individual CoNS species to these interactions. Staphylococcus hominis is the second most frequently isolated CoNS from healthy skin, and there is emerging evidence to suggest that it may play an important role in excluding pathogens, including Staphylococcus aureus, from colonizing or infecting the skin. Here, we identified that S. hominis makes 6 unique peptide inhibitors of the S. aureus global virulence factor regulation system (). Additionally, we found that one of these peptides can prevent topical or necrotic S. aureus skin injury in a mouse model. Our results demonstrate a specific and broadly protective role for this ubiquitous, yet underappreciated skin commensal.
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http://dx.doi.org/10.1128/mbio.00930-22DOI Listing
May 2022

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds.

PLoS Comput Biol 2022 02 2;18(2):e1009828. Epub 2022 Feb 2.

Department of Pediatrics, University of California, San Diego, California, United States of America.

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N. europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N. europaea, iGC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.
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http://dx.doi.org/10.1371/journal.pcbi.1009828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8853641PMC
February 2022

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data.

Metabolites 2021 Dec 24;12(1). Epub 2021 Dec 24.

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA.

Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.
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http://dx.doi.org/10.3390/metabo12010014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8778254PMC
December 2021

Linking anaerobic gut bacteria and cardiovascular disease.

Nat Microbiol 2022 01;7(1):14-15

Department of Pediatrics, University of California, San Diego, San Diego, CA, USA.

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http://dx.doi.org/10.1038/s41564-021-01009-4DOI Listing
January 2022

Dietary Neu5Ac Intervention Protects Against Atherosclerosis Associated With Human-Like Neu5Gc Loss-Brief Report.

Arterioscler Thromb Vasc Biol 2021 11 30;41(11):2730-2739. Epub 2021 Sep 30.

Glycobiology Research and Training Center (K.K., J.K.C., K.V.G., C.D., J.H., K.Z., N.V., A.V., P.L.S.M.G.), University of California, San Diego, La Jolla.

Objective: Species-specific pseudogenization of the CMAH gene during human evolution eliminated common mammalian sialic acid N-glycolylneuraminic acid (Neu5Gc) biosynthesis from its precursor N-acetylneuraminic acid (Neu5Ac). With metabolic nonhuman Neu5Gc incorporation into endothelia from red meat, the major dietary source, anti-Neu5Gc antibodies appeared. Human-like Ldlr-/-Cmah-/- mice on a high-fat diet supplemented with a Neu5Gc-enriched mucin, to mimic human red meat consumption, suffered increased atherosclerosis if human-like anti-Neu5Gc antibodies were elicited.

Approach And Results: We now ask whether interventional Neu5Ac feeding attenuates metabolically incorporated Neu5Gc-mediated inflammatory acceleration of atherogenesis in this Cmah-/-Ldlr-/- model system. Switching to a Neu5Gc-free high-fat diet or adding a 5-fold excess of Collocalia mucoid-derived Neu5Ac in high-fat diet protects against accelerated atherosclerosis. Switching completely from a Neu5Gc-rich to a Neu5Ac-rich diet further reduces severity. Remarkably, feeding Neu5Ac-enriched high-fat diet alone has a substantial intrinsic protective effect against atherosclerosis in Ldlr-/- mice even in the absence of dietary Neu5Gc but only in the human-like Cmah-null background.

Conclusions: Interventional Neu5Ac feeding can mitigate or prevent the red meat/Neu5Gc-mediated increased risk for atherosclerosis, and has an intrinsic protective effect, even in the absence of Neu5Gc feeding. These findings suggest that similar interventions should be tried in humans and that Neu5Ac-enriched diets alone should also be investigated further.
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http://dx.doi.org/10.1161/ATVBAHA.120.315280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8551057PMC
November 2021

Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics.

Methods Mol Biol 2021 ;2327:87-92

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Host DNA makes up the majority of DNA in a saliva sample. Therefore, shotgun metagenomics can be an inefficient way to evaluate the microbial populations of saliva since often <10% of the sequencing reads are microbial. In this chapter, we describe a method to deplete human DNA from fresh or frozen saliva samples, allowing for more efficient shotgun metagenomic sequencing of the salivary microbial community.
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http://dx.doi.org/10.1007/978-1-0716-1518-8_6DOI Listing
January 2022

Biotechnology for secure biocontainment designs in an emerging bioeconomy.

Curr Opin Biotechnol 2021 10 3;71:25-31. Epub 2021 Jun 3.

National Renewable Energy Laboratory, Golden, CO, United States. Electronic address:

Genetically modified organisms (GMOs) have emerged as an integral component of a sustainable bioeconomy, with an array of applications in agriculture, bioenergy, and biomedicine. However, the rapid development of GMOs and associated synthetic biology approaches raises a number of biosecurity concerns related to environmental escape of GMOs, detection thereof, and impact upon native ecosystems. A myriad of genetic safeguards have been deployed in diverse microbial hosts, ranging from classical auxotrophies to global genome recoding. However, to realize the full potential of microbes as biocatalytic platforms in the bioeconomy, a deeper understanding of the fundamental principles governing microbial responsiveness to biocontainment constraints, and interactivity of GMOs with the environment, is required. Herein, we review recent analytical biotechnological advances and strategies to assess biocontainment and microbial bioproductivity, as well as opportunities for predictive systems biodesigns towards securing a viable bioeconomy.
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http://dx.doi.org/10.1016/j.copbio.2021.05.004DOI Listing
October 2021

The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection.

bioRxiv 2021 Mar 26. Epub 2021 Mar 26.

We identify the prolyl-tRNA synthetase (PRS) inhibitor halofuginone , a compound in clinical trials for anti-fibrotic and anti-inflammatory applications , as a potent inhibitor of SARS-CoV-2 infection and replication. The interaction of SARS-CoV-2 spike protein with cell surface heparan sulfate (HS) promotes viral entry . We find that halofuginone reduces HS biosynthesis, thereby reducing spike protein binding, SARS-CoV-2 pseudotyped virus, and authentic SARS-CoV-2 infection. Halofuginone also potently suppresses SARS-CoV-2 replication post-entry and is 1,000-fold more potent than Remdesivir . Inhibition of HS biosynthesis and SARS-CoV-2 infection depends on specific inhibition of PRS, possibly due to translational suppression of proline-rich proteins. We find that pp1a and pp1ab polyproteins of SARS-CoV-2, as well as several HS proteoglycans, are proline-rich, which may make them particularly vulnerable to halofuginone's translational suppression. Halofuginone is orally bioavailable, has been evaluated in a phase I clinical trial in humans and distributes to SARS-CoV-2 target organs, including the lung, making it a near-term clinical trial candidate for the treatment of COVID-19.
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http://dx.doi.org/10.1101/2021.03.22.436522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8010724PMC
March 2021

Intestinal α1-2-Fucosylation Contributes to Obesity and Steatohepatitis in Mice.

Cell Mol Gastroenterol Hepatol 2021 22;12(1):293-320. Epub 2021 Feb 22.

Department of Medicine, University of California San Diego, La Jolla, California; Department of Medicine, VA San Diego Healthcare System, San Diego, California. Electronic address:

Background & Aims: Fucosyltransferase 2 (Fut2)-mediated intestinal α1- 2-fucosylation is important for host-microbe interactions and has been associated with several diseases, but its role in obesity and hepatic steatohepatitis is not known. The aim of this study was to investigate the role of Fut2 in a Western-style diet-induced mouse model of obesity and steatohepatitis.

Methods: Wild-type (WT) and Fut2-deficient littermate mice were used and features of the metabolic syndrome and steatohepatitis were assessed after 20 weeks of Western diet feeding.

Results: Intestinal α1-2-fucosylation was suppressed in WT mice after Western diet feeding, and supplementation of α1-2-fucosylated glycans exacerbated obesity and steatohepatitis in these mice. Fut2-deficient mice were protected from Western diet-induced features of obesity and steatohepatitis despite an increased caloric intake. These mice have increased energy expenditure and thermogenesis, as evidenced by a higher core body temperature. Protection from obesity and steatohepatitis associated with Fut2 deficiency is transmissible to WT mice via microbiota exchange; phenotypic differences between Western diet-fed WT and Fut2-deficient mice were reduced with antibiotic treatment. Fut2 deficiency attenuated diet-induced bile acid accumulation by altered relative abundance of bacterial enzyme 7-α-hydroxysteroid dehydrogenases metabolizing bile acids and by increased fecal excretion of secondary bile acids. This also was associated with increased intestinal farnesoid X receptor/fibroblast growth factor 15 signaling, which inhibits hepatic synthesis of bile acids. Dietary supplementation of α1-2-fucosylated glycans abrogates the protective effects of Fut2 deficiency.

Conclusions: α1-2-fucosylation is an important host-derived regulator of intestinal microbiota and plays an important role for the pathogenesis of obesity and steatohepatitis in mice.
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http://dx.doi.org/10.1016/j.jcmgh.2021.02.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166943PMC
January 2022

Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health.

Gut Microbes 2021 Jan-Dec;13(1):1-18

Department of Pediatrics, University of California , San Diego, La Jolla, USA.

Gut microbiome composition depends heavily upon diet and has strong ties to human health. Dietary carbohydrates shape the gut microbiome by providing a potent nutrient source for particular microbes. This review explores how dietary carbohydrates in general, including individual monosaccharides and complex polysaccharides, influence the gut microbiome with subsequent effects on host health and disease. In particular, the effects of sialic acids, a prominent and influential class of monosaccharides, are discussed. Complex plant carbohydrates, such as dietary fiber, generally promote microbial production of compounds beneficial to the host while preventing degradation of host carbohydrates from colonic mucus. In contrast, simple and easily digestible sugars such as glucose are often associated with adverse effects on health and the microbiome. The monosaccharide class of sialic acids exerts a powerful but nuanced effect on gut microbiota. Sialic acid consumption (in monosaccharide form, or as part of human milk oligosaccharides or certain animal-based foods) drives the growth of organisms with sialic acid metabolism capabilities. Minor chemical modifications of Neu5Ac, the most common form of sialic acid, can alter these effects. All aspects of carbohydrate composition are therefore relevant to consider when designing dietary therapeutic strategies to alter the gut microbiome.
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http://dx.doi.org/10.1080/19490976.2020.1869502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7899658PMC
January 2022

Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load.

mSystems 2021 Feb 16;6(1). Epub 2021 Feb 16.

Department of Pediatrics, University of California, San Diego, La Jolla, California, USA

Evaluating microbial community composition through next-generation sequencing has become increasingly accessible. However, metagenomic sequencing data sets provide researchers with only a snapshot of a dynamic ecosystem and do not provide information about the total microbial number, or load, of a sample. Additionally, DNA can be detected long after a microorganism is dead, making it unsafe to assume that all microbial sequences detected in a community came from living organisms. By combining relic DNA removal by propidium monoazide (PMA) with microbial quantification with flow cytometry, we present a novel workflow to quantify live microbial load in parallel with metagenomic sequencing. We applied this method to unstimulated saliva samples, which can easily be collected longitudinally and standardized by passive collection time. We found that the number of live microorganisms detected in saliva was inversely correlated with salivary flow rate and fluctuated by an order of magnitude throughout the day in healthy individuals. In an acute perturbation experiment, alcohol-free mouthwash resulted in a massive decrease in live bacteria, which would have been missed if we did not consider dead cell signal. While removing relic DNA from saliva samples did not greatly impact the microbial composition, it did increase our resolution among samples collected over time. These results provide novel insight into the dynamic nature of host-associated microbiomes and underline the importance of applying scale-invariant tools in the analysis of next-generation sequencing data sets. Human microbiomes are dynamic ecosystems often composed of hundreds of unique microbial taxa. To detect fluctuations over time in the human oral microbiome, we developed a novel workflow to quantify live microbial cells with flow cytometry in parallel with next-generation sequencing, and applied this method to over 150 unstimulated, timed saliva samples. Microbial load was inversely correlated with salivary flow rate and fluctuated by an order of magnitude within a single participant throughout the day. Removing relic DNA improved our ability to distinguish samples over time and revealed that the percentage of sequenced bacteria in a given saliva sample that are alive can range from nearly 0% up to 100% throughout a typical day. These findings highlight the dynamic ecosystem of the human oral microbiome and the benefit of removing relic DNA signals in longitudinal microbiome study designs.
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http://dx.doi.org/10.1128/mSystems.01182-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8561659PMC
February 2021

The sum is greater than the parts: exploiting microbial communities to achieve complex functions.

Curr Opin Biotechnol 2021 02 6;67:149-157. Epub 2021 Feb 6.

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0403, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA. Electronic address:

Multi-species microbial communities are ubiquitous in nature. The widespread prevalence of these communities is due to highly elaborated interactions among their members thereby accomplishing metabolic functions that are unattainable by individual members alone. Harnessing these communal capabilities is an emerging field in biotechnology. The rational intervention of microbial communities for the purpose of improved function has been facilitated in part by developments in multi-omics approaches, synthetic biology, and computational methods. Recent studies have demonstrated the benefits of rational interventions to human and animal health as well as agricultural productivity. Emergent technologies, such as in situ modification of complex microbial community and community metabolic modeling, represent an avenue to engineer sustainable microbial communities. In this opinion, we review relevant computational and experimental approaches to study and engineer microbial communities and discuss their potential for biotechnological applications.
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http://dx.doi.org/10.1016/j.copbio.2021.01.013DOI Listing
February 2021

Microbiome Signatures in a Fast- and Slow-Progressing Gastric Cancer Murine Model and Their Contribution to Gastric Carcinogenesis.

Microorganisms 2021 Jan 17;9(1). Epub 2021 Jan 17.

Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.

Gastric cancer is the third most common cause of death from cancer in the world and infection with () is the main cause of gastric cancer. In addition to infection, the overall stomach microbiota has recently emerged as a potential factor in gastric cancer progression. Previously we had established that mice deficient in myeloid differentiation primary response gene 88 (MyD88, ) rapidly progressed to neoplasia when infected with . Thus, in order to assess the role of the microbiota in this fast-progressing gastric cancer model we investigated changes of the gastric microbiome in mice with different genotypic backgrounds: wild type (WT), MyD88-deficient (), mice deficient in the Toll/interleukin-1 receptor (TIR) domain-containing adaptor-inducing interferon-β (TRIF, ), and MyD88- and TRIF-deficient (/ , double knockout (DKO)) mice. We compared changes in alpha diversity, beta diversity, relative abundance, and log-fold differential of relative abundance ratios in uninfected and infected mice and studied their correlations with disease progression to gastric cancer . We observed an overall reduction in microbial diversity post-infection with across all genotypes. Campylobacterales were observed in all infected mice, with marked reduction in abundance at 3 and 6 months in mice. A sharp increase in Lactobacillales in infected and DKO mice at 3 and 6 months was observed as compared to and WT mice, hinting at a possible role of these bacteria in gastric cancer progression. This was further reinforced upon comparison of Lactobacillales log-fold differentials with histological data, indicating that Lactobacillales are closely associated with infection and gastric cancer progression. Our study suggests that differences in genotypes could influence the stomach microbiome and make it more susceptible to the development of gastric cancer upon infection. Additionally, increase in Lactobacillales could contribute to faster development of gastric cancer and might serve as a potential biomarker for the fast progressing form of gastric cancer.
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http://dx.doi.org/10.3390/microorganisms9010189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7829848PMC
January 2021

Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems.

mSystems 2020 Oct 20;5(5). Epub 2020 Oct 20.

Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA

Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.
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http://dx.doi.org/10.1128/mSystems.00658-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7577295PMC
October 2020

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity.

bioRxiv 2020 Aug 18. Epub 2020 Aug 18.

The human microbiota has a close relationship with human disease and it remodels components of the glycocalyx including heparan sulfate (HS). Studies of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) spike protein receptor binding domain suggest that infection requires binding to HS and angiotensin converting enzyme 2 (ACE2) in a codependent manner. Here, we show that commensal host bacterial communities can modify HS and thereby modulate SARS-CoV-2 spike protein binding and that these communities change with host age and sex. Common human-associated commensal bacteria whose genomes encode HS-modifying enzymes were identified. The prevalence of these bacteria and the expression of key microbial glycosidases in bronchoalveolar lavage fluid (BALF) was lower in adult COVID-19 patients than in healthy controls. The presence of HS-modifying bacteria decreased with age in two large survey datasets, FINRISK 2002 and American Gut, revealing one possible mechanism for the observed increase in COVID-19 susceptibility with age. , bacterial glycosidases from unpurified culture media supernatants fully blocked SARS-CoV-2 spike binding to human H1299 protein lung adenocarcinoma cells. HS-modifying bacteria in human microbial communities may regulate viral adhesion, and loss of these commensals could predispose individuals to infection. Understanding the impact of shifts in microbial community composition and bacterial lyases on SARS-CoV-2 infection may lead to new therapeutics and diagnosis of susceptibility.
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http://dx.doi.org/10.1101/2020.08.17.238444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7444296PMC
August 2020

Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts.

NPJ Syst Biol Appl 2020 08 4;6(1):24. Epub 2020 Aug 4.

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.

Candidatus Liberibacter asiaticus (CLas) has been associated with Huanglongbing, a lethal vector-borne disease affecting citrus crops worldwide. While comparative genomics has provided preliminary insights into the metabolic capabilities of this uncultured microorganism, a comprehensive functional characterization is currently lacking. Here, we reconstructed and manually curated genome-scale metabolic models for the six CLas strains A4, FL17, gxpsy, Ishi-1, psy62, and YCPsy, in addition to a model of the closest related culturable microorganism, L. crescens BT-1. Predictions about nutrient requirements and changes in growth phenotypes of CLas were confirmed using in vitro hairy root-based assays, while the L. crescens BT-1 model was validated using cultivation assays. Host-dependent metabolic phenotypes were revealed using expression data obtained from CLas-infected citrus trees and from the CLas-harboring psyllid Diaphorina citri Kuwayama. These results identified conserved and unique metabolic traits, as well as strain-specific interactions between CLas and its hosts, laying the foundation for the development of model-driven Huanglongbing management strategies.
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http://dx.doi.org/10.1038/s41540-020-00142-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7403731PMC
August 2020

Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth.

Nat Commun 2020 07 30;11(1):3803. Epub 2020 Jul 30.

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.

Microbial communities comprised of phototrophs and heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.
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http://dx.doi.org/10.1038/s41467-020-17612-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393147PMC
July 2020

Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph DJ.

Metab Eng Commun 2020 Dec 30;11:e00132. Epub 2020 May 30.

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.

Nitrogen fixation is an important metabolic process carried out by microorganisms, which converts molecular nitrogen into inorganic nitrogenous compounds such as ammonia (NH). These nitrogenous compounds are crucial for biogeochemical cycles and for the synthesis of essential biomolecules, i.e. nucleic acids, amino acids and proteins. is a bacterial non-photosynthetic model organism to study aerobic nitrogen fixation (diazotrophy) and hydrogen production. Moreover, the diazotroph can produce biopolymers like alginate and polyhydroxybutyrate (PHB) that have important industrial applications. However, many metabolic processes such as partitioning of carbon and nitrogen metabolism in remain unknown to date. Genome-scale metabolic models (M-models) represent reliable tools to unravel and optimize metabolic functions at genome-scale. M-models are mathematical representations that contain information about genes, reactions, metabolites and their associations. M-models can simulate optimal reaction fluxes under a wide variety of conditions using experimentally determined constraints. Here we report on the development of a M-model of the wild type bacterium DJ (DT1278) which consists of 2,003 metabolites, 2,469 reactions, and 1,278 genes. We validated the model using high-throughput phenotypic and physiological data, testing 180 carbon sources and 95 nitrogen sources. DT1278 was able to achieve an accuracy of 89% and 91% for growth with carbon sources and nitrogen source, respectively. This comprehensive M-model will help to comprehend metabolic processes associated with nitrogen fixation, ammonium assimilation, and production of organic nitrogen in an environmentally important microorganism.
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http://dx.doi.org/10.1016/j.mec.2020.e00132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292883PMC
December 2020

Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants.

Commun Biol 2020 05 22;3(1):259. Epub 2020 May 22.

Department of Pediatrics, Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.

Lung macrophages mature after birth, placing newborn infants, particularly those born preterm, within a unique window of susceptibility to disease. We hypothesized that in preterm infants, lung macrophage immaturity contributes to the development of bronchopulmonary dysplasia (BPD), the most common serious complication of prematurity. By measuring changes in lung macrophage gene expression in preterm patients at risk of BPD, we show here that patients eventually developing BPD had higher inflammatory mediator expression even on the first day of life. Surprisingly, the ex vivo response to LPS was similar across all samples. Our analysis did however uncover macrophage signature genes whose expression increased in the first week of life specifically in patients resilient to disease. We propose that these changes describe the dynamics of human lung macrophage differentiation. Our study therefore provides new mechanistic insight into both neonatal lung disease and human developmental immunology.
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http://dx.doi.org/10.1038/s42003-020-0985-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244484PMC
May 2020

Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes.

NPJ Syst Biol Appl 2020 05 15;6(1):14. Epub 2020 May 15.

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.

Cells can sense changes in their extracellular environment and subsequently adapt their biomass composition. Nutrient abundance defines the capability of the cell to produce biomass components. Under nutrient-limited conditions, resource allocation dramatically shifts to carbon-rich molecules. Here, we used dynamic biomass composition data to predict changes in growth and reaction flux distributions using the available genome-scale metabolic models of five eukaryotic organisms (three heterotrophs and two phototrophs). We identified temporal profiles of metabolic fluxes that indicate long-term trends in pathway and organelle function in response to nitrogen depletion. Surprisingly, our calculations of model sensitivity and biosynthetic cost showed that free energy of biomass metabolites is the main driver of biosynthetic cost and not molecular weight, thus explaining the high costs of arginine and histidine. We demonstrated how metabolic models can accurately predict the complexity of interwoven mechanisms in response to stress over the course of growth.
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http://dx.doi.org/10.1038/s41540-020-0135-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229059PMC
May 2020

Genomic and Transcriptomic Evidence Supports Methane Metabolism in .

mSystems 2020 Mar 17;5(2). Epub 2020 Mar 17.

State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China

Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal have long been considered nonmethanogenic and their evolutionary history remains elusive. Here, three high-quality metagenomic-assembled genomes (MAGs) retrieved from high-temperature oil reservoir and hot springs, together with three newly assembled MAGs from previously reported hot spring metagenomes, are demonstrated to represent a novel genus of , " Methanomixophus." All " Methanomixophus" MAGs encode an M methyltransferase (MTR) complex and a traditional type of methyl-coenzyme M reductase (MCR) complex, which is different from the divergent MCR complexes found in " Polytropus marinifundus." In addition, " Methanomixophus dualitatem" MAGs preserve the genomic capacity for dissimilatory sulfate reduction. Comparative phylogenetic analysis supports a laterally transferred origin for an MCR complex and vertical heritage of the MTR complex in this lineage. Metatranscriptomic analysis revealed concomitant activity of hydrogen-dependent methylotrophic methanogenesis and heterotrophic fermentation within populations of " Methanomixophus hydrogenotrophicum" in a high-temperature oil reservoir. Current understanding of the diversity, biology, and ecology of is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of " Methanomixophus" MAGs not only expands the known range of metabolic versatility of the members of but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider than previously anticipated.
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http://dx.doi.org/10.1128/mSystems.00651-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380581PMC
March 2020

Interplay of Staphylococcal and Host Proteases Promotes Skin Barrier Disruption in Netherton Syndrome.

Cell Rep 2020 03;30(9):2923-2933.e7

Department of Dermatology, University of California, San Diego, San Diego, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, San Diego, CA 92093, USA. Electronic address:

Netherton syndrome (NS) is a monogenic skin disease resulting from loss of function of lymphoepithelial Kazal-type-related protease inhibitor (LEKTI-1). In this study we examine if bacteria residing on the skin are influenced by the loss of LEKTI-1 and if interaction between this human gene and resident bacteria contributes to skin disease. Shotgun sequencing of the skin microbiome demonstrates that lesional skin of NS subjects is dominated by Staphylococcus aureus (S. aureus) and Staphylococcus epidermidis (S. epidermidis). Isolates of either species from NS subjects are able to induce skin inflammation and barrier damage on mice. These microbes promote skin inflammation in the setting of LEKTI-1 deficiency due to excess proteolytic activity promoted by S. aureus phenol-soluble modulin α as well as increased bacterial proteases staphopain A and B from S. aureus or EcpA from S. epidermidis. These findings demonstrate the critical need for maintaining homeostasis of host and microbial proteases to prevent a human skin disease.
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http://dx.doi.org/10.1016/j.celrep.2020.02.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7183042PMC
March 2020

Blockade of IL-17 signaling reverses alcohol-induced liver injury and excessive alcohol drinking in mice.

JCI Insight 2020 02 13;5(3). Epub 2020 Feb 13.

Department of Surgery, and.

Chronic alcohol abuse has a detrimental effect on the brain and liver. There is no effective treatment for these patients, and the mechanism underlying alcohol addiction and consequent alcohol-induced damage of the liver/brain axis remains unresolved. We compared experimental models of alcoholic liver disease (ALD) and alcohol dependence in mice and demonstrated that genetic ablation of IL-17 receptor A (IL-17ra-/-) or pharmacological blockade of IL-17 signaling effectively suppressed the increased voluntary alcohol drinking in alcohol-dependent mice and blocked alcohol-induced hepatocellular and neurological damage. The level of circulating IL-17A positively correlated with the alcohol use in excessive drinkers and was further increased in patients with ALD as compared with healthy individuals. Our data suggest that IL-17A is a common mediator of excessive alcohol consumption and alcohol-induced liver/brain injury, and targeting IL-17A may provide a novel strategy for treatment of alcohol-induced pathology.
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http://dx.doi.org/10.1172/jci.insight.131277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098802PMC
February 2020

Author Correction: Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities.

Nat Microbiol 2019 Dec;4(12):2578

Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41564-019-0621-4DOI Listing
December 2019

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities.

Nat Microbiol 2019 12 7;4(12):2184-2191. Epub 2019 Oct 7.

Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.

Phototrophic communities of photosynthetic algae or cyanobacteria and heterotrophic bacteria or fungi are pervasive throughout the environment. How interactions between members contribute to the resilience and affect the fitness of phototrophic communities is not fully understood. Here, we integrated metatranscriptomics, metabolomics and phenotyping with computational modelling to reveal condition-dependent secretion and cross-feeding of metabolites in a synthetic community. We discovered that interactions between members are highly dynamic and are driven by the availability of organic and inorganic nutrients. Environmental factors, such as ammonia concentration, influenced community stability by shifting members from collaborating to competing. Furthermore, overall fitness was dependent on genotype and streamlined genomes improved growth of the entire community. Our mechanistic framework provides insights into the physiology and metabolic response to environmental and genetic perturbation of these ubiquitous microbial associations.
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http://dx.doi.org/10.1038/s41564-019-0567-6DOI Listing
December 2019

Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity.

NPJ Syst Biol Appl 2019 24;5:33. Epub 2019 Sep 24.

1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA.

Nutrient availability is critical for growth of algae and other microbes used for generating valuable biochemical products. Determining the optimal levels of nutrient supplies to cultures can eliminate feeding of excess nutrients, lowering production costs and reducing nutrient pollution into the environment. With the advent of omics and bioinformatics methods, it is now possible to construct genome-scale models that accurately describe the metabolism of microorganisms. In this study, a genome-scale model of the green alga (CZ946) was applied to predict feeding of multiple nutrients, including nitrate and glucose, under both autotrophic and heterotrophic conditions. The objective function was changed from optimizing growth to instead minimizing nitrate and glucose uptake rates, enabling predictions of feed rates for these nutrients. The metabolic model control (MMC) algorithm was validated for autotrophic growth, saving 18% nitrate while sustaining algal growth. Additionally, we obtained similar growth profiles by simultaneously controlling glucose and nitrate supplies under heterotrophic conditions for both high and low levels of glucose and nitrate. Finally, the nitrate supply was controlled in order to retain protein and chlorophyll synthesis, albeit at a lower rate, under nitrogen-limiting conditions. This model-driven cultivation strategy doubled the total volumetric yield of biomass, increased fatty acid methyl ester (FAME) yield by 61%, and enhanced lutein yield nearly 3 fold compared to nitrogen starvation. This study introduces a control methodology that integrates omics data and genome-scale models in order to optimize nutrient supplies based on the metabolic state of algal cells in different nutrient environments. This approach could transform bioprocessing control into a systems biology-based paradigm suitable for a wide range of species in order to limit nutrient inputs, reduce processing costs, and optimize biomanufacturing for the next generation of desirable biotechnology products.
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http://dx.doi.org/10.1038/s41540-019-0110-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6760154PMC
April 2020

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.

Nat Microbiol 2019 12 23;4(12):2082-2089. Epub 2019 Sep 23.

Department of Pediatrics, University of California, San Diego, CA, USA.

Dietary habits have been associated with alterations of the human gut resident microorganisms contributing to obesity, diabetes and cancer. In Western diets, red meat is a frequently eaten food, but long-term consumption has been associated with increased risk of disease. Red meat is enriched in N-glycolylneuraminic acid (Neu5Gc) that cannot be synthesized by humans. However, consumption can cause Neu5Gc incorporation into cell surface glycans, especially in carcinomas. As a consequence, an inflammatory response is triggered when Neu5Gc-containing glycans encounter circulating anti-Neu5Gc antibodies. Although bacteria can use free sialic acids as a nutrient source, it is currently unknown if gut microorganisms contribute to releasing Neu5Gc from food. We found that a Neu5Gc-rich diet induces changes in the gut microbiota, with Bacteroidales and Clostridiales responding the most. Genome assembling of mouse and human shotgun metagenomic sequencing identified bacterial sialidases with previously unobserved substrate preference for Neu5Gc-containing glycans. X-ray crystallography revealed key amino acids potentially contributing to substrate preference. Additionally, we verified that mouse and human sialidases were able to release Neu5Gc from red meat. The release of Neu5Gc from red meat using bacterial sialidases could reduce the risk of inflammatory diseases associated with red meat consumption, including colorectal cancer and atherosclerosis.
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http://dx.doi.org/10.1038/s41564-019-0564-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879853PMC
December 2019

Functional and Proteomic Analysis of Virulence Upon Loss of Its Native Cas9 Nuclease.

Front Microbiol 2019 22;10:1967. Epub 2019 Aug 22.

Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States.

The public health impact of (group A , GAS) as a top 10 cause of infection-related mortality in humans contrasts with its benefit to biotechnology as the main natural source of Cas9 nuclease, the key component of the revolutionary CRISPR-Cas9 gene editing platform. Despite widespread knowledge acquired in the last decade on the molecular mechanisms by which GAS Cas9 achieves precise DNA targeting, the functions of Cas9 in the biology and pathogenesis of its native organism remain unknown. In this study, we generated an isogenic serotype M1 GAS mutant deficient in Cas9 protein and compared its behavior and phenotypes to the wild-type parent strain. Absence of Cas9 was linked to reduced GAS epithelial cell adherence, reduced growth in human whole blood , and attenuation of virulence in a murine necrotizing skin infection model. Virulence defects of the GAS Δ strain were explored through quantitative proteomic analysis, revealing a significant reduction in the abundance of key GAS virulence determinants. Similarly, deletion of affected the expression of several known virulence regulatory proteins, indicating that Cas9 impacts the global architecture of GAS gene regulation.
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http://dx.doi.org/10.3389/fmicb.2019.01967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714885PMC
August 2019

Modelling approaches for studying the microbiome.

Nat Microbiol 2019 08 23;4(8):1253-1267. Epub 2019 Jul 23.

Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.

Advances in metagenome sequencing of the human microbiome have provided a plethora of new insights and revealed a close association of this complex ecosystem with a range of human diseases. However, there is little knowledge about how the different members of the microbial community interact with each other and with the host, and we lack basic mechanistic understanding of these interactions related to health and disease. Mathematical modelling has been demonstrated to be highly advantageous for gaining insights into the dynamics and interactions of complex systems and in recent years, several modelling approaches have been proposed to enhance our understanding of the microbiome. Here, we review the latest developments and current approaches, and highlight how different modelling strategies have been applied to unravel the highly dynamic nature of the human microbiome. Furthermore, we discuss present limitations of different modelling strategies and provide a perspective of how modelling can advance understanding and offer new treatment routes to impact human health.
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http://dx.doi.org/10.1038/s41564-019-0491-9DOI Listing
August 2019
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