bluuebunny/crossref_metadata_2025_split huggingface dataset:
Back to the future: bacteriophages as promising therapeutic tools
Authors: Domingo‐Calap P. , Georgel P. , Bahram S. 
Published: February 2016

AbstractBacteriophages (phages), natural predators of bacteria, are becoming increasingly attractive in medical and pharmaceutical applications. After their discovery almost a century ago, they have been particularly instrumental in the comprehension of basic molecular biology and genetics processes. The more recent emergence of multi‐drug‐resistant bacteria requires novel therapeutic strategies, and phages are being (re)considered as promising potential antibacterial tools. Furthermore, phages are also used for other purposes, e.g. vaccine production, gene/drug carriers, bacterial detection and typing. These new alternative approaches using phages are of major interest and have allowed unexpected developments, from the decipherment of fundamental biological processes to potential clinical applications.
High‐throughput sequencing of cerebrospinal fluid for diagnosis of chronic Propionibacterium acnes meningitis in an allogeneic stem cell transplant recipient
Authors: Wylie K.M. , Blanco‐Guzman M. , Wylie T.N. , Lawrence S.J. , Ghobadi A. , DiPersio J.F. , Storch G.A. 
Published: February 2016

AbstractBackgroundA 40‐year‐old man with chronic myelogenous leukemia presented multiple times over a period of 3 years with episodes of confusion, wide‐based gait and falls because of recurrent hydrocephalus despite repeated therapeutic lumbar punctures. These problems occurred in the context of persistent cerebrospinal fluid (CSF) pleocytosis and leptomeningeal enhancement. Extensive diagnostic workups and therapeutic trials had failed to identify a clinically plausible cause or produce any significant improvement in the CSF and neuroimaging abnormalities.MethodsWe used high‐throughput metagenomic shotgun sequencing to identify microbes in 2 CSF samples collected from the patient during his illness. These results were compared to sequence data from 1 CSF sample collected during treatment and 5 control CSF samples from other patients.ResultsWe found sequences representing 53% and 67% of the Propionibacterium acnes genome in 2 CSF samples collected from the patient during his illness. Directed antimicrobial therapy was administered for 6 weeks with resolution of CSF and neuroimaging abnormalities. Sequencing of a sample obtained during treatment demonstrated that the P. acnes levels were decreased to background levels. After insertion of a ventriculo‐peritoneal shunt, the patient returned to baseline status.ConclusionsHigh‐throughput metagenomic shotgun sequencing revealed P. acnes as the cause of chronic meningitis that had eluded conventional attempts at diagnosis. Treatment directed at this organism resulted in cure of the infection and clinical improvement.
Experimental transfusion‐induced Babesia microti infection: dynamics of parasitemia and immune responses in a rhesus macaque model
Authors: Gumber Sanjeev , Nascimento Fernanda S. , Rogers Kenneth A. , Bishop Henry S. , Rivera Hilda N. , Xayavong Maniphet V. , Devare Sushil G. , Schochetman Gerald , Amancha Praveen K. , Qvarnstrom Yvonne , Wilkins Patricia P. , Villinger François 
Published: February 2016

BACKGROUNDBabesiosis is an emerging tick‐borne infection in humans. The increasing numbers of reported cases of transfusion‐associated babesiosis (TAB), primarily caused by Babesia microti, represents a concern for the safety of the US blood supply.STUDY DESIGN AND METHODSThis study investigated kinetics of parasitemia and innate immune responses and dynamics of antibody responses during B. microti infection in rhesus macaques (RMs) using blood smears, quantitative polymerase chain reaction (qPCR), flow cytometry, and indirect fluorescent antibody testing. A total of six monkeys were transfused with either hamster or monkey‐passaged B. microti–infected red blood cells (two and four monkeys, respectively) simulating TAB.RESULTSThe prepatent period in monkeys inoculated with hamster‐passaged B. microti was 35 days compared with 4 days in monkeys transfused with monkey‐passaged B. microti; the latter monkeys also had markedly higher parasitemia levels. The duration of the window period from the first detected parasitemia by qPCR analysis to the first detected antibody response ranged from 10 to 17 days. Antibody responses fluctuated during the course of the infection. Innate responses assessed by the frequencies of monocytes and activated B cells correlated with the kinetics and magnitude of parasitemia. On Day 14, additional activation peaks were noted for CD14+CD16+ and CD14–CD16+ monocytes and for CD11c+ myeloid dendritic cells, but only in animals transfused with monkey‐passaged B. microti. Parasitemia persisted in these immunocompetent animals, similar to human infection.CONCLUSIONThe results suggest that transfusion‐associated transmission of B. microti leads to rapid onset of parasitemia (Day 4) in RMs, detectable antibody response 14 days later, and persistent parasitemia.
Epidemiology of Toxocariasis in England and Wales
Authors: Halsby K. , Senyonjo L. , Gupta S. , Ladbury G. , Suvari M. , Chiodini P. , Morgan D. 
Published: February 2016

SummaryToxocara infection occurs through ingestion of parasite eggs excreted by dogs and cats, and can cause severe morbidity. The burden of disease in England and Wales is not well described, and the impact of public health campaigns conducted in the mid‐1990s is uncertain. This paper uses data from two extensive databases to explore the trends in this disease in England and Wales from the 1970s to 2009.
Invasive Pasteurella multocida Infections – Report of Five Cases at a Minnesota Hospital, 2014
Authors: Talley P. , Snippes‐Vagnone P. , Smith K. 
Published: February 2016

SummaryDuring October 2014, the Minnesota Department of Health was notified of five Hospital A patients with Pasteurella multocida bacteraemia; three had died. Human soft tissue infection with P. multocida typically results from cat or dog bites or scratches. Invasive infection, defined as a P. multocida isolate from a usually sterile site, is rare. We evaluated P. multocida isolations at Hospital A, compared with other Minnesota hospitals to understand invasive infection trends. A case was defined as clinically confirmed P. multocida in a Minnesota resident during 2012–2014. All hospital laboratories were queried; Fisher's exact test was used for comparison. Medical charts were reviewed for 2014 Hospital A patients with P. multocida infections. The Minnesota clinical laboratories survey response rate was 79% (63/80). At Hospital A, proportion of P. multocida isolates from usually sterile sites increased from 0% (0/2) during 2012 to 11% (1/9) during 2013, and to 86% (5/6) during 2014. The proportion of patients with P. multocida isolated from sterile sites was 35% (6/17) at Hospital A compared with 10% (58/583) statewide during 2012–2014 combined (P < 0.05). Among 2014 Hospital A patients with invasive P. multocida infection, all five were men; median age was 70 (range: 44–78) years. Four were temporally clustered within a 33‐day period; three of those had bacteraemia on admission, making hospital acquisition possible in only one. Among five bacteraemia patients, four had cirrhosis and/or skin ulcerations, and three died. The proportion of invasive P. multocida cases was substantially higher at Hospital A during 2014. No epidemiologic links between patients were found. Three had known pet exposure. Collaborative educational efforts of chronically ill pet owners by physicians and veterinarians can acknowledge the health benefits of pet ownership, while minimizing risk for serious invasive zoonotic infections, including those caused by P. multocida.
Effect of Dietary Oxalate on the Gut Microbiota of the Mammalian Herbivore Neotoma albigula
Authors: Miller Aaron W. , Oakeson Kelly F. , Dale Colin , Dearing M. Denise 
Published: February 2016

ABSTRACT

Diet is one of the primary drivers that sculpts the form and function of the mammalian gut microbiota. However, the enormous taxonomic and metabolic diversity held within the gut microbiota makes it difficult to isolate specific diet-microbe interactions. The objective of the current study was to elucidate interactions between the gut microbiota of the mammalian herbivore
Neotoma albigula
and dietary oxalate, a plant secondary compound (PSC) degraded exclusively by the gut microbiota. We quantified oxalate degradation in
N. albigula
fed increasing amounts of oxalate over time and tracked the response of the fecal microbiota using high-throughput sequencing. The amount of oxalate degraded
in vivo
was linearly correlated with the amount of oxalate consumed. The addition of dietary oxalate was found to impact microbial species diversity by increasing the representation of certain taxa, some of which are known to be capable of degrading oxalate (e.g.,
Oxalobacter
spp.). Furthermore, the relative abundances of 117 operational taxonomic units (OTU) exhibited a significant correlation with oxalate consumption. The results of this study indicate that dietary oxalate induces complex interactions within the gut microbiota that include an increase in the relative abundance of a community of bacteria that may contribute either directly or indirectly to oxalate degradation in mammalian herbivores.
Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS
Authors: He Shaomei , Tominski Claudia , Kappler Andreas , Behrens Sebastian , Roden Eric E. 
Published: February 2016

ABSTRACT

Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458–1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family
Gallionellaceae
, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochrome
c
system identified in neutrophilic microaerobic Fe(II)-oxidizing
Sideroxydans lithotrophicus
ES-1] in a
Gallionellaceae
sp., and findings of other putative genes involving cytochrome
c
and multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this
Gallionellaceae
sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration.
Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases
Authors: Terrón-González Laura , Martín-Cabello Guadalupe , Ferrer Manuel , Santero Eduardo 
Published: February 2016

ABSTRACT
A metagenomic library of a petroleum-contaminated soil was constructed in a fosmid vector that allowed heterologous expression of metagenomic DNA. The library, consisting of 6.5 Gb of metagenomic DNA, was screened for extradiol dioxygenase (Edo) activity using catechol and 2,3-dihydroxybiphenyl as the substrates. Fifty-eight independent clones encoding extradiol dioxygenase activity were identified. Forty-one different Edo-encoding genes were identified. The population of Edo genes was not dominated by a particular gene or by highly similar genes; rather, the genes had an even distribution and high diversity. Phylogenetic analyses revealed that most of the genes could not be ascribed to previously defined subfamilies of Edos. Rather, the Edo genes led to the definition of 10 new subfamilies of type I Edos. Phylogenetic analysis of type II enzymes defined 7 families, 2 of which harbored the type II Edos that were found in this work. Particularly striking was the diversity found in family I.3 Edos; 15 out of the 17 sequences assigned to this family belonged to 7 newly defined subfamilies. A strong bias was found that depended on the substrate used for the screening: catechol mainly led to the detection of Edos belonging to the I.2 family, while 2,3-dihydroxybiphenyl led to the detection of most other Edos. Members of the I.2 family showed a clear substrate preference for monocyclic substrates, while those from the I.3 family showed a broader substrate range and high activity toward 2,3-dihydroxybiphenyl. This metagenomic analysis has substantially increased our knowledge of the existing biodiversity of Edos.
Oxidation of Molecular Hydrogen by a Chemolithoautotrophic Beggiatoa Strain
Authors: Kreutzmann Anne-Christin , Schulz-Vogt Heide N. 
Published: February 2016

ABSTRACT

A chemolithoautotrophic strain of the family
Beggiatoaceae
,
Beggiatoa
sp. strain 35Flor, was found to oxidize molecular hydrogen when grown in a medium with diffusional gradients of oxygen, sulfide, and hydrogen. Microsensor profiles and rate measurements suggested that the strain oxidized hydrogen aerobically when oxygen was available, while hydrogen consumption under anoxic conditions was presumably driven by sulfur respiration.
Beggiatoa
sp. 35Flor reached significantly higher biomass in hydrogen-supplemented oxygen-sulfide gradient media, but hydrogen did not support growth of the strain in the absence of reduced sulfur compounds. Nevertheless, hydrogen oxidation can provide
Beggiatoa
sp. 35Flor with energy for maintenance and assimilatory purposes and may support the disposal of internally stored sulfur to prevent physical damage resulting from excessive sulfur accumulation. Our knowledge about the exposure of natural populations of
Beggiatoaceae
to hydrogen is very limited, but significant amounts of hydrogen could be provided by nitrogen fixation, fermentation, and geochemical processes in several of their typical habitats such as photosynthetic microbial mats and submarine sites of hydrothermal fluid flow.

IMPORTANCE
Reduced sulfur compounds are certainly the main electron donors for chemolithoautotrophic
Beggiatoaceae
, but the traditional focus on this topic has left other possible inorganic electron donors largely unexplored. In this paper, we provide evidence that hydrogen oxidation has the potential to strengthen the ecophysiological plasticity of
Beggiatoaceae
in several ways. Moreover, we show that hydrogen oxidation by members of this family can significantly influence biogeochemical gradients and therefore should be considered in environmental studies.
Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility
Authors: Vigneron Adrien , Alsop Eric B. , Chambers Brian , Lomans Bartholomeus P. , Head Ian M. , Tsesmetzis Nicolas 
Published: February 2016

ABSTRACTOffshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularlyDesulfovibriospecies, dominated the biofilm microbial communities. However, other bacteria, such asPelobacter,Pseudomonas, andGeotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms.
Engineering Escherichia coli for Microbial Production of Butanone
Authors: Srirangan Kajan , Liu Xuejia , Akawi Lamees , Bruder Mark , Moo-Young Murray , Chou C. Perry 
Published: February 2016

ABSTRACT

To expand the chemical and molecular diversity of biotransformation using whole-cell biocatalysts, we genetically engineered a pathway in
Escherichia coli
for heterologous production of butanone, an important commodity ketone. First, a 1-propanol-producing
E. coli
host strain with its sleeping beauty mutase (Sbm) operon being activated was used to increase the pool of propionyl-coenzyme A (propionyl-CoA). Subsequently, molecular heterofusion of propionyl-CoA and acetyl-CoA was conducted to yield 3-ketovaleryl-CoA via a CoA-dependent elongation pathway. Lastly, 3-ketovaleryl-CoA was channeled into the clostridial acetone formation pathway for thioester hydrolysis and subsequent decarboxylation to form butanone. Biochemical, genetic, and metabolic factors affecting relative levels of ketogenesis, acidogenesis, and alcohologenesis under selected fermentative culture conditions were investigated. Using the engineered
E. coli
strain for batch cultivation with 30 g liter
−1
glycerol as the carbon source, we achieved coproduction of 1.3 g liter
−1
butanone and 2.9 g liter
−1
acetone. The results suggest that approximately 42% of spent glycerol was utilized for ketone biosynthesis, and thus they demonstrate potential industrial applicability of this microbial platform.
Mechanisms of Bacterial (Serratia marcescens) Attachment to, Migration along, and Killing of Fungal Hyphae
Authors: Hover Tal , Maya Tal , Ron Sapir , Sandovsky Hani , Shadkchan Yana , Kijner Nitzan , Mitiagin Yulia , Fichtman Boris , Harel Amnon , Shanks Robert M. Q. , Bruna Roberto E. , García-Véscovi Eleonora , Osherov Nir 
Published: February 2016

ABSTRACTWe have found a remarkable capacity for the ubiquitous Gram-negative rod bacteriumSerratia marcescensto migrate along and kill the mycelia of zygomycete molds. This migration was restricted to zygomycete molds and several basidiomycete species. No migration was seen on any molds of the phylum Ascomycota.S. marcescensmigration did not require fungal viability or surrounding growth medium, as bacteria migrated along aerial hyphae as well.S. marcescensdid not exhibit growth tropism toward zygomycete mycelium. Bacterial migration along hyphae proceeded only when the hyphae grew into the bacterial colony.S. marcescenscells initially migrated along the hyphae, forming attached microcolonies that grew and coalesced to generate a biofilm that covered and killed the mycelium. Flagellum-defective strains ofS. marcescenswere able to migrate along zygomycete hyphae, although they were significantly slower than the wild-type strain and were delayed in fungal killing. Bacterial attachment to the mycelium does not necessitate type 1 fimbrial adhesion, since mutants defective in this adhesin migrated equally well as or faster than the wild-type strain. Killing does not depend on the secretion ofS. marcescenschitinases, as mutants in which all three chitinase genes were deleted retained wild-type killing abilities. A better understanding of the mechanisms by whichS. marcescensbinds to, spreads on, and kills fungal hyphae might serve as an excellent model system for such interactions in general; fungal killing could be employed in agricultural fungal biocontrol.
Text messaging reminders for influenza vaccine in primary care: a cluster randomised controlled trial (TXT4FLUJAB)
Authors: Herrett Emily , Williamson Elizabeth , van Staa Tjeerd , Ranopa Michael , Free Caroline , Chadborn Tim , Goldacre Ben , Smeeth Liam 
Published: February 2016

Objectives(1) To develop methods for conducting cluster randomised trials of text messaging interventions utilising routine electronic health records at low cost; (2) to assess the effectiveness of text messaging influenza vaccine reminders in increasing vaccine uptake in patients with chronic conditions.DesignCluster randomised trial with general practices as clusters.SettingEnglish primary care.Participants156 general practices, who used text messaging software, who had not previously used text message influenza vaccination reminders. Eligible patients were aged 18–64 in ‘at-risk’ groups.InterventionsPractices were randomly allocated to either an intervention or standard care arm in the 2013 influenza season (September to December). Practices in the intervention arm were asked to send a text message influenza vaccination reminder to their at-risk patients under 65. Practices in the standard care arm were asked to continue their influenza campaign as planned.BlindingPractices were not blinded. Analysis was performed blinded to practice allocation.Main outcome measuresPractice-level influenza vaccine uptake among at-risk patients aged 18–64 years.Results77 practices were randomised to the intervention group (76 analysed, n at-risk patients=51 121), 79 to the standard care group (79 analysed, n at-risk patients=51 136). The text message increased absolute vaccine uptake by 2.62% (95% CI −0.09% to 5.33%), p=0.058, though this could have been due to chance. Within intervention clusters, a median 21.0% (IQR 10.2% to 47.0%) of eligible patients were sent a text message. The number needed to treat was 7.0 (95% CI −0.29 to 14.3).ConclusionsPatient follow-up using routine electronic health records is a low cost method of conducting cluster randomised trials. Text messaging reminders are likely to result in modest improvements in influenza vaccine uptake, but levels of patients being texted need to markedly increase if text messaging reminders are to have much effect.Trial registration numberISRCTN48840025.