Publications by authors named "Ruben A T Mars"

14 Publications

  • Page 1 of 1

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community.

Nat Microbiol 2021 02 4;6(2):196-208. Epub 2021 Jan 4.

European Molecular Biology Laboratory, Heidelberg, Germany.

Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures or synthetic assemblies. Here, we show how kefir, a natural milk-fermenting community of prokaryotes (predominantly lactic and acetic acid bacteria) and yeasts (family Saccharomycetaceae), realizes stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microorganisms) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open the niche for the followers by making available metabolites such as amino acids and lactate. Through metabolomics, transcriptomics and large-scale mapping of inter-species interactions, we show how microorganisms poorly suited for milk survive in-and even dominate-the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.
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http://dx.doi.org/10.1038/s41564-020-00816-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610452PMC
February 2021

Bacterially Derived Tryptamine Increases Mucus Release by Activating a Host Receptor in a Mouse Model of Inflammatory Bowel Disease.

iScience 2020 Dec 13;23(12):101798. Epub 2020 Nov 13.

Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.

Recent studies emphasize the role of microbial metabolites in regulating gastrointestinal (GI) physiology through activation of host receptors, highlighting the potential for inter-kingdom signaling in treating GI disorders. In this study, we show that tryptamine, a tryptophan-derived bacterial metabolite, stimulates mucus release from goblet cells via activation of G-protein-coupled receptor (GPCR) 5-HT4R. Germ-free mice colonized with engineered optimized to produce tryptamine (Trp D+) exhibit decreased weight loss and increased mucus release following dextran sodium sulfate treatment when compared with mice colonized with control (Trp D-). Additional beneficial effects in preventing barrier disruption and lower disease activity index were seen only in female mice, highlighting sex-specific effects of the bacterial metabolite. This study demonstrates potential for the precise modulation of mucus release by microbially produced 5-HT4 GPCR agonist as a therapeutic strategy to treat inflammatory conditions of the GI tract.
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http://dx.doi.org/10.1016/j.isci.2020.101798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7702010PMC
December 2020

Functional Gastrointestinal Disorders and the Microbiome-What Is the Best Strategy for Moving Microbiome-based Therapies for Functional Gastrointestinal Disorders into the Clinic?

Gastroenterology 2021 Jan 28;160(2):538-555. Epub 2020 Nov 28.

Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota. Electronic address:

There have been numerous human studies reporting associations between the intestinal microbiome and functional gastrointestinal disorders (FGIDs), and independently animal studies have explored microbiome-driven mechanisms underlying FGIDs. However, there is often a disconnect between human and animal studies, which hampers translation of microbiome findings to the clinic. Changes in the microbiota composition of patients with FGIDs are generally subtle, whereas changes in microbial function, reflected in the fecal metabolome, appear to be more precise indicators of disease subtype-specific mechanisms. Although we have made significant progress in characterizing the microbiome, to effectively translate microbiome science in a timely manner, we need concurrent and iterative longitudinal studies in humans and animals to determine the precise microbial functions that can be targeted to address specific pathophysiological processes in FGIDs. A systems approach integrating multiple data layers rather than evaluating individual data layers of symptoms, physiological changes, or -omics data in isolation will allow for validation of mechanistic insights from animal studies while also allowing new discovery. Patient stratification for clinical trials based on functional microbiome alterations and/or pathophysiological measurements may allow for more accurate determination of efficacy of individual microbiome-targeted interventions designed to correct an underlying abnormality. In this review, we outline current approaches and knowledge, and identify gaps, to provide a potential roadmap for accelerating translation of microbiome science toward microbiome-targeted personalized treatments for FGIDs.
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http://dx.doi.org/10.1053/j.gastro.2020.10.058DOI Listing
January 2021

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome.

Cell 2020 09 10;182(6):1460-1473.e17. Epub 2020 Sep 10.

Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA. Electronic address:

The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. VIDEO ABSTRACT.
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http://dx.doi.org/10.1016/j.cell.2020.08.007DOI Listing
September 2020

Tryptic Shaving of Unveils Immunodominant Epitopes on the Bacterial Cell Surface.

J Proteome Res 2020 08 25;19(8):2997-3010. Epub 2020 Jun 25.

Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands.

The opportunistic pathogen has become a major threat for human health and well-being by developing resistance to antibiotics and by fast evolution into new lineages that rapidly spread within the healthy human population. This calls for development of active or passive immunization strategies to prevent or treat acute phase infections. Since no such anti-staphylococcal immunization approaches are available for clinical implementation, the present studies were aimed at identifying new leads for their development. For this purpose, we profiled the cell-surface-exposed staphylococcal proteome under infection-mimicking conditions by combining two approaches for "bacterial shaving" with immobilized or soluble trypsin and subsequent mass spectrometry analysis of liberated peptides. In parallel, non-covalently cell-wall-bound proteins extracted with potassium thiocyanate and the exoproteome fraction were analyzed by gel-free proteomics. All data are available through ProteomeXchange accession PXD000156. To pinpoint immunodominant bacterial-surface-exposed epitopes, we screened selected cell-wall-attached proteins of for binding of immunoglobulin G from patients who have been challenged by different types of due to chronic wound colonization. The combined results of these analyses highlight particular cell-surface-exposed proteins with highly immunogenic exposed epitopes as potential targets for development of protective anti-staphylococcal immunization strategies.
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http://dx.doi.org/10.1021/acs.jproteome.0c00043DOI Listing
August 2020

Impact of air quality on the gastrointestinal microbiome: A review.

Environ Res 2020 07 7;186:109485. Epub 2020 Apr 7.

Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA; Department of Cardiovascular Diseases, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA. Electronic address:

Background: Poor air quality is increasingly associated with several gastrointestinal diseases suggesting a possible association between air quality and the human gut microbiome. However, details on this remain largely unexplored as current available research is scarce. The aim of this comprehensive rigorous review was to summarize the existing reports on the impact of indoor or outdoor airborne pollutants on the animal and human gut microbiome and to outline the challenges and suggestions to expand this field of research.

Methods And Results: A comprehensive search of several databases (inception to August 9, 2019, humans and animals, English language only) was designed and conducted by an experienced librarian to identify studies describing the impact of air pollution on the human gut microbiome. The retrieved articles were assessed independently by two reviewers. This process yielded six original research papers on the animal GI gastrointestinal microbiome and four on the human gut microbiome. β-diversity analyses from selected animal studies demonstrated a significantly different composition of the gut microbiota between control and exposed groups but changes in α-diversity were less uniform. No consistent findings in α or β-diversity were reported among the human studies. Changes in microbiota at the phylum level disclosed substantial discrepancies across animal and human studies.

Conclusions: A different composition of the gut microbiome, particularly in animal models, is associated with exposure to air pollution. Air pollution is associated with various taxa changes, which however do not follow a clear pattern. Future research using standardized methods are critical to replicate these initial findings and advance this emerging field.
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http://dx.doi.org/10.1016/j.envres.2020.109485DOI Listing
July 2020

Disentangling metabolic functions of bacteria in the honey bee gut.

PLoS Biol 2017 Dec 12;15(12):e2003467. Epub 2017 Dec 12.

Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.

It is presently unclear how much individual community members contribute to the overall metabolic output of a gut microbiota. To address this question, we used the honey bee, which harbors a relatively simple and remarkably conserved gut microbiota with striking parallels to the mammalian system and importance for bee health. Using untargeted metabolomics, we profiled metabolic changes in gnotobiotic bees that were colonized with the complete microbiota reconstituted from cultured strains. We then determined the contribution of individual community members in mono-colonized bees and recapitulated our findings using in vitro cultures. Our results show that the honey bee gut microbiota utilizes a wide range of pollen-derived substrates, including flavonoids and outer pollen wall components, suggesting a key role for degradation of recalcitrant secondary plant metabolites and pollen digestion. In turn, multiple species were responsible for the accumulation of organic acids and aromatic compound degradation intermediates. Moreover, a specific gut symbiont, Bifidobacterium asteroides, stimulated the production of host hormones known to impact bee development. While we found evidence for cross-feeding interactions, approximately 80% of the identified metabolic changes were also observed in mono-colonized bees, with Lactobacilli being responsible for the largest share of the metabolic output. These results show that, despite prolonged evolutionary associations, honey bee gut bacteria can independently establish and metabolize a wide range of compounds in the gut. Our study reveals diverse bacterial functions that are likely to contribute to bee health and provide fundamental insights into how metabolic activities are partitioned within gut communities.
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http://dx.doi.org/10.1371/journal.pbio.2003467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726620PMC
December 2017

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression.

Microbiol Mol Biol Rev 2016 12 26;80(4):1029-1057. Epub 2016 Oct 26.

Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands

Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5' untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis. A recent study identified 1,583 putative regulatory RNAs in B. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5' ends of mRNA molecules. These can include 5' secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis.
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http://dx.doi.org/10.1128/MMBR.00026-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116874PMC
December 2016

The reduction in small ribosomal subunit abundance in ethanol-stressed cells of Bacillus subtilis is mediated by a SigB-dependent antisense RNA.

Biochim Biophys Acta 2015 Oct 24;1853(10 Pt A):2553-9. Epub 2015 Jun 24.

Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands. Electronic address:

One of the best-characterized general stress responses in bacteria is the σB-mediated stress response of the Gram-positive soil bacterium Bacillus subtilis. The σB regulon contains approximately 200 protein-encoding genes and 136 putative regulatory RNAs. One of these σB-dependent RNAs, named S1136-S1134, was recently mapped as being transcribed from the S1136 promoter on the opposite strand of the essential rpsD gene, which encodes the ribosomal primary-binding protein S4. Accordingly, S1136-S1134 transcription results in an rpsD-overlapping antisense RNA (asRNA). Upon exposure of B. subtilis to ethanol, the S1136 promoter was found to be induced, while rpsD transcription was downregulated. By quantitative PCR, we show that the activation of transcription from the S1136 promoter is directly responsible for the downregulation of rpsD upon ethanol exposure. We also show that this downregulation of rpsD leads to a reduced level of the small (30S) ribosomal subunit upon ethanol stress. The activation of the S1136 promoter thus represents the first example of antisense transcription-mediated regulation in the general stress response of B. subtilis and implicates the reduction of ribosomal protein abundance as a new aspect in the σB-dependent stress response. We propose that the observed reduction in the level of the small ribosomal subunit, which contains the ribosome-decoding center, may protect B. subtilis cells against misreading and spurious translation of possibly toxic aberrant peptides under conditions of ethanol stress.
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http://dx.doi.org/10.1016/j.bbamcr.2015.06.009DOI Listing
October 2015

Small regulatory RNA-induced growth rate heterogeneity of Bacillus subtilis.

PLoS Genet 2015 Mar 19;11(3):e1005046. Epub 2015 Mar 19.

Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.

Isogenic bacterial populations can consist of cells displaying heterogeneous physiological traits. Small regulatory RNAs (sRNAs) could affect this heterogeneity since they act by fine-tuning mRNA or protein levels to coordinate the appropriate cellular behavior. Here we show that the sRNA RnaC/S1022 from the Gram-positive bacterium Bacillus subtilis can suppress exponential growth by modulation of the transcriptional regulator AbrB. Specifically, the post-transcriptional abrB-RnaC/S1022 interaction allows B. subtilis to increase the cell-to-cell variation in AbrB protein levels, despite strong negative autoregulation of the abrB promoter. This behavior is consistent with existing mathematical models of sRNA action, thus suggesting that induction of protein expression noise could be a new general aspect of sRNA regulation. Importantly, we show that the sRNA-induced diversity in AbrB levels generates heterogeneity in growth rates during the exponential growth phase. Based on these findings, we hypothesize that the resulting subpopulations of fast- and slow-growing B. subtilis cells reflect a bet-hedging strategy for enhanced survival of unfavorable conditions.
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http://dx.doi.org/10.1371/journal.pgen.1005046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366234PMC
March 2015

The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism.

Nucleic Acids Res 2014 Oct 12;42(18):11393-407. Epub 2014 Sep 12.

Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, P.O. box 30001, 9700 RB Groningen, the Netherlands.

Expression of particular drug transporters in response to antibiotic pressure is a critical element in the development of bacterial multidrug resistance, and represents a serious concern for human health. To obtain a better understanding of underlying regulatory mechanisms, we have dissected the transcriptional activation of the ATP-binding cassette (ABC) transporter BmrC/BmrD of the Gram-positive model bacterium Bacillus subtilis. By using promoter-GFP fusions and live cell array technology, we demonstrate a temporally controlled transcriptional activation of the bmrCD genes in response to antibiotics that target protein synthesis. Intriguingly, bmrCD expression only occurs during the late-exponential and stationary growth stages, irrespective of the timing of the antibiotic challenge. We show that this is due to tight transcriptional control by the transition state regulator AbrB. Moreover, our results show that the bmrCD genes are co-transcribed with bmrB (yheJ), a small open reading frame immediately upstream of bmrC that harbors three alternative stem-loop structures. These stem-loops are apparently crucial for antibiotic-induced bmrCD transcription. Importantly, the antibiotic-induced bmrCD expression requires translation of bmrB, which implies that BmrB serves as a regulatory leader peptide. Altogether, we demonstrate for the first time that a ribosome-mediated transcriptional attenuation mechanism can control the expression of a multidrug ABC transporter.
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http://dx.doi.org/10.1093/nar/gku832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191407PMC
October 2014

Is proteomics a reliable tool to probe the oxidative folding of bacterial membrane proteins?

Antioxid Redox Signal 2013 Apr 11;18(10):1159-64. Epub 2012 Jun 11.

Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.

The oxidative folding of proteins involves disulfide bond formation, which is usually catalyzed by thiol-disulfide oxidoreductases (TDORs). In bacteria, this process takes place in the cytoplasmic membrane and other extracytoplasmic compartments. While it is relatively easy to study oxidative folding of water-soluble proteins on a proteome-wide scale, this has remained a major challenge for membrane proteins due to their high hydrophobicity. Here, we have assessed whether proteomic techniques can be applied to probe the oxidative folding of membrane proteins using the Gram-positive bacterium Bacillus subtilis as a model organism. Specifically, we investigated the membrane proteome of a B. subtilis bdbCD mutant strain, which lacks the primary TDOR pair BdbC and BdbD, by gel-free mass spectrometry. In total, 18 membrane-associated proteins showed differing behavior in the bdbCD mutant and the parental strain. These included the ProA protein involved in osmoprotection. Consistent with the absence of ProA, the bdbCD mutant was found to be sensitive to osmotic shock. We hypothesize that membrane proteomics is a potentially effective approach to profile oxidative folding of bacterial membrane proteins.
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http://dx.doi.org/10.1089/ars.2012.4664DOI Listing
April 2013

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.

Science 2012 Mar;335(6072):1103-6

INRA, UR1077, Mathématique Informatique et Génome, Jouy-en-Josas, France.

Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.
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http://dx.doi.org/10.1126/science.1206848DOI Listing
March 2012