bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coadministration of the Campylobacter jejuni N-Glycan-Based Vaccine with Probiotics Improves Vaccine Performance in Broiler Chickens
Authors: Nothaft H. , Perez-Muñoz M. E. , Gouveia G. J. , Duar R. M. , Wanford J. J. , Lango-Scholey L. , Panagos C. G. , Srithayakumar V. , Plastow G. S. , Coros C. , Bayliss C. D. , Edison A. S. , Walter J. , Szymanski C. M. 
Published: September 2017

ABSTRACT

Source attribution studies report that the consumption of contaminated poultry is the primary source for acquiring human campylobacteriosis. Oral administration of an engineered
Escherichia coli
strain expressing the
Campylobacter jejuni
N-glycan reduces bacterial colonization in specific-pathogen-free leghorn chickens, but only a fraction of birds respond to vaccination. Optimization of the vaccine for commercial broiler chickens has great potential to prevent the entry of the pathogen into the food chain. Here, we tested the same vaccination approach in broiler chickens and observed similar efficacies in pathogen load reduction, stimulation of the host IgY response, the lack of
C. jejuni
resistance development, uniformity in microbial gut composition, and the bimodal response to treatment. Gut microbiota analysis of leghorn and broiler vaccine responders identified one member of
Clostridiales
cluster XIVa,
Anaerosporobacter mobilis
, that was significantly more abundant in responder birds. In broiler chickens, coadministration of the live vaccine with
A. mobilis
or
Lactobacillus reuteri
, a commonly used probiotic, resulted in increased vaccine efficacy, antibody responses, and weight gain. To investigate whether the responder-nonresponder effect was due to the selection of a
C. jejuni
“supercolonizer mutant” with altered phase-variable genes, we analyzed all poly(G)-containing loci of the input strain compared to nonresponder colony isolates and found no evidence of phase state selection. However, untargeted nuclear magnetic resonance (NMR)-based metabolomics identified a potential biomarker negatively correlated with
C. jejuni
colonization levels that is possibly linked to increased microbial diversity in this subgroup. The comprehensive methods used to examine the bimodality of the vaccine response provide several opportunities to improve the
C. jejuni
vaccine and the efficacy of any vaccination strategy.

IMPORTANCE
Campylobacter jejuni
is a common cause of human diarrheal disease worldwide and is listed by the World Health Organization as a high-priority pathogen.
C. jejuni
infection typically occurs through the ingestion of contaminated chicken meat, so many efforts are targeted at reducing
C. jejuni
levels at the source. We previously developed a vaccine that reduces
C. jejuni
levels in egg-laying chickens. In this study, we improved vaccine performance in meat birds by supplementing the vaccine with probiotics. In addition, we demonstrated that
C. jejuni
colonization levels in chickens are negatively correlated with the abundance of clostridia, another group of common gut microbes. We describe new methods for vaccine optimization that will assist in improving the
C. jejuni
vaccine and other vaccines under development.
Genetic Diversity of Infectious Laryngotracheitis Virus duringIn VivoCoinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome
Authors: Loncoman Carlos A. , Hartley Carol A. , Coppo Mauricio J. C. , Vaz Paola K. , Diaz-Méndez Andrés , Browning Glenn F. , García Maricarmen , Spatz Stephen , Devlin Joanne M. 
Published: September 2017

ABSTRACTRecombination is a feature of many alphaherpesviruses that infect people and animals. Infectious laryngotracheitis virus (ILTV;Gallid alphaherpesvirus 1) causes respiratory disease in chickens, resulting in significant production losses in poultry industries worldwide. Natural (field) ILTV recombination is widespread, particularly recombination between attenuated ILTV vaccine strains to create virulent viruses. These virulent recombinants have had a major impact on animal health. Recently, the development of a single nucleotide polymorphism (SNP) genotyping assay for ILTV has helped to understand ILTV recombination in laboratory settings. In this study, we applied this SNP genotyping assay to further examine ILTV recombination in the natural host. Following coinoculation of specific-pathogen-free chickens, we examined the resultant progeny for evidence of viral recombination and characterized the diversity of the recombinants over time. The results showed that ILTV replication and recombination are closely related and that the recombinant viral progeny are most diverse 4 days after coinoculation, which is the peak of viral replication. Further, the locations of recombination breakpoints in a selection of the recombinant progeny, and in field isolates of ILTV from different geographical regions, were examined following full-genome sequencing and used to identify recombination hot spots in the ILTV genome.IMPORTANCEAlphaherpesviruses are common causes of disease in people and animals. Recombination enables genome diversification in many different species of alphaherpesviruses, which can lead to the evolution of higher levels of viral virulence. Using the alphaherpesvirus infectious laryngotracheitis virus (ILTV), we performed coinfections in the natural host (chickens) to demonstrate high levels of virus recombination. Higher levels of diversity in the recombinant progeny coincided with the highest levels of virus replication. In the recombinant progeny, and in field isolates, recombination occurred at greater frequency in recombination hot spot regions of the virus genome. Our results suggest that control measures that aim to limit viral replication could offer the potential to limit virus recombination and thus the evolution of virulence. The development and use of vaccines that are focused on limiting virus replication, rather than vaccines that are focused more on limiting clinical disease, may be indicated in order to better control disease.
A Distinctive and Host-Restricted Gut Microbiota in Populations of a Cactophilic Drosophila Species
Authors: Martinson Vincent G. , Carpinteyro-Ponce Javier , Moran Nancy A. , Markow Therese A. 
Published: September 2017

ABSTRACT

Almost all animals possess gut microbial communities, but the nature of these communities varies immensely. For example, in social bees and mammals, the composition is relatively constant within species and is dominated by specialist bacteria that do not live elsewhere; in laboratory studies and field surveys of
Drosophila melanogaster
, however, gut communities consist of bacteria that are ingested with food and that vary widely among individuals and localities. We addressed whether an ecological specialist in its natural habitat has a microbiota dominated by gut specialists or by environmental bacteria.
Drosophila nigrospiracula
is a species that is endemic to the Sonoran Desert and is restricted to decaying tissues of two giant columnar cacti,
Pachycereus pringlei
(cardón cactus) and
Carnegiea gigantea
(saguaro cactus). We found that the
D. nigrospiracula
microbiota differs strikingly from that of the cactus tissue on which the flies feed. The most abundant bacteria in the flies are rare or completely absent in the cactus tissue and are consistently abundant in flies from different cacti and localities. Several of these fly-associated bacterial groups, such as the bacterial order
Orbales
and the genera
Serpens
and
Dysgonomonas
, have been identified in prior surveys of insects from the orders Hymenoptera, Coleoptera, Lepidoptera, and Diptera, including several
Drosophila
species. Although the functions of these bacterial groups are mostly unexplored,
Orbales
species studied in bees are known to break down plant polysaccharides and use the resulting sugars. Thus, these bacterial groups appear to be specialized to the insect gut environment, where they may colonize through direct host-to-host transmission in natural settings.

IMPORTANCE
Flies in the genus
Drosophila
have become laboratory models for microbiota research, yet the bacteria commonly used in these experiments are rarely found in wild-caught flies and instead represent bacteria also present in the food. This study shows that an ecologically specialized
Drosophila
species possesses a distinctive microbiome, composed of bacterial types absent from the flies' natural food but widespread in other wild-caught insects. This study highlights the importance of fieldwork-informed microbiota research.
Alterations in gp37 Expand the Host Range of a T4-Like Phage
Authors: Chen Mianmian , Zhang Lei , Abdelgader Sheikheldin Adam , Yu Li , Xu Juntian , Yao Huochun , Lu Chengping , Zhang Wei 
Published: September 2017

ABSTRACTThe use of phages as antibacterial agents is limited by their generally narrow host ranges. The aim of this study was to make a T4-like phage, WG01, obtain the host range of another T4-like phage, QL01, by replacing its host-determinant gene region with that of QL01. This process triggered a direct expansion of the WG01 host range. The offspring of WG01 obtained the host ranges of both QL01 and WG01, as well as the ability to infect eight additional host bacteria in comparison to the wild-type strains. WQD had the widest host range; therefore, the corresponding fragments, named QD, could be used for constructing a homologous sequence library. Moreover, after a sequencing analysis of gene 37, we identified two different mechanisms responsible for the expanded host range: (i) the first generation of WG01 formed chimeras without mutations, and (ii) the second generation of WG01 mutants formed from the chimeras. The expansion of the host range indicated that regions other than the C-terminal region may indirectly change the receptor specificity by altering the supportive capacity of the binding site. Additionally, we also found the novel means by which subsequent generations expanded their host ranges, namely, by exchanging gene 37 to acquire a wider temperature range for lysis. The method developed in this work offers a quick way to change or expand the host range of a phage. Future clinical applications for screening phages against a given clinical isolate could be achieved after acquiring more suitable homologous sequences.IMPORTANCET4-like phages have been established as safe in numerous phage therapy applications. The primary drawbacks to the use of phages as therapeutic agents include their highly specific host ranges. Thus, changing or expanding the host range of T4-like phages is beneficial for selecting phages for phage therapy. In this study, the host range of the T4-like phage WG01 was expanded using genetic manipulation. The WG01 derivatives acquired a novel means of expanding their host ranges by acquiring a wider temperature range for lysis. A region was located that had the potential to be used as a sequence region for homologous sequence recombination.
Biochemical Characteristics and Variable Alginate-Degrading Modes of a Novel Bifunctional Endolytic Alginate Lyase
Authors: Cheng Yuanyuan , Wang Dandan , Gu Jingyan , Li Junge , Liu Huihui , Li Fuchuan , Han Wenjun 
Published: September 2017

ABSTRACT

Bifunctional alginate lyases can efficiently degrade alginate comprised of mannuronate (M) and guluronate (G), but their substrate-degrading modes have not been thoroughly elucidated to date. In this study, we present Aly1 as a novel bifunctional endolytic alginate lyase of the genus
Flammeovirga
. The recombinant enzyme showed optimal activity at 50°C and pH 6.0. The enzyme produced unsaturated disaccharide (UDP2) and trisaccharide fractions as the final main alginate digests. Primary substrate preference tests and further structure identification of various size-defined final oligosaccharide products demonstrated that Aly1 is a bifunctional alginate lyase and prefers G to M. Tetrasaccharide-size fractions are the smallest substrates, and M, G, and UDP2 fractions are the minimal product types. Remarkably, Aly1 can vary its substrate-degrading modes in accordance with the terminus types, molecular sizes, and M/G contents of alginate substrates, producing a series of small size-defined saturated oligosaccharide products from the nonreducing ends of single or different saturated sugar chains and yielding unsaturated products in distinct but restricted patterns. The action mode changes can be partially inhibited by fluorescent labeling at the reducing ends of oligosaccharide substrates. Deletion of the noncatalytic region (NCR) of Aly1 caused weak changes of biochemical characteristics but increased the degradation proportions of small size-defined saturated M-enriched oligosaccharide substrates and unsaturated tetrasaccharide fractions without any size changes of degradable oligosaccharides, thereby enhancing the M preference and enzyme activity. Therefore, our results provided insight into the variable action mode of a novel bifunctional endolytic alginate lyase to inform accurate enzyme use.

IMPORTANCE
The elucidated endolytic alginate lyases usually degrade substrates into various size-defined unsaturated oligosaccharide products (≥UDP2), and exolytic enzymes yield primarily unsaturated monosaccharide products. However, it is poorly understood whether endolytic enzymes can produce monosaccharide product types when degrading alginate. In this study, we demonstrated that Aly1, a bifunctional alginate lyase of
Flammeovirga
sp. strain MY04, is endolytic and monosaccharide producing. Using various sugar chains as testing substrates, we also proved that key factors causing Aly1's action mode changes are the terminus types, molecular sizes, and M/G contents of substrates. Furthermore, the NCR fragment's effects on Aly1's biochemical characteristics and alginate-degrading modes and corresponding mechanisms were discovered by gene truncation and enzyme comparison. In summary, this study provides a novel bifunctional endolytic tool and a variable action mode for accurate use in alginate degradation.
The Type IX Secretion System Is Required for Virulence of the Fish Pathogen Flavobacterium columnare
Authors: Li Nan , Zhu Yongtao , LaFrentz Benjamin R. , Evenhuis Jason P. , Hunnicutt David W. , Conrad Rachel A. , Barbier Paul , Gullstrand Connor W. , Roets Jack E. , Powers Jonathan L. , Kulkarni Surashree S. , Erbes Devon H. , García Julio C. , Nie Pin , McBride Mark J. 
Published: September 2017

ABSTRACT

Flavobacterium columnare
, a member of the phylum
Bacteroidetes
, causes columnaris disease in wild and aquaculture-reared freshwater fish. The mechanisms responsible for columnaris disease are not known. Many members of the phylum
Bacteroidetes
use type IX secretion systems (T9SSs) to secrete enzymes, adhesins, and proteins involved in gliding motility. The
F. columnare
genome has all of the genes needed to encode a T9SS.
gldN
, which encodes a core component of the T9SS, was deleted in wild-type strains of
F. columnare
. The
F. columnare
Δ
gldN
mutants were deficient in the secretion of several extracellular proteins and lacked gliding motility. The Δ
gldN
mutants exhibited reduced virulence in zebrafish, channel catfish, and rainbow trout, and complementation restored virulence. PorV is required for the secretion of a subset of proteins targeted to the T9SS. An
F. columnare
Δ
porV
mutant retained gliding motility but exhibited reduced virulence. Cell-free spent media from exponentially growing cultures of wild-type and complemented strains caused rapid mortality, but spent media from Δ
gldN
and Δ
porV
mutants did not, suggesting that soluble toxins are secreted by the T9SS.

IMPORTANCE
Columnaris disease, caused by
F. columnare
, is a major problem for freshwater aquaculture. Little is known regarding the virulence factors produced by
F. columnare
, and control measures are limited. Analysis of targeted gene deletion mutants revealed the importance of the type IX protein secretion system (T9SS) and of secreted toxins in
F. columnare
virulence. T9SSs are common in members of the phylum
Bacteroidetes
and likely contribute to the virulence of other animal and human pathogens.
5-year disease progression of patients across the glaucoma spectrum assessed by structural and functional tools
Authors: Seth Natasha Gautam , Kaushik Sushmita , Kaur Savleen , Raj Srishti , Pandav Surinder Singh 
Published: September 2017

BackgroundAssessment of spectral-domain optical coherence tomography (SD-OCT) compared with visual fields, to detect progression across the glaucoma spectrum.MethodsIn this study, adult glaucoma suspects and patients, with baseline retinal nerve fibre layer (RNFL) thickness on SD-OCT and reliable visual field (VF) tests on Humphrey Field Analyser (HFA) prior to March 2010, were recruited. Functional and structural progression over at least 5 years was compared using Glaucoma Progression Analysis (GPA) and VF index (VFI) on HFA and Guided Progression Analysis (GPA-OCT) on SD-OCT, respectively. Agreement of progression detection between the two modalities was computed using κ statistics.Results122 subjects (63 glaucoma suspects; 59 glaucoma patients) were enrolled. Of 18 suspects who progressed to glaucoma, 13 showed progression by GPA-OCT, 4 by GPA, 7 by VFI and 2 were concordant. In the 14 glaucoma patients who progressed, GPA-OCT detected progression in 6, GPA in five and VFI in six. GPA-OCT had poor agreement with GPA in glaucoma suspects (Kappa 0.15; p=0.13) and patients (Kappa 0.10; p=0.45). VFI had better agreement with GPA-OCT in glaucoma suspects (Kappa 0.34; p=0.01) than glaucoma patients (Kappa 0.12; p=0.36). Progressors by VF in both groups had similar percentage change from baseline RNFL thickness (−9.9% vs −8.6% p=0.46), even though the absolute change was significantly greater in suspects(−8.75µ vs−6.4µ p=0.03).ConclusionStructural change appears to be more useful to detect progression in glaucoma suspects, while functional change is a better indicator as the disease progresses. Percentage change from baseline RNFL thickness was a better measure than absolute change in RNFL.
Effect of low-dose versus higher-dose antenatal iron supplementation on child health outcomes at 36 months of age in Viet Nam: longitudinal follow-up of a cluster randomised controlled trial
Authors: Hanieh Sarah , Ha Tran T , Simpson Julie A , Braat Sabine , Thuy Tran T , Tran Thach D , King Janet , Tuan Tran , Fisher Jane , Biggs Beverley-Ann 
Published: September 2017

IntroductionIntermittent iron-folic acid supplementation (IFA) is currently recommended for pregnant women in populations where anaemia prevalence among pregnant women is <20% or if daily iron is not acceptable. The effect of providing lower doses of antenatal elemental iron through intermittent regimes on longer-term health outcomes in childhood is unclear.MethodsA prospective cohort study conducted between May 2012 and May 2014 in Viet Nam among children of 36 months of age, born to women previously enrolled in a cluster randomised controlled trial of antenatal micronutrient supplementation (daily IFA (60 mg elemental iron) vs twice-weekly IFA (60 mg elemental iron) vs twice-weekly multiple micronutrient (MMN) supplementation (60 mg elemental iron)). Primary outcomes were height-for-age z-scores (HAZ), according to WHO growth standards and cognitive composite scores (Bayley Scales of Infant and Toddler Development, third edition) at 36 months of age.ResultsA total of 1017 children born to mothers enrolled in the cluster randomised trial were assessed at 36 months of age. Adjusted mean differences (MDs) in HAZ were –0.14 (95% CI –0.28 to –0.01) and –0.15 (95% CI –0.29 to –0.01) in children born to mothers who received twice-weekly IFA or MMN compared with those who received daily IFA. Children born to mothers who received twice-weekly MMN had lower composite motor scores compared with those who received daily IFA (MD –2.07, 95% CI –4.11 to –0.03). There were no differences in composite cognitive scores in the twice-weekly compared with daily regimens.ConclusionsLow-dose antenatal IFA supplementation (120 mg elemental iron per week) resulted in lower HAZ and motor composite scores in children compared with higher-dose antenatal IFA supplementation (420 mg elemental iron per week). This highlights the importance of adequate iron stores during pregnancy and the need for careful monitoring when lower-dose antenatal iron regimens are used.Trial registration numberAustralia New Zealand Clinical Trials Registry: 12610000944033.
Effects of nutrition interventions during pregnancy on low birth weight: an overview of systematic reviews
Authors: da Silva Lopes Katharina , Ota Erika , Shakya Prakash , Dagvadorj Amarjargal , Balogun Olukunmi Omobolanle , Peña-Rosas Juan Pablo , De-Regil Luz Maria , Mori Rintaro 
Published: September 2017

IntroductionLow birth weight (LBW, birth weight less than 2500 g) is associated with infant mortality and childhood morbidity. Poor maternal nutritional status is one of several contributing factors to LBW. We systematically reviewed the evidence for nutrition-specific (addressing the immediate determinants of nutrition) and nutrition-sensitive (addressing the underlying cause of undernutrition) interventions to reduce the risk of LBW and/or its components: preterm birth (PTB) and small-for-gestational age (SGA).MethodsWe conducted a comprehensive literature search in MEDLINE, EMBASE, CINAHL and the Cochrane Database of Systematic Reviews (September 2015). Systematic reviews of randomised controlled trials focusing on nutritional interventions before and during pregnancy to reduce LBW and its components were eligible for inclusion into the overview review. We assessed the methodological quality of the included reviews usingA Measurement Tool to Assess Reviews(AMSTAR), PROSPERO: CRD42015024814.ResultsWe included 23 systematic reviews which comprised 34 comparisons. Sixteen reviews were of high methodological quality, six of moderate and only one review of low quality. Six interventions were associated with a decreased risk of LBW: oral supplementation with (1) vitamin A, (2) low-dose calcium, (3) zinc, (4) multiple micronutrients (MMN), nutritional education and provision of preventive antimalarials. MMN and balanced protein/energy supplementation had a positive effect on SGA, while high protein supplementation increased the risk of SGA. High-dose calcium, zinc or long-chain n-3 fatty acid supplementation and nutritional education decreased the risk of PTB.ConclusionImproving women’s nutritional status positively affected LBW, SGA and PTB. Based on current evidence, especially MMN supplementation and preventive antimalarial drugs during pregnancy may be considered for policy and practice. However, for most interventions evidence was derived from a small number of trials and/or participants. There is a need to further explore the evidence of nutrition-specific and nutrition-sensitive interventions in order to reach the WHO’s goal of a 30% reduction in the global rate of LBW by 2025.