Publications by authors named "Loy A"

218 Publications

An overview of biomass thermochemical conversion technologies in Malaysia.

Sci Total Environ 2019 Aug 18;680:105-123. Epub 2019 Apr 18.

Department of Chemical and Environmental Engineering, University of Nottingham, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.

The rising pressure on both cleaner production and sustainable development have been the main driving force that pushes mankind to seek for alternative greener and sustainable feedstocks for chemical and energy production. The biomass 'waste-to-wealth' concept which convert low value biomass into value-added products which contain high economic potential, have attracted the attentions from both academicians and industry players. With a tropical climate, Malaysia has a rich agricultural sector and dense tropical rainforest, giving rise to abundance of biomass which most of them are underutilized. Hence, the biomass 'waste-to-wealth' conversion through various thermochemical conversion technologies and the prospective challenges towards commercialization in Malaysia are reviewed in this paper. In this paper, a critical review about the maturity status of the four most promising thermochemical conversion routes in Malaysia (i.e. gasification, pyrolysis, liquefaction and hydroprocessing) is given. The current development of thermochemical conversion technologies for biomass conversion in Malaysia is also reviewed and benchmarked against global progress. Besides, the core technical challenges in commercializing these green technologies are highlighted as well. Lastly, the future outlook for successful commercialization of these technologies in Malaysia is included.
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http://dx.doi.org/10.1016/j.scitotenv.2019.04.211DOI Listing
August 2019

Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.

Cell Host Microbe 2019 05 18;25(5):681-694.e8. Epub 2019 Apr 18.

Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site LMU Munich, 80336 Munich, Germany. Electronic address:

The microbiota and the gastrointestinal mucus layer play a pivotal role in protection against non-typhoidal Salmonella enterica serovar Typhimurium (S. Tm) colitis. Here, we analyzed the course of Salmonella colitis in mice lacking a functional mucus layer in the gut. Unexpectedly, in contrast to mucus-proficient littermates, genetically deficient mice were protected against Salmonella-induced gut inflammation in the streptomycin colitis model. This correlated with microbiota alterations and enrichment of the bacterial phylum Deferribacteres. Using gnotobiotic mice associated with defined bacterial consortia, we causally linked Mucispirillum schaedleri, currently the sole known representative of Deferribacteres present in the mammalian microbiota, to host protection against S. Tm colitis. Inhibition by M. schaedleri involves interference with S. Tm invasion gene expression, partly by competing for anaerobic electron acceptors. In conclusion, this study establishes M. schaedleri, a core member of the murine gut microbiota, as a key antagonist of S. Tm virulence in the gut.
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http://dx.doi.org/10.1016/j.chom.2019.03.004DOI Listing
May 2019

Pseudomonas aeruginosa severe skin infection in a toddler with X-linked agammaglobulinemia due to a novel BTK mutation.

Infez Med 2019 Mar;27(1):73-76

Infectious Disease Unit, Istituto Giannina Gaslini, University of Genoa, Italy.

Agammaglobulinemia is a congenital deficit of humoral immunity characterized by a decreased level or complete absence of immunoglobulins and profound reduction of B-lymphocytes associated with an increased risk of life-threatening bacterial infection. We report a case of invasive Pseudomonas aeruginosa severe skin and soft tissue infection treated with vacuum-assisted closure and antibiotics in a toddler with a previously unreported mutation of the Bruton tyrosin kinase gene.
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March 2019

Historical Factors Associated With Past Environments Influence the Biogeography of Thermophilic Endospores in Arctic Marine Sediments.

Front Microbiol 2019 28;10:245. Epub 2019 Feb 28.

School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, United Kingdom.

Selection by the local, contemporary environment plays a prominent role in shaping the biogeography of microbes. However, the importance of historical factors in microbial biogeography is more debatable. Historical factors include past ecological and evolutionary circumstances that may have influenced present-day microbial diversity, such as dispersal and past environmental conditions. Diverse thermophilic sulfate-reducing are present as dormant endospores in marine sediments worldwide where temperatures are too low to support their growth. Therefore, they are dispersed to here from elsewhere, presumably a hot, anoxic habitat. While dispersal through ocean currents must influence their distribution in cold marine sediments, it is not clear whether even earlier historical factors, related to the source habitat where these organisms were once active, also have an effect. We investigated whether these historical factors may have influenced the diversity and distribution of thermophilic endospores by comparing their diversity in 10 Arctic fjord surface sediments. Although community composition varied spatially, clear biogeographic patterns were only evident at a high level of taxonomic resolution (>97% sequence similarity of the 16S rRNA gene) achieved with oligotyping. In particular, the diversity and distribution of oligotypes differed for the two most prominent OTUs (defined using a standard 97% similarity cutoff). One OTU was dominated by a single ubiquitous oligotype, while the other OTU consisted of ten more spatially localized oligotypes that decreased in compositional similarity with geographic distance. These patterns are consistent with differences in historical factors that occurred when and where the taxa were once active, prior to sporulation. Further, the influence of history on biogeographic patterns was only revealed by analyzing microdiversity within OTUs, suggesting that populations within standard OTU-level groupings do not necessarily share a common ecological and evolutionary history.
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http://dx.doi.org/10.3389/fmicb.2019.00245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403435PMC
February 2019

Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member.

mBio 2019 02 12;10(1). Epub 2019 Feb 12.

Department of Biology, University of Konstanz, Konstanz, Germany

Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize " Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under -like conditions for 50 days by -targeted qPCR and metatranscriptomics. The population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 10 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of " Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days. The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.
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http://dx.doi.org/10.1128/mBio.02189-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372793PMC
February 2019

Prolonged antibiotic administration for surgical site infection in pediatric laryngotracheal surgery.

Laryngoscope 2019 Nov 27;129(11):2634-2639. Epub 2018 Dec 27.

Infectious Diseases Unit, Scientific Institute for Research, Hospitalization, and Health Care, Istituto Giannina Gaslini, Genoa, Italy.

Objectives/hypothesis: Incidence of surgical site infection (SSI) after laryngotracheal (LT) surgery is relatively high, especially in children.

Study Design: Retrospective and prospective cohort study.

Methods: Clinical records of children who underwent open LT surgery at the Istituto Giannina Gaslini Children's Hospital from January 2008 to August 2017 were reviewed for development of SSI. Standard antibiotic prophylaxis was administered until February 2015. In March 2015, an antibiotic treatment tailored on pathogens isolated from surveillance cultures and prolonged until extubation was introduced. Incidence and risk factors for SSI before and after the new protocol implementation were analyzed by means of univariate and multivariable analyses.

Results: A total of 57 procedures were analyzed. SSI incidence was 36% in patients receiving standard prophylaxis and 4% in those treated with the new strategy (P = .004), with an absolute benefit increase of 32% (95% confidence interval: 11%-52%), in absence of any difference in clinical conditions between the two groups.

Conclusions: The new management protocol had a highly favorable impact on the development of an SSI.

Level Of Evidence: 2b Laryngoscope, 129:2634-2639, 2019.
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http://dx.doi.org/10.1002/lary.27699DOI Listing
November 2019

OpenMICE: an open spatial and temporal data set of small mammals in south-central Italy based on owl pellet data.

Ecology 2018 12 15;99(12):2874. Epub 2018 Oct 15.

EnvixLab, Dipartimento Bioscienze e Territorio, Università degli Studi del Molise, Contrada Fonte Lappone, Pesche, I86090, Italy.

The use of database technologies as a tool for implementing data for quantitative ecological studies and biodiversity conservation planning has recently attracted the attention of the biological community. Despite the fact that the number of biodiversity data sets is quickly rising, online databases of small mammals are still scarce, especially for Mediterranean ecosystems. We implemented the first standardized and accessible georeferenced European database of small mammal occurrences, abundances, and functional traits. Data derived from owl pellets was obtained from different sources, including original field surveys, publications, gray literature, existing databases, and museum collections. The OpenMICE database covers the years 1972 to 2017 and includes nearly 50,000 individuals from 23 species (13 Rodentia and 10 Eulipotyphla) at 190 sites in south-central Italy. Our specific goals in compiling this data set were as follows: (1) to make data that is usually accessible to a restricted audience widely available; (2) to identify the gaps in knowledge about small mammal communities and guide future sampling and conservation efforts; and (3) to gain a first insight into small mammal diversity and abundance in the study area. The potential applications of our spatial relational database are many, from individual-based to community-based models as potential indicators of environmental changes at different geographical scales. Given the long-term support for data storage, the OpenMICE database could be further expanded to include other geographical contexts and implemented with new information and traits. We would appreciate that researchers cite this paper if using all or part of the data set. We also request that researchers and teachers inform us of how they are using the data. We intend to keep it up to date as novel studies become available (see Data Availability).
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http://dx.doi.org/10.1002/ecy.2506DOI Listing
December 2018

Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment.

Environ Microbiol 2018 08 3;20(8):2927-2940. Epub 2018 Sep 3.

Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria.

Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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http://dx.doi.org/10.1111/1462-2920.14297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175234PMC
August 2018

Stable-Isotope Probing of Human and Animal Microbiome Function.

Trends Microbiol 2018 12 9;26(12):999-1007. Epub 2018 Jul 9.

Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, Austria.

Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.
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http://dx.doi.org/10.1016/j.tim.2018.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249988PMC
December 2018

Kinetics and thermodynamic analysis in one-pot pyrolysis of rice hull using renewable calcium oxide based catalysts.

Bioresour Technol 2018 Oct 6;265:180-190. Epub 2018 Jun 6.

College of Forest Products and Paper Science, University of the Philippines Los Baños, College, Laguna 4031, Philippines.

Thermodynamic and kinetic parameters of catalytic pyrolysis of rice hull (RH) pyrolysis using two different types of renewable catalysts namely natural limestone (LS) and eggshells (ES) using thermogravimetric analysis (TG) approach at different heating rates of 10-100 K min in temperature range of 323-1173 K are investigated. Catalytic pyrolysis mechanism of both catalysts had shown significant effect on the degradation of RH. Model free kinetic of iso-conversional method (Flynn-Wall-Ozawa) and multi-step reaction model (Distributed Activation Energy Model) were employed into present study. The average activation energy was found in the range of 175.4-177.7 kJ mol (RH), 123.3-132.5 kJ mol (RH-LS), and 96.1-100.4 kJ mol (RH-ES) respectively. The syngas composition had increased from 60.05 wt% to 63.1 wt% (RH-LS) and 63.4 wt% (RH-ES). However, the CO content had decreased from 24.1 wt% (RH) to 20.8 wt% (RH-LS) and 19.9 wt% (RH-ES).
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http://dx.doi.org/10.1016/j.biortech.2018.06.003DOI Listing
October 2018

CD3ε Expression Defines Functionally Distinct Subsets of Vδ1 T Cells in Patients With Human Immunodeficiency Virus Infection.

Front Immunol 2018 2;9:940. Epub 2018 May 2.

Discipline of Immunology, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland.

Human γδ T cells expressing the Vδ1 T cell receptor (TCR) recognize self and microbial antigens and stress-inducible molecules in a major histocompatibility complex-unrestricted manner and are an important source of innate interleukin (IL)-17. Vδ1 T cells are expanded in the circulation and intestines of patients with human immunodeficiency virus (HIV) infection. In this study, we show that patients with HIV have elevated frequencies, but not absolute numbers, of circulating Vδ1 T cells compared to control subjects. This increase was most striking in the patients with co-infection. Using flow cytometry and confocal microscopy, we identify two populations of Vδ1 T cells, based on low and high expression of the ε chain of the CD3 protein complex responsible for transducing TCR-mediated signals (denoted CD3ε and CD3ε Vδ1 T cells). Both Vδ1 T cell populations expressed the CD3 ζ-chain, also used for TCR signaling. Using lines of Vδ1 T cells generated from healthy donors, we show that CD3ε can be transiently downregulated by activation but that its expression is restored over time in culture in the presence of exogenous IL-2. Compared to CD3ε Vδ1 T cells, CD3ε Vδ1 T cells more frequently expressed terminally differentiated phenotypes and the negative regulator of T cell activation, programmed death-1 (PD-1), but not lymphocyte-activation gene 3, and upon stimulation , only the CD3ε subset of Vδ1 T cells, produced IL-17. Thus, while HIV can infect and kill IL-17-producing CD4 T cells, Vδ1 T cells are another source of IL-17, but many of them exist in a state of exhaustion, mediated either by the induction of PD-1 or by downregulation of CD3ε expression.
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http://dx.doi.org/10.3389/fimmu.2018.00940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940748PMC
July 2019

Heparin inhibits intracellular Mycobacterium tuberculosis bacterial replication by reducing iron levels in human macrophages.

Sci Rep 2018 05 8;8(1):7296. Epub 2018 May 8.

Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA.

Iron is a crucial micronutrient for both mammals and their associated pathogens, and extensive literature has shown that Mycobacterium tuberculosis (Mtb) bacilli inhibited from acquiring iron from the host are severely attenuated. In contrast, increased dietary iron concentrations or patients with hemochromatosis have long been associated with a more severe tuberculosis (TB) disease outcome. We have observed that upon macrophage infection, Mtb bacilli strongly promote intracellular iron sequestration, both through increased expression of hepcidin, a key mammalian iron regulatory protein, and downregulation of the iron exporter protein, ferroportin. Heparin is a highly sulfated glycosaminoglycan released by mast cells and basophils at sites of tissue injury. During Mtb infection, heparin alters intracellular trafficking in alveolar epithelial cells and decreases extrapulmonary dissemination but recently, heparin also has been reported to inhibit hepcidin expression in hepatocytes, decreasing intracellular iron availability. In this report, we demonstrate that heparin significantly reduces hepcidin expression in macrophages infected with Mtb bacilli. Heparin-treated macrophages have higher ferroportin expression compared to untreated macrophages, promoting iron export and decreasing iron availability to intracellular bacilli. Thus, here we describe a novel immunomodulatory effect and potential therapeutic role for heparin against mycobacterial infection in human macrophages.
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http://dx.doi.org/10.1038/s41598-018-25480-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940867PMC
May 2018

Thermogravimetric kinetic modelling of in-situ catalytic pyrolytic conversion of rice husk to bioenergy using rice hull ash catalyst.

Bioresour Technol 2018 Aug 7;261:213-222. Epub 2018 Apr 7.

Resilience Development Initiative, Jl. Imperial Imperial 2, No. 52, Bandung 40135, Indonesia.

The thermal degradation behaviour and kinetic parameter of non-catalytic and catalytic pyrolysis of rice husk (RH) using rice hull ash (RHA) as catalyst were investigated using thermogravimetric analysis at four different heating rates of 10, 20, 50 and 100 K/min. Four different iso conversional kinetic models such as Kissinger, Friedman, Kissinger-Akahira-Sunose (KAS) and Ozawa-Flynn-Wall (OFW) were applied in this study to calculate the activation energy (E) and pre-exponential value (A) of the system. The E of non-catalytic and catalytic pyrolysis was found to be in the range of 152-190 kJ/mol and 146-153 kJ/mol, respectively. The results showed that the catalytic pyrolysis of RH had resulted in a lower E as compared to non-catalytic pyrolysis of RH and other biomass in literature. Furthermore, the high Gibb's free energy obtained in RH implied that it has the potential to serve as a source of bioenergy production.
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http://dx.doi.org/10.1016/j.biortech.2018.04.020DOI Listing
August 2018

Peatland Acidobacteria with a dissimilatory sulfur metabolism.

ISME J 2018 06 23;12(7):1729-1742. Epub 2018 Feb 23.

Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria.

Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.
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http://dx.doi.org/10.1038/s41396-018-0077-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018796PMC
June 2018

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle.

ISME J 2018 06 21;12(7):1715-1728. Epub 2018 Feb 21.

Department of Earth and Planetary Science, Berkeley, CA, USA.

A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.
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http://dx.doi.org/10.1038/s41396-018-0078-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018805PMC
June 2018

Draft Genome Sequence of 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.

Genome Announc 2018 Jan 25;6(4). Epub 2018 Jan 25.

Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.

The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of that reveals expected and novel metabolic potential for the genus , including genes for sulfur oxidation.
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http://dx.doi.org/10.1128/genomeA.01524-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786683PMC
January 2018

Granulated sugar for adjuvant treatment of surgical wound infection due to multi-drug-resistant pathogens in a child with sarcoma: a case report and literature review.

Infez Med 2017 Dec;25(4):358-361

Infectious Diseases Unit, Istituto Giannina Gaslini - Ospedale Pediatrico IRCCS, Genova, Italy.

The use of sugar for treating wounds which are difficult to heal and positive to resistant pathogens has already been documented. The authors describe the successful treatment by direct instillation of granular sugar in the antibiotic-resistant infected surgical site wound of a child with sarcoma. Sugar instillation in the extended spectrum beta-lactamase (ESBL)-producing Enterobacter cloacae positive wound, in addition to systemic treatment with meropenem and levofloxacin, allowed culture negativization in six days and complete wound healing in 30 days. These results make the use of sugar an attractive option for wounds which are difficult to treat, even in an immunocompromised child.
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December 2017

Epidemiology of Infectious Complications During Extracorporeal Membrane Oxygenation in Children: A Single-Center Experience in 46 Runs.

Pediatr Infect Dis J 2018 07;37(7):624-626

Neonatal and Pediatric Intensive care Unit, Istituto Giannina Gaslini Children's Hospital, Genoa, Italy.

Background: Infections represent a severe complication of extracorporeal membrane oxygenation (ECMO). Aim of the present study was to describe the epidemiology of infections acquired during ECMO in a tertiary care children's hospital.

Methods: Retrospective analysis of clinical records of patients undergoing ECMO between January 2009 and December 2016. For each patient, data were collected on clinical characteristics, modality of ECMO support, site and etiology of documented infections, survival within 1 week after ECMO weaning and/or at pediatric intensive care unit discharge. These data were employed to evaluate overall infection prevalence, infection rate expressed as episodes/1000 days of support and cumulative risk estimates of infections occurring during ECMO.

Results: During the study period, a total of 46 ECMO procedures were performed. The overall prevalence of documented infections was 33%, with an infection rate of 27.22 and a cumulative risk of 55%. Bloodstream infection represented the most frequently documented (53%), followed by pneumonia (40%). Coagulase-negative staphylococci and Pseudomonas aeruginosa prevailed as isolated pathogens. Overall survival was 59%, and 46% among those developing infections during ECMO.

Conclusions: ECMO is a procedure at high risk for infections. Our data, limited to 1 center, represent a recent benchmark for further investigations.
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http://dx.doi.org/10.1097/INF.0000000000001873DOI Listing
July 2018

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.

Environ Microbiol 2017 Dec 4;19(12):4939-4952. Epub 2017 Dec 4.

School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK.

Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.
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http://dx.doi.org/10.1111/1462-2920.13971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767755PMC
December 2017

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay.

Appl Environ Microbiol 2017 Dec 16;83(23). Epub 2017 Nov 16.

Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark

Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.
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http://dx.doi.org/10.1128/AEM.01547-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5691419PMC
December 2017

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters.

Microbiome 2017 09 22;5(1):126. Epub 2017 Sep 22.

Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.

Background: Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown.

Results: We performed a multifaceted analysis of microbiota and DOM diversity in 12 natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than 10 species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM.

Conclusions: The bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.
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http://dx.doi.org/10.1186/s40168-017-0344-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610417PMC
September 2017

Management of Lyme Disease in European Children: a Review for Practical Purpose.

Curr Infect Dis Rep 2017 Aug;19(8):27

Istituto Giannina Gaslini - Ospedale Pediatrico IRCCS, Largo G. Gaslini 5, 16147, Genoa, Italy.

Purpose Of Review: Lyme disease is a tick-borne zoonosis transmitted through a bite of a tick carrying a spirochete belonging to Borrelia species. In the last 20 years, the reported incidence of Lyme disease is increased by three times in Europe. Clinically, the illness develops through a primary stage with a typical skin rash (erythema marginatum), then a secondary stage with possible neurologic or cardiac involvement. The last stage (chronic Lyme disease) is mainly represented by arthritis or late neurological complications but nowadays is rarely seen due to precocious antibiotic use.

Recent Findings: The diagnosis of Lyme disease is essentially based on history in agreement with tick exposure (living/recent traveling in endemic area or tick bite) and clinical findings compatible with the disease. At present, no laboratory diagnostic tool available can neither establish nor exclude the diagnosis of Lyme disease. The management of Lyme disease should comprise a prophylactic administration of antibiotic in selected population (patients exposed to a tick bite in endemic regions) in which the typical signs of Lyme disease are not yet appeared; conversely, patients with current signs of Lyme disease should undergo a standard therapeutic course. First-line therapy should be oral tetracycline or oral penicillin/cephalosporin (in pediatric populations, beta-lactamic drugs are preferred). In severe courses, intravenous route should be preferred. The aim of this review is to provide an updated guide to the management of pediatric Lyme patients, from prophylaxis to first- and second-line therapy in European setting.
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http://dx.doi.org/10.1007/s11908-017-0582-9DOI Listing
August 2017

HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis.

Cancer Res 2017 05 20;77(9):2424-2438. Epub 2017 Feb 20.

Christian Doppler Laboratory for Molecular Cancer Chemoprevention, Division of Gastroenterology and Hepatology, Department of Medicine 3, Medical University of Vienna, Vienna, Austria.

HuR is an RNA-binding protein implicated in immune homeostasis and various cancers, including colorectal cancer. HuR binding to AU-rich elements within the 3' untranslated region of mRNAs encoding oncogenes, growth factors, and various cytokines leads message stability and translation. In this study, we evaluated HuR as a small-molecule target for preventing colorectal cancer in high-risk groups such as those with familial adenomatosis polyposis (FAP) or inflammatory bowel disease (IBD). In human specimens, levels of cytoplasmic HuR were increased in colonic epithelial cells from patients with IBD, IBD-cancer, FAP-adenoma, and colorectal cancer, but not in patients with IBD-dysplasia. Intraperitoneal injection of the HuR small-molecule inhibitor MS-444 in AOM/DSS mice, a model of IBD and inflammatory colon cancer, augmented DSS-induced weight loss and increased tumor multiplicity, size, and invasiveness. MS-444 treatment also abrogated tumor cell apoptosis and depleted tumor-associated eosinophils, accompanied by a decrease in IL18 and eotaxin-1. In contrast, HuR inhibition in APC mice, a model of FAP and colon cancer, diminished the number of small intestinal tumors generated. In this setting, fecal microbiota, evaluated by 16S rRNA gene amplicon sequencing, shifted to a state of reduced bacterial diversity, with an increased representation of , and Taken together, our results indicate that HuR activation is an early event in FAP-adenoma but is not present in IBD-dysplasia. Furthermore, our results offer a preclinical proof of concept for HuR inhibition as an effective means of FAP chemoprevention, with caution advised in the setting of IBD. .
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http://dx.doi.org/10.1158/0008-5472.CAN-15-1726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826591PMC
May 2017

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

Environ Microbiol Rep 2017 08 5;9(4):323-344. Epub 2017 May 5.

Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network "Chemistry meets Microbiology", University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria.

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.
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http://dx.doi.org/10.1111/1758-2229.12538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573963PMC
August 2017

Physical Activity is Associated with Metabolic Health in Men Living with HIV.

AIDS Behav 2018 Jun;22(6):1965-1971

Department of Cardiology, Saint James's Hospital, Dublin, Ireland.

Metabolic health is a cause for concern among those living with HIV, especially those on antiretroviral therapy. Physical activity (PA) is known to benefit metabolic health, however, few studies have objectively measured PA or investigated the relationship between PA and metabolic health among those living with HIV. In this study, PA and indices of metabolic health among twenty men living with HIV and twenty age matched HIV-negative men were measured. PA was measured using Actigraph accelerometers. Components of the metabolic syndrome and insulin resistance were measured using routine laboratory methods. Men living with HIV were significantly more physically active than HIV-negative men, and were reaching public PA guidelines. Significant inverse correlations between moderate PA and both insulin resistance (ρ -0.847; p < 0.001) and triglycerides (ρ -0.575; p = 0.013) were seen in those living with HIV. Results of this study emphasize the importance of an active lifestyle for those living with HIV.
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http://dx.doi.org/10.1007/s10461-017-1715-8DOI Listing
June 2018

Lifestyle and Horizontal Gene Transfer-Mediated Evolution of , a Core Member of the Murine Gut Microbiota.

mSystems 2017 Jan-Feb;2(1). Epub 2017 Jan 31.

Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Austria.

is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species , which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The genome has been shaped by extensive horizontal gene transfer, primarily from intestinal - and , indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium , which is associated with inflammation in widely used mouse models. We found that has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.
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http://dx.doi.org/10.1128/mSystems.00171-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5285517PMC
January 2017

Environmental Enteric Dysfunction and Growth Failure/Stunting in Global Child Health.

Pediatrics 2016 12 4;138(6). Epub 2016 Nov 4.

International Atomic Energy Agency, Vienna, Austria.

Approximately 25% of the world's children aged <5 years have stunted growth, which is associated with increased mortality, cognitive dysfunction, and loss of productivity. Reducing by 40% the number of stunted children is a global target for 2030. The pathogenesis of stunting is poorly understood. Prenatal and postnatal nutritional deficits and enteric and systemic infections clearly contribute, but recent findings implicate a central role for environmental enteric dysfunction (EED), a generalized disturbance of small intestinal structure and function found at a high prevalence in children living under unsanitary conditions. Mechanisms contributing to growth failure in EED include intestinal leakiness and heightened permeability, gut inflammation, dysbiosis and bacterial translocation, systemic inflammation, and nutrient malabsorption. Because EED has multiple causal pathways, approaches to manage it need to be multifaceted. Potential interventions to tackle EED include: (1) reduction of exposure to feces and contact with animals through programs such as improved water, sanitation, and hygiene; (2) breastfeeding and enhanced dietary diversity; (3) probiotics and prebiotics; (4) nutrient supplements, including zinc, polyunsaturated fatty acids, and amino acids; (5) antiinflammatory agents such as 5-aminosalicyclic acid; and (6) antibiotics in the context of acute malnutrition and infection. Better understanding of the underlying causes of EED and development of noninvasive, practical, simple, and affordable point-of-care diagnostic tools remain key gaps. "Omics" technologies (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) and stable isotope techniques (eg, C breath tests) targeted at children and their intestinal microbiota will enhance our ability to successfully identify, manage, and prevent this disorder.
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http://dx.doi.org/10.1542/peds.2016-0641DOI Listing
December 2016

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium.

Nat Microbiol 2016 Nov 21;2:16215. Epub 2016 Nov 21.

Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany.

Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse-Microbiota (Oligo-MM), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM. By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the mouse intestinal bacterial collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genome-guided design can be used to generate insights into microbe-microbe and microbe-host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine.
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http://dx.doi.org/10.1038/nmicrobiol.2016.215DOI Listing
November 2016