Publications

@article{MUROVEC2018428,

title = {1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms},

author = {Boštjan Murovec and Damjan Makuc and Sabina Kolbl Repinc and Zala Prevoršek and Domen Zavec and Robert Šket and Klemen Pečnik and Janez Plavec and Blaž Stres},

url = {http://www.sciencedirect.com/science/article/pii/S0301479718305991},

doi = {https://doi.org/10.1016/j.jenvman.2018.05.068},

issn = {0301-4797},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Environmental Management},

volume = {222},

pages = {428 - 435},

abstract = {In this study, nuclear magnetic resonance (1H NMR) spectroscopic profiling was used to provide a more comprehensive view of microbial metabolites associated with poor reactor performance in a full-scale 4 MW mesophilic agricultural biogas plant under fully operational and also under inhibited conditions. Multivariate analyses were used to assess the significance of differences between reactors whereas artificial neural networks (ANN) were used to identify the key metabolites responsible for inhibition and their network of interaction. Based on the results of nm-MDS ordination the subsamples of each reactor were similar, but not identical, despite homogenization of the full-scale reactors before sampling. Hence, a certain extent of variability due to the size of the system under analysis was transferred into metabolome analysis. Multivariate analysis showed that fully active reactors were clustered separately from those containing inhibited reactor metabolites and were significantly different. Furthermore, the three distinct inhibited states were significantly different from each other. The inhibited metabolomes were enriched in acetate, caprylate, trimethylamine, thymine, pyruvate, alanine, xanthine and succinate. The differences in the metabolic fingerprint between inactive and fully active reactors observed in this study resembled closely the metabolites differentiating the (sub) acute rumen acidosis inflicted and healthy rumen metabolomes, creating thus favorable conditions for the growth and activity of pathogenic bacteria. The consistency of our data with those reported before for rumen ecosystems shows that 1H NMR based metabolomics is a reliable approach for the evaluation of metabolic events at full-scale biogas reactors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fphys.2018.00198,

title = {Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis},

author = {Robert Šket and Tadej Debevec and Susanne Kublik and Michael Schloter and Anne Schoeller and Boštjan Murovec and Katarina Vogel Mikuš and Damjan Makuc and Klemen Pečnik and Janez Plavec and Igor B Mekjavić and Ola Eiken and Zala Prevoršek and Blaž Stres},

url = {https://www.frontiersin.org/article/10.3389/fphys.2018.00198},

doi = {10.3389/fphys.2018.00198},

issn = {1664-042X},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Frontiers in Physiology},

volume = {9},

pages = {198},

abstract = {We explored the metagenomic, metabolomic and trace metal makeup of intestinal microbiota and environment in healthy male participants during the run-in (5 day) and the following three 21-day interventions: normoxic bedrest (NBR), hypoxic bedrest (HBR) and hypoxic ambulation (HAmb) which were carried out within a controlled laboratory environment (circadian rhythm, fluid and dietary intakes, microbial bioburden, oxygen level, exercise). The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for the NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg (~4000 m simulated altitude) for HBR and HAmb interventions, respectively. Shotgun metagenomes were analyzed at various taxonomic and functional levels, 1H- and 13C -metabolomes were processed using standard quantitative and human expert approaches, whereas metals were assessed using X-ray fluorescence spectrometry. Inactivity and hypoxia resulted in a significant increase in the genus Bacteroides in HBR, in genes coding for proteins involved in iron acquisition and metabolism, cell wall, capsule, virulence, defense and mucin degradation, such as beta-galactosidase (EC3.2.1.23), α-L-fucosidase (EC3.2.1.51), Sialidase (EC3.2.1.18) and α-N-acetylglucosaminidase (EC3.2.1.50). In contrast, the microbial metabolomes, intestinal element and metal profiles, the diversity of bacterial, archaeal and fungal microbial communities were not significantly affected. The observed progressive decrease in defecation frequency and concomitant increase in the electrical conductivity (EC) preceded or took place in absence of significant changes at the taxonomic, functional gene, metabolome and intestinal metal profile levels. The fact that the genus Bacteroides and proteins involved in iron acquisition and metabolism, cell wall, capsule, virulence and mucin degradation were enriched at the end of HBR suggest that both constipation and EC decreased intestinal metal availability leading to modified expression of co-regulated genes in Bacteroides genomes. Bayesian network analysis was used to derive the first hierarchical model of initial inactivity mediated deconditioning steps over time. The PlanHab wash-out period corresponded to a profound life-style change (i.e. reintroduction of exercise) that resulted in stepwise amelioration of the negative physiological symptoms, indicating that exercise apparently prevented the crosstalk between the microbial physiology, mucin degradation and proinflammatory immune activities in the host.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1371/journal.pone.0188556,

title = {Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study},

author = {Robert Šket and Nicole Treichel and Susanne Kublik and Tadej Debevec and Ola Eiken and Igor Mekjavić and Michael Schloter and Marius Vital and Jenna Chandler and James M Tiedje and Boštjan Murovec and Zala Prevoršek and Matevž Likar and Blaž Stres},

url = {https://doi.org/10.1371/journal.pone.0188556},

doi = {10.1371/journal.pone.0188556},

year  = {2017},

date = {2017-01-01},

journal = {PLOS ONE},

volume = {12},

number = {12},

pages = {1-26},

publisher = {Public Library of Science},

abstract = {We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4000 m simulated altitude), respectively. A number of parameters linked to intestinal environment such as defecation frequency, intestinal electrical conductivity (IEC), sterol and polyphenol content and diversity, indole, aromaticity and spectral characteristics of dissolved organic matter (DOM) were measured (64 variables). The structure and diversity of bacterial microbial community was assessed using 16S rRNA amplicon sequencing. Inactivity negatively affected frequency of defecation and in combination with hypoxia increased IEC (p < 0.05). In contrast, sterol and polyphenol diversity and content, various characteristics of DOM and aromatic compounds, the structure and diversity of bacterial microbial community were not significantly affected over time. A new in-house PlanHab database was established to integrate all measured variables on host physiology, diet, experiment, immune and metabolic markers (n = 231). The observed progressive decrease in defecation frequency and concomitant increase in IEC suggested that the transition from healthy physiological state towards the developed symptoms of low magnitude obesity-related syndromes was dose dependent on the extent of time spent in inactivity and preceded or took place in absence of significant rearrangements in bacterial microbial community. Species B. thetaiotamicron, B. fragilis, B. dorei and other Bacteroides with reported relevance for dysbiotic medical conditions were significantly enriched in HBR, characterized with most severe inflammation symptoms, indicating a shift towards host mucin degradation and proinflammatory immune crosstalk.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fphys.2017.00250,

title = {Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study},

author = {Robert Šket and Nicole Treichel and Tadej Debevec and Ola Eiken and Igor Mekjavic and Michael Schloter and Marius Vital and Jenna Chandler and James M Tiedje and Boštjan Murovec and Zala Prevoršek and Blaž Stres},

url = {https://www.frontiersin.org/article/10.3389/fphys.2017.00250},

doi = {10.3389/fphys.2017.00250},

issn = {1664-042X},

year  = {2017},

date = {2017-01-01},

journal = {Frontiers in Physiology},

volume = {8},

pages = {250},

abstract = {We explored the assembly of intestinal microbiota in healthy male participants during the run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bedrest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4000 m simulated altitude), respectively. A number of parameters linked to intestinal transit spanning Bristol Stool Scale, defecation rates, zonulin, α1-antitrypsin, eosinophil derived neurotoxin, bile acids, reducing sugars, short chain fatty acids, total soluble organic carbon, water content, diet composition and food intake were measured (167 variables). The abundance, structure and diversity of butyrate producing microbial community were assessed using the two primary bacterial butyrate synthesis pathways, butyryl-CoA: acetate CoA-transferase (but) and butyrate kinase (buk) genes. Inactivity negatively affected fecal consistency and in combination with hypoxia aggravated the state of gut inflammation (p < 0.05). In contrast, gut permeability, various metabolic markers, the structure, diversity and abundance of butyrate producing microbial community were not significantly affected. Rearrangements in the butyrate producing microbial community structure were explained by experimental setup (13.4 %), experimentally structured metabolites (12.8 %) and gut metabolite-immunological markers (11.9 %), with 61.9% remaining unexplained. Many of the measured parameters were found to be correlated and were hence omitted from further analyses. The observed progressive increase in two immunological intestinal markers suggested that the transition from healthy physiological state towards the developed symptoms of low magnitude obesity-related syndromes was primarily driven by the onset of inactivity (lack of exercise in NBR) that were exacerbated by systemic hypoxia (HBR) and significantly alleviated by exercise, despite hypoxia (HAmb). Butyrate producing community in colon exhibited apparent resilience towards short-term modifications in host exercise or hypoxia. Progressive constipation (decreased intestinal motility) and increased local inflammation marker suggest that changes in microbial colonization and metabolism were taking place at the location of small intestine.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MUROVEC2015320,

title = {Job-shop local-search move evaluation without direct consideration of the criterion’s value},

author = {Boštjan Murovec},

url = {http://www.sciencedirect.com/science/article/pii/S0377221714007309},

doi = {https://doi.org/10.1016/j.ejor.2014.08.044},

issn = {0377-2217},

year  = {2015},

date = {2015-01-01},

journal = {European Journal of Operational Research},

volume = {241},

number = {2},

pages = {320 - 329},

abstract = {This article focuses on the evaluation of moves for the local search of the job-shop problem with the makespan criterion. We reason that the omnipresent ranking of moves according to their resulting value of a criterion function makes the local search unnecessarily myopic. Consequently, we introduce an alternative evaluation that relies on a surrogate quantity of the move’s potential, which is related to, but not strongly coupled with, the bare criterion. The approach is confirmed by empirical tests, where the proposed evaluator delivers a new upper bound on the well-known benchmark test yn2. The line of the argumentation also shows that by sacrificing accuracy the established makespan estimators unintentionally improve on the move evaluation in comparison to the exact makespan calculation, in contrast to the belief that the reliance on estimation degrades the optimization results.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MUROVEC2015217,

title = {Methane Yield Database: Online infrastructure and bioresource for methane yield data and related metadata},

author = {Boštjan Murovec and Sabina Kolbl and Blaž Stres},

url = {http://www.sciencedirect.com/science/article/pii/S0960852415005040},

doi = {https://doi.org/10.1016/j.biortech.2015.04.021},

issn = {0960-8524},

year  = {2015},

date = {2015-01-01},

journal = {Bioresource Technology},

volume = {189},

pages = {217 - 223},

abstract = {The aim of this study was to develop and validate a community supported online infrastructure and bioresource for methane yield data and accompanying metadata collected from published literature. In total, 1164 entries described by 15,749 data points were assembled. Analysis of data collection showed little congruence in reporting of methodological approaches. The largest identifiable source of variation in reported methane yields was represented by authorship (i.e. substrate batches within particular substrate class) within which experimental scales (volumes (0.02–5l), incubation temperature (34–40°C) and % VS of substrate played an important role (p<0.0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1371/journal.pone.0076440,

title = {Recently Deglaciated High-Altitude Soils of the Himalaya: Diverse Environments, Heterogenous Bacterial Communities and Long-Range Dust Inputs from the Upper Troposphere},

author = {Blaz Stres and Woo Jun Sul and Bostjan Murovec and James M Tiedje},

url = {https://doi.org/10.1371/journal.pone.0076440},

doi = {10.1371/journal.pone.0076440},

year  = {2013},

date = {2013-01-01},

journal = {PLOS ONE},

volume = {8},

number = {9},

pages = {1-10},

publisher = {Public Library of Science},

abstract = {Background The Himalaya with its altitude and geographical position forms a barrier to atmospheric transport, which produces much aqueous-particle monsoon precipitation and makes it the largest continuous ice-covered area outside polar regions. There is a paucity of data on high-altitude microbial communities, their native environments and responses to environmental-spatial variables relative to seasonal and deglaciation events. Methodology/Principal Findings Soils were sampled along altitude transects from 5000 m to 6000 m to determine environmental, spatial and seasonal factors structuring bacterial communities characterized by 16 S rRNA gene deep sequencing. Dust traps and fresh-snow samples were used to assess dust abundance and viability, community structure and abundance of dust associated microbial communities. Significantly different habitats among the altitude-transect samples corresponded to both phylogenetically distant and closely-related communities at distances as short as 50 m showing high community spatial divergence. High within-group variability that was related to an order of magnitude higher dust deposition obscured seasonal and temporal rearrangements in microbial communities. Although dust particle and associated cell deposition rates were highly correlated, seasonal dust communities of bacteria were distinct and differed significantly from recipient soil communities. Analysis of closest relatives to dust OTUs, HYSPLIT back-calculation of airmass trajectories and small dust particle size (4–12 µm) suggested that the deposited dust and microbes came from distant continental, lacustrine and marine sources, e.g. Sahara, India, Caspian Sea and Tibetan plateau. Cyanobacteria represented less than 0.5% of microbial communities suggesting that the microbial communities benefitted from (co)deposited carbon which was reflected in the psychrotolerant nature of dust-particle associated bacteria. Conclusions/Significance The spatial, environmental and temporal complexity of the high-altitude soils of the Himalaya generates ongoing disturbance and colonization events that subject heterogeneous microniches to stochastic colonization by far away dust associated microbes and result in the observed spatially divergent bacterial communities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MUROVEC2013847,

title = {Towards commoditized smart-camera design},

author = {Boštjan Murovec and Janez Perš and Rok Mandeljc and Vildana Sulić Kenk and Stanislav Kovačič},

url = {http://www.sciencedirect.com/science/article/pii/S1383762113000799},

doi = {https://doi.org/10.1016/j.sysarc.2013.05.010},

issn = {1383-7621},

year  = {2013},

date = {2013-01-01},

journal = {Journal of Systems Architecture},

volume = {59},

number = {10, Part A},

pages = {847 - 858},

abstract = {We propose a set of design principles for a cost-effective embedded smart camera. Our aim is to alleviate the shortcomings of the existing designs, such as excessive reliance on battery power and wireless networking, over-emphasized focus on specific use cases, and use of specialized technologies. In our opinion, these shortcomings prevent widespread commercialization and adoption of embedded smart cameras, especially in the context of visual-sensor networks. The proposed principles lead to a distinctively different design, which relies on commoditized, standardized and widely-available components, tools and knowledge. As an example of using these principles in practice, we present a smart camera, which is inexpensive, easy to build and support, capable of high-speed communication and enables rapid transfer of computer-vision algorithms to the embedded world.},

note = {Smart Camera Architecture},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MUROVEC2010175,

title = {DNA encoding for an efficient 'Omics processing},

author = {Boštjan Murovec and James M Tiedje and Blaž Stres},

url = {http://www.sciencedirect.com/science/article/pii/S0169260710000660},

doi = {https://doi.org/10.1016/j.cmpb.2010.03.014},

issn = {0169-2607},

year  = {2010},

date = {2010-01-01},

journal = {Computer Methods and Programs in Biomedicine},

volume = {100},

number = {2},

pages = {175 - 190},

abstract = {The exponential growth of available DNA sequences and the increased interoperability of biological information is triggering intergovernmental efforts aimed at increasing the access, dissemination, and analysis of sequence data. Achieving the efficient storage and processing of DNA material is an important goal that parallels well with the foreseen coding standardization on the horizon. This paper proposes novel coding approaches, for both the dissemination and processing of sequences, where the speed of the DNA processing is shown to be boosted by exploring more than the normally utilized eight bits for encoding a single nucleotide. Further gains are achieved by encoding the nucleotides together with their trailing alignment information as a single 64-bit data structure. The paper also proposes a slight modification to the established FASTA scheme in order to improve on its representation of alignment information. The significance of the propositions is confirmed by the encouraging results from empirical tests.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1093/bioinformatics/btp254,

title = {BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer–enzyme–sequence databases},

author = {Blaž Stres and James M Tiedje and Boštjan Murovec},

url = {https://doi.org/10.1093/bioinformatics/btp254},

doi = {10.1093/bioinformatics/btp254},

issn = {1367-4803},

year  = {2009},

date = {2009-01-01},

journal = {Bioinformatics},

volume = {25},

number = {12},

pages = {1556-1558},

abstract = {Summary: BEsTRF (Best Estimated T-RF) provides a standalone environment for analyzing primers-enzymes-gene section combinations used in terminal-restriction fragment length polymorphism (T-RFLP) for its optimal resolution. User-defined sequence databases of several hundred thousand DNA sequences can be explored and the resolution of user-specified sets of primers and restriction endonucleases can be analyzed on either forward or reverse terminal fragments. Sequence quality, primer mismatches, insertions and deletions can be controlled and each primer pair-specific sequence collections can be exported for downstream analyses. The configuration for a novel T-RFLP population profiling using rpoB gene (DNA-directed RNA polymerase, beta subunit) on forward fluorescently labeled primer are presented.Availability: BEsTRF is freely available at http://lie.fe.uni-lj.si/bestrf and can be downloaded from the same site. The online protocol, numerous primer and enzyme dictionaries, sequence collections and results generated during this work for various genes are available at our website http://lie.fe.uni-lj.si/bestrf.Contact:blaz.stres@bfro.uni-lj.si},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MUROVEC2004220,

title = {A repairing technique for the local search of the job-shop problem},

author = {Boštjan Murovec and Peter Šuhel},

url = {http://www.sciencedirect.com/science/article/pii/S0377221702007336},

doi = {https://doi.org/10.1016/S0377-2217(02)00733-6},

issn = {0377-2217},

year  = {2004},

date = {2004-01-01},

journal = {European Journal of Operational Research},

volume = {153},

number = {1},

pages = {220 - 238},

abstract = {The local search technique has become a widely used tool for solving many combinatorial optimization problems. In the case of the job-shop the implementation of such a technique is not straightforward at all due to the existence of the technological constraints among the operations that belong to the same job. Their presence renders a certain set of schedules infeasible. Consequently, special attention is required when defining optimization algorithms to prevent the possibility of reaching an infeasible schedule during execution. Traditionally, the problem is tackled on the neighborhood level by using only a limited set of moves for which feasibility inherently holds. This paper proposes an alternative way to avoid infeasibility by incorporating a repairing technique into the mechanism for applying moves to a schedule. Whenever an infeasible move is being applied, a repairing mechanism rearranges the underlying schedule in such a way that the feasibility of the move is restored. The possibility of reaching infeasible solutions is, therefore, eliminated on the lowest possible conceptual level. Consequently, neighborhood functions need not to be constrained to a limited set of feasible moves any more.},

note = {Timetabling and Rostering},

keywords = {},

pubstate = {published},

tppubtype = {article}

}