Diego Chaves‐Moreno

Helmholtz Centre for Infection Research

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Dietmar H. Pieper

Helmholtz Centre for Infection Research

Ruy Jáuregui

AgResearch

Andrew P. A. Oxley

Deakin University

Melissa L. Wos‐Oxley

Deakin University

Eva Medina

Helmholtz Centre for Infection Research

Karsten Becker

Universitätsmedizin Greifswald

Silke Kahl

Helmholtz Centre for Infection Research

Silke Niemann

University Hospital Münster

Iris Plumeier

Helmholtz Centre for Infection Research

Daiana de Lima-Morales

Hospital de Clínicas de Porto Alegre

Cooperative Institutions

Helmholtz Centre for Infection Research

University Hospital Münster

Technical University of Munich

University of Münster

Center for Integrated Protein Science Munich

Czech Academy of Sciences, Institute of Microbiology

German Center for Infection Research

Institute of Medical Microbiology and Hygiene

Universität Greifswald

Universitätsmedizin Greifswald

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Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw

Scientific Reports (2015)

Diego Javier Jiménez Diego Chaves‐Moreno Jan Dirk van Elsas

Abstract Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2 Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohydrate transporters (ABC, TonB and phosphotransferases), two-component sensing systems and β-glucosidases/galactosidases in the two consortia as compared to the forest soil inoculum. Additionally, “profiling” of carbohydrate-active enzymes showed significant enrichments of several genes encoding glycosyl hydrolases of families GH2, GH43, GH92 and GH95. Sequence analyses revealed these to be most strongly affiliated to genes present on the genomes of Sphingobacterium , Bacteroides , Flavobacterium and Pedobacter spp . Assembly of the RWS and TWS metagenomes generated 16,536 and 15,902 contigs of ≥10 Kb, respectively. Thirteen contigs, containing 39 glycosyl hydrolase genes, constitute novel (hemi)cellulose utilization loci with affiliation to sequences primarily found in the Bacteroidetes. Overall, this study provides deep insight in the plant polysaccharide degrading capabilities of microbial consortia bred from forest soil, highlighting their biotechnological potential.

10.1038/srep13845

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Citations (72)

Exploring the bacterial assemblages along the human nasal passage

Environmental Microbiology (2016)

Melissa L. Wos‐Oxley Diego Chaves‐Moreno Ruy Jáuregui Andrew P. A. Oxley Ursula Kaspar

Summary The human nasal passage, from the anterior nares through the nasal vestibule to the nasal cavities, is an important habitat for opportunistic pathogens and commensals alike. This work sampled four different anatomical regions within the human nasal passage across a large cohort of individuals ( n = 79) comprising individuals suffering from chronic nasal inflammation clinically known as chronic rhinosinusitis (CRS) and individuals not suffering from inflammation (CRS‐free). While individuals had their own unique bacterial fingerprint that was consistent across the anatomical regions, these bacterial fingerprints formed into distinct delineated groups comprising core bacterial members, which were consistent across all four swabbed anatomical regions irrespective of health status. The most significant observed pattern was the difference between the global bacterial profiles of swabbed and tissue biopsy samples from the same individuals, being also consistent across different anatomical regions. Importantly, no statistically significant differences could be observed concerning the global bacterial communities, any of the bacterial species or the range of diversity indices used to compare between CRS and CRS‐free individuals, and between two CRS phenotypes (without nasal polyps and with nasal polyps). Thus, the role of bacteria in the pathogenesis of sinusitis remains uncertain.

Nasal vestibule

Nasal Polyps

Chronic Rhinosinusitis

Commensalism

10.1111/1462-2920.13378

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Importance of superoxide dismutases A and M for protection ofStaphylococcus aureusin the oxidative stressful environment of cystic fibrosis airways

Cellular Microbiology (2020)

Janina Treffon Diego Chaves‐Moreno Silke Niemann Dietmar H. Pieper Thomas J. Vogl

Staphylococcus aureus is one of the earliest pathogens that persists the airways of cystic fibrosis (CF) patients and contributes to increased inflammation and decreased lung function. In contrast to other staphylococci, S. aureus possesses two superoxide dismutases (SODs), SodA and SodM, with SodM being unique to S. aureus. Both SODs arm S. aureus for its fight against oxidative stress, a by-product of inflammatory reactions. Despite complex investigations, it is still unclear if both enzymes are crucial for the special pathogenicity of S. aureus. To investigate the role of both SODs during staphylococcal persistence in CF airways, we analysed survival and gene expression of S. aureus CF isolates and laboratory strains in different CF-related in vitro and ex vivo settings. Bacteria located in inflammatory and oxidised CF sputum transcribed high levels of sodA and sodM. Especially expression values of sodM were remarkably higher in CF sputum than in bacterial in vitro cultures. Interestingly, also S. aureus located in airway epithelial cells expressed elevated transcript numbers of both SODs, indicating that S. aureus is exposed to oxidative stress at various sites within CF airways. Both enzymes promoted survival of S. aureus during polymorphonuclear leukocyte killing and seem to act compensatory, thereby giving evidence that the interwoven interaction of SodA and SodM contributes to S. aureus virulence and facilitates S. aureus persistence within CF airways.

10.1111/cmi.13158

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The Hologenome of Haliclona fulva (Porifera, Demospongiae) Reveals an Abundant and Diverse Viral Community

Frontiers in Marine Science (2021)

Erika García-Bonilla Diego Chaves‐Moreno Diego Riaño-Pachón Wilson Terán Alberto Acosta

Viruses are among the most abundant biological entities in the ocean, largely responsible of modulating nutrients fluxes and influencing microbial composition and functioning. In marine invertebrate holobionts like sponges and their associated microbiomes, little is known about virome composition. Here, we characterized the Haliclona fulva hologenome, an encrusting low-microbial abundance sponge found across the Western Mediterranean Sea (35–40 m of depth) producer of a large metabolic repertoire of bioactive compounds and harboring a distinct and stable associated microbiome. Assembled contigs from shotgun metagenome sequences obtained from H. fulva specimens were comprehensively analyzed regarding taxonomic and functional content revealing its remarkable and abundant viral community dominated by single-stranded DNA (ssDNA) virus. Viral families consistently detected in contigs are Circoviridae, Phycodnaviridae, Poxviridae, Herelleviridae, Mimiviridae, Microviridae, and notably the first reported encounter of Nanoviridae and Genomoviridae in Porifera, expanding their known host range. The relative abundance of inferred bacteriophages/prophages was low, suggesting that the prokaryotic community in this sponge has a limited host range and susceptibility. H. fulva showed a distinct viral composition supporting the general proposition of specific and coevolving viromes in marine holobionts.

Human virome

Holobiont

Sponge

10.3389/fmars.2021.736817

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High Nuclease Activity of Long Persisting Staphylococcus aureus Isolates Within the Airways of Cystic Fibrosis Patients Protects Against NET-Mediated Killing

Frontiers in Immunology (2019)

Susann Herzog Felix Dach Nicole de Buhr Silke Niemann Jannik Schlagowski

Staphylococcus aureus is one of the first and one of the most prevalent pathogens cultured from the airways of cystic fibrosis (CF) patients, which can persist therefor extended periods. Airway infections in CF patients are characterized by a strong inflammatory response of highly recruited neutrophils. One killing mechanism of neutrophils is the formation of neutrophil extracellular traps (NETs), which capture and eradicate bacteria by extracellular fibers of neutrophil chromatin decorated with antimicrobial granule proteins. S. aureus secretes nuclease, which can degrade NETs. We hypothesized, that S. aureus adapts to the airways of CF patients during persistent infection by escaping from NET-mediated killing via an increase of nuclease activity. Sputum samples of CF patients with chronic S. aureus infection were visualized by confocal microscopy after immuno-fluorescence staining of DNA-histone-1-complexes as a specific marker for NETs, S. aureus bacteria and overall DNA structures. Nuclease activity was analyzed in sequential isogenic long persisting S. aureus isolates from an individual CF patient using a FRET- based nuclease activity assay. NET-killing assays were performed with clinical S. aureus isolates to evaluate killing and bacterial survival depending on nuclease activity. To confirm the role of nuclease during NET-mediated killing, a clinical isolate with low nuclease activity was transformed with a nuclease expression vector (pCM28nuc). Two sputa from a CF patient were subjected to RNA-sequence analysis to evaluate the activity of nuclease in vivo. In sputa, S. aureus was associated to extracellular DNA structures. Nuclease activity in clinical S. aureus isolates increased in a time- and phenotype-dependent manner. NET-mediated killing was significantly higher in S. aureus isolates with low compared to isolates with high nuclease activity. Importantly, transformation of the clinical isolate with low nuclease activity with pCM28nuc conferred protection against NET-mediated killing confirming the beneficial role of nuclease for protection against NETs. Also, nuclease expression in in vivo sputa was high, which underlines the important role of nuclease within the highly inflamed CF airways. In conclusion, our data show that S. aureus adapts to the neutrophil-rich environment of CF airways with increasing nuclease expression most likely to avoid NET-killing during long-term persistence.

Nuclease

Neutrophil Extracellular Traps

Micrococcal nuclease

10.3389/fimmu.2019.02552

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Citations (34)

Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics

Microorganisms (2019)

C. Pineda-Quiroga Daniel Borda-Molina Diego Chaves‐Moreno R. Ruíz Raquel Atxaerandio

Diet has an essential influence in the establishment of the cecum microbial communities in poultry, so its supplementation with safe additives, such as probiotics, prebiotics, and synbiotics might improve animal health and performance. This study showed the ceca microbiome modulations of laying hens, after feeding with dry whey powder as prebiotics, Pediococcus acidilactici as probiotics, and the combination of both as synbiotics. A clear grouping of the samples induced per diet was observed (p < 0.05). Operational taxonomic units (OTUs) identified as Olsenella spp., and Lactobacillus crispatus increased their abundance in prebiotic and synbiotic treatments. A core of the main functions was shared between all metagenomes (45.5%), although the genes encoding for the metabolism of butanoate, propanoate, inositol phosphate, and galactose were more abundant in the prebiotic diet. The results indicated that dietary induced-changes in microbial composition did not imply a disturbance in the principal biological roles, while the specific functions were affected.

Prebiotic

Synbiotics

Cecum

Pediococcus acidilactici

Lactobacillus crispatus

10.3390/microorganisms7050123

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Citations (29)