A gut commensal microbiome-host protein network map reveals bacterial modulation of human immune signaling

Complex diseases such as cardiovascular illnesses, cancer, respiratory diseases, and diabetes have been on the rise worldwide contributing to 70% of all deaths. While these illnesses are superficially not associated with microbial organisms accumulating research links bacteria of the gut microbiome to a diverse range of complex diseases. Especially Pseudomonadota, the third most abundant phylum in the gut, has been associated with several of those illnesses e.g., metabolic sicknesses and cancer. However, the underlying mechanisms mediating the bacterial impact on host health remain largely unknown. Pathogenic representatives of the Pseudomonadota phylum are well-known for employing a type three secretion system (T3SS) to manipulate host cells and thereby mediate infectious diseases. Prominent examples are Salmonella, Shigella, enterohemorrhagic Escherichia coli (EHEC), and enteropathogenic Escherichia coli (EPEC) as well as Yersinia pestis responsible for wiping out one-third of the European population during the plague. Yet, T3SSs have also been detected in plant mutualists e.g., rhizobia strains of the rhizobia-legume symbiosis. Furthermore, bacteria that do not exhibit a pathogenic or mutualistic lifestyle also seem to encode for T3SSs. Work outside of this thesis as part of the same project detected T3SSs also in commensal Pseudomonadota of the human gut microbiome. However, the impact of the T3SS effectors on the host cell and subsequently host health is not known. Therefore, this thesis aimed to elucidate the impact of T3SS effectors expressed by commensal gut Pseudomonadota on host functions in the context of human health and disease. To assess the impact of bacterial effectors on the human host a network map of protein-protein interactions (PPIs) between gut commensal bacterial effectors and human proteins was generated. To this end, an ORFeome collection of bacterial effectors was established by cloning 959 T3SS effectors from known, culturable strains as well as from metagenomic data of the human gut. Testing these bacterial effectors against the human ORFeome v9.1 collection consisting of 17,408 protein-coding genes with a systematic, high-throughput yeast two-hybrid (Y2H) pipeline gave rise to the human-microbiome meta-interactome map (HuMMI). The network consists of 1,263 interactions mediated by 289 effectors and 430 human proteins. HuMMI was subjected to a detailed quality control to assess the reliability of the used pipeline and the quality of the interactions. For this purpose, reference sets were assembled to benchmark the Y2H and an orthogonal assay, which was employed to re-test a subset of HuMMI. In addition, the saturation of HuMMI i.e., the percentage of discovered interactions compared to all detectable interactions, was assessed by a Y2H repeat screen. After demonstrating the reliability of the employed Y2H pipeline and the comparability of HuMMI to well-documented, literature-curated-interactions, validation experiments in vitro were conducted based on the functional analysis of the effector targets. As the bacterial effectors targeted human proteins involved in immune signaling their impact on the transcription factor nuclear factor kappa B (NF-κB) was assessed. A cell-based reporter assay was employed testing the ability of the effectors to modulate NF-κB activity. Five effectors significantly activated NF-κB, while three effectors seemed to inhibit the transcription factor significantly. Further impacts on human immune signaling by T3SS effectors were shown by collaborators reporting increased ICAM1 expression as well as up- and downregulation of pro-inflammatory cytokine secretion from a colon cell line upon effector transfection. The opposing effects of bacterial effectors on immune signaling pathways suggest different influences of gut commensal T3SS effectors on the human host. In conclusion, this study introduced a novel mechanism by which gut commensals might impact the human host. T3SS effectors potentially affect human immune signaling locally and systemically via cytokine secretion potentially affecting the risk of complex disease. Thereby, this works launches the investigation into gut commensal T3SS effectors and their impacts on host health and disease

Prevalence of Arthritis in Africa: A Systematic Review and Meta-Analysis

Objective In this systematic review, we estimate the prevalence of six types of arthritis in Africa; namely rheumatoid arthritis, osteoarthritis, juvenile arthritis, psoriatic arthritis, gout, and ankylosing spondylitis. Methods We comprehensively searched literature on 31 August 2014 in MEDLINE, EMBASE, Web of Science and the Cochrane Library to identify eligible studies from 1975 up to 31 July 2014. Two review authors independently selected studies, extracted data, and appraised studies. We carried out random effects meta-analysis of prevalence of arthritis and assessed heterogeneity through subgroup analyses. We performed separate analyses for population- and hospital-based studies, as well as rural and urban settings. Main Findings We included 27 cross-sectional studies (20 population-based and 7 hospital-based) from Africa reporting on the prevalence of arthritis. The majority of the studies were from South Africa (44.4%, 12/27). Rheumatoid arthritis in urban settings ranged from 0.1% in Algeria, 0.6% in the DRC, to a meta-analysis overall prevalence of 2.5% in South Africa, and in rural settings ranged from a meta-analysis overall prevalence of 0.07% in South Africa, 0.3% in Egypt, to 0.4% in Lesotho. Osteoarthritis was the most prevalent form of arthritis and in urban settings it was 55.1% in South Africa and in rural settings, all in South Africa, ranged from 29.5%, 29.7%, up to 82.7% among adults aged over 65 years. Other results include highest prevalence of 33.1% for knee osteoarthritis in rural South Africa, 0.1% for ankylosing spondylitis in rural South Africa, 4.4% for psoriatic arthritis in urban South Africa, 0.7% for gout in urban South Africa, and 0.3% for juvenile idiopathic arthritis in urban Egypt. A third of the included studies had a low risk of bias (33.3%, 9/27), 40.8% (11/27) moderate risk, and 25.9% (7/27) had a high risk of bias. Conclusions In this systematic review, we have identified the paucity of latest prevalence data on arthritis in Africa. More studies are needed to address the prevalence and the true burden of this disease in Africa

An exploratory trial implementing a community-based child oral health promotion intervention for Australian families from refugee and migrant backgrounds: a protocol paper for Teeth Tales

Introduction: Inequalities are evident in early childhood caries rates with the socially disadvantaged experiencing greater burden of disease. This study builds on formative qualitative research, conducted in the Moreland/Hume local government areas of Melbourne, Victoria 2006–2009, in response to community concerns for oral health of children from refugee and migrant backgrounds. Development of the community-based intervention described here extends the partnership approach to cogeneration of contemporary evidence with continued and meaningful involvement of investigators, community, cultural and government partners. This trial aims to establish a model for child oral health promotion for culturally diverse communities in Australia.<p></p> Methods and analysis: This is an exploratory trial implementing a community-based child oral health promotion intervention for Australian families from refugee and migrant backgrounds. Families from an Iraqi, Lebanese or Pakistani background with children aged 1–4 years, residing in metropolitan Melbourne, were invited to participate in the trial by peer educators from their respective communities using snowball and purposive sampling techniques. Target sample size was 600. Moreland, a culturally diverse, inner-urban metropolitan area of Melbourne, was chosen as the intervention site. The intervention comprised peer educator led community oral health education sessions and reorienting of dental health and family services through cultural Competency Organisational Review (CORe).<p></p> Ethics and dissemination: Ethics approval for this trial was granted by the University of Melbourne Human Research Ethics Committee and the Department of Education and Early Childhood Development Research Committee. Study progress and output will be disseminated via periodic newsletters, peer-reviewed research papers, reports, community seminars and at National and International conferences.<p></p&gt

Aestipascuomyces dupliciliberans gen. nov, sp. nov., the First Cultured Representative of the Uncultured SK4 Clade from Aoudad Sheep and Alpaca

We report on the isolation of the previously-uncultured Neocallimastigomycota SK4 lineage, by two independent research groups, from a wild aoudad sheep rumen sample (Texas, USA) and an alpaca fecal sample (Baden-Württemberg, Germany). Isolates from both locations showed near-identical morphological and microscopic features, forming medium-sized (2–5 mm) white filamentous colonies with a white center of sporangia, on agar roll tubes and a heavy biofilm in liquid media. Microscopic analysis revealed monocentric thalli, and spherical polyflagellated zoospores with 7–20 flagella. Zoospore release occurred through an apical pore as well as by sporangial wall rupturing, a duality that is unique amongst described anaerobic gut fungal strains. Isolates were capable of growing on a wide range of mono-, oligo-, and polysaccharide substrates as the sole carbon source. Phylogenetic assessment based on the D1–D2 28S large rRNA gene subunit (D1–D2 LSU) and internal transcribed spacer-1 (ITS-1) regions demonstrated high sequence identity (minimum identity of 99.07% and 96.96%, respectively) between all isolates; but low sequence identity (92.4% and 86.7%, respectively) to their closest cultured relatives. D1–D2 LSU phylogenetic trees grouped the isolates as a new monophyletic clade within the Orpinomyces–Neocallimastix–Pecoramyces–Feramyces–Ghazallamyces supragenus group. D1–D2 LSU and ITS-1 sequences recovered from the obtained isolates were either identical or displayed extremely high sequence similarity to sequences recovered from the same aoudad sheep sample on which isolation was conducted, as well as several sequences recovered from domestic sheep and few other herbivores. Interestingly, members of the SK4 clade seem to be encountered preferably in animals grazing on summer pasture. We hence propose accommodating these novel isolates in a new genus, Aestipascuomyces (derived from the Latin word for “summer pasture”), and a new species, A. dupliciliberans. The type strain is Aestipascuomycesdupliciliberans strain R4

Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples:Insights into Community Composition and Novel Lineages

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara)

Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples:Insights into Community Composition and Novel Lineages

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara)

No time to die : comparative study on preservation protocols for anaerobic fungi

Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to anaerobically degrade recalcitrant lignocellulosic biomass through mechanic and enzymatic means. While their biotechnological potential is well-recognized, applied research on AF is still hampered by the time-consuming and cost-intensive laboratory routines required to isolate, maintain, and preserve AF cultures. Reliable long-term preservation of specific AF strains would aid basic as well as applied research, but commonly used laboratory protocols for AF preservation can show erratic survival rates and usually exhibit only moderate resuscitation success for up to one or two years after preservation. To address both, the variability, and the preservation issues, we have set up a cross-laboratory, year-long study. We tested five different protocols for the preservation of AF. The experiments were performed at three different laboratories (Austria, Germany, Switzerland) with the same three morphologically distinct AF isolates (Anaeromyces mucronatus, Caeocmyces sp., and Neocallimastix cameroonii) living in stable co-culture with their naturally occurring, syntrophic methanogens. We could show that handling greatly contributes to the variability of results, especially in Anaeromyces mucronatus. Cryopreservation of (mature) biomass in liquid nitrogen had the highest overall survival rates (85–100%, depending on the strain and laboratory). Additionally, preservation on agar at 39°C had surprisingly high survival rates for up to 9 months, if pieces of agar containing mature AF thalli were resuscitated. This low-cost, low-effort method could replace consecutive batch cultivation for periods of up to 6 months, while long-term preservation is best done by cryopreservation in liquid nitrogen. Regardless of the method, however, preserving several replicates (>three) of the same strain is highly advisable

Sub-population analysis based on temporal features of high content images

Background: High content screening techniques are increasingly used to understand the regulation and progression of cell motility. The demand of new platforms, coupled with availability of terabytes of data has challenged the traditional technique of identifying cell populations by manual methods and resulted in development of high-dimensional analytical methods. Results: In this paper, we present sub-populations analysis of cells at the tissue level by using dynamic features of the cells. We used active contour without edges for segmentation of cells, which preserves the cell morphology, and autoregressive modeling to model cell trajectories. The sub-populations were obtained by clustering static, dynamic and a combination of both features. We were able to identify three unique sub-populations in combined clustering. Conclusion: We report a novel method to identify sub-populations using kinetic features and demonstrate that these features improve sub-population analysis at the tissue level. These advances will facilitate the application of high content screening data analysis to new and complex biological problems.Computation and Systems Biology Programme of Singapore--Massachusetts Institute of Technology Allianc

Crop Updates 2003 - Cereals

This session covers twenty one papers from different authors: PLENARY 1. Recognising and responding to new market opportunities in the grains industry, Graham Crosbie, Manager, Grain Products Research, Crop Breeding, Plant Industries, Department of Agriculture 2. Stripe rust – where to now for the WA wheat industry? Robert Loughman1, Colin Wellings2 and Greg Shea11Department of Agriculture, 2University of Sydney Plant Breeding Institute, Cobbitty (on secondment from NSW Agriculture) 3. Benefits of a Grains Biosecurity Plan, Dr Simon McKirdy, Plant Health Australia, Mr Greg Shea, Department of Agriculture 4. Can we improve the drought tolerance of our crops? Neil C. Turner, CSIRO Plant Industry, Wembley 5. The silence of the lambing, Ross Kingwell, Department of Agriculture AGRONOMY AND VARIETIES 6. Maximising performance of wheat varieties, Brenda Shackley, Wal Anderson, Darshan Sharma, Mohammad Amjad, Steve Penny Jr, Melanie Kupsch, Anne Smith, Veronika Reck, Pam Burgess, Glenda Smith and Elizabeth Tierney, Department of Agriculture 7. Wheat variety performance in wet and dry, Peter Burgess 8. e-VarietyGuide for stripe rust – an updated version (1.02 – 2003), Moin Salam, Megan Collins, Art Diggle and Robert Loughman, Department of Agriculture 9. Baudin and Hamelin – new generation of malting barley developed in Western Australia, Blakely Paynter, Roslyn Jettner and Kevin Young, Department of Agriculture 10. Oaten hay production, Jocelyn Ball, Natasha Littlewood and Lucy Anderton, Department of Agriculture 11. Improving waterlogging tolerance in wheat and barley, Irene Waters and Tim Setter, Department of Agriculture 12. Broadscale variety comparisons featuring new wheat varieties, Jeff Russell, Department of Agriculture, Centre for Cropping Systems BIOTECHNOLOGY 13. Barley improvement in the Western Region – the intergration of biotechnologies, Reg Lance, Chengdao Li and Sue Broughton, Department of Agriculture 14. The Western Australian State Agricultural Biotechnology Centre – what we are and what we do, Michael Jones, WA State Agricultural Biotechnology Centre, Murdoch University 15. Protein and DNA methods for variety identification, Dr Grace Zawko, Saturn Biotech Limited 16. The Centre for High-throughput Agricultural Genetic Analysis (CHAGA), Keith Gregg, CHAGA, Murdoch University NUTRITION 17. Potassium – topdressed, drilled or banded? Stephen Loss, Patrick Gethin, Ryan Guthrie, Daniel Bell, Wesfarmers CSBP 18. Liquid phosphorus fertilisers in WA, Stephen Loss, Frank Ripper, Ryan Guthrie, Daniel Bell and Patrick Gethin, Wesfarmers CSBP 19. Wheat nutrition in the high rainfall cropping zone, Narelle Hill1and Laurence Carslake2, 1Department of Agriculture, 2Wesfarmers Landmark PESTS AND DISEASES 20. Managenent options for root lesion nematode in West Australian cropping systems, Vivien Vanstone, Sean Kelly and Helen Hunter, Department of Agriculture STORAGE 21. Aeration can profit your grain enterprise, Christopher R. Newman, Department of Agricultur