Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae

Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys6bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (;47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons

The Interplay Between Use of Biological Therapies, Psychological State, and the Microbiome in IBD

BackgroundThis study examines longitudinal bio-psychological dynamics and their interplay in IBD patients undergoing conventional and biological therapies.MethodsFifty IBD participants (24 UC, 26 CD) in clinical remission were followed for 12 months. Complete longitudinal datasets, biological samples, validated scores of psychological status were collected monthly for analysis of association. Microbiome analysis was performed to identify microbial dynamics and signatures. Patients were grouped on disease phenotype (CD, UC) and mode of treatment (biological therapies, non-biological treatment). General linear models, mixed models, cluster analysis, and analyses of variance were used to examine the longitudinal trends of the variables and their associations over time. Results were corrected for multiple testing.ResultsResults substantiated different interactions between biological therapy and longitudinal trends of inflammatory biomarkers in remission CD and UC patients as well as significant differences between CD and UC patients in their psychological measures during clinical remission, with UC patients having inferior condition compared to CD. A significant reduction in microbial diversity in CD patients compared to UC was identified. Results characterized considerable differences in longitudinal microbial profile between those taking and not taking biological treatment in UC patients, but not in CD patients.ConclusionA different trajectory of interdependence was identified between psychological state, sleep, and microbial dynamics with mode of treatment when compared between CD and UC patients. Further studies should investigate the causal relationships between bio-psychological factors for improved treatment purposes

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Rainfall-mediated biogeochemical changes at a legacy radionuclide waste disposal site

Poster to be presented at the 16th International Symposium on Microbial Ecology in Montreal (21–26 Aug 2016).<br

The isolation of fungi from low-pH, high ionic strength uranium mine process water

Presentation at the 6th International Symposium on Biohydrometallurgy. 19 June 2012. Falmouth, UK.<br><br>Contents of the presentation were later published as:<br><div> <div>Vázquez-Campos X, Kinsela AS, Waite TD, Collins RN, Neilan BA. (2014). <i>Fodinomyces uranophilus</i> gen. nov. sp. nov. and <i>Coniochaeta fodinicola</i> sp. nov., two uranium mine inhabiting Ascomycota fungi from northern Australia. <i>Mycologia</i> <b>106</b>: 1073–1089.<br><div> <div>Vázquez-Campos X, Kinsela AS, Collins RN, Neilan BA, Aoyagi N, Waite TD. (2015). Uranium binding mechanisms of the acid-tolerant fungus <i>Coniochaeta fodinicola</i>. <i>Environ Sci Technol</i> <b>49</b>: 8487–8496.</div> </div></div></div><br

Supplementary files for LFLS metagenome paper

<p>Supplementary file 1. Spreadsheet with YSI data.</p> <p>Supplementary file 2. Krona HTML file with the taxonomy.</p> <p>Supplementary file 3. Spreadsheet with the relative abundances of all the RXNs.</p> <p>Supplementary file 4. Table with the raw HUMAnN2 output.</p

Characterisation of Bacteriophage vB_SmaM_Ps15 Infective to <i>Stenotrophomonas maltophilia</i> Clinical Ocular Isolates

Recent acknowledgment that multidrug resistant Stenotrophomonas maltophilia strains can cause severe infections has led to increasing global interest in addressing its pathogenicity. While being primarily associated with hospital-acquired respiratory tract infections, this bacterial species is also relevant to ophthalmology, particularly to contact lens-related diseases. In the current study, the capacity of Stenotrophomonas phage vB_SmaM_Ps15 to infect ocular S. maltophilia strains was investigated to explore its future potential as a phage therapeutic. The phage proved to be lytic to a range of clinical isolates collected in Australia from eye swabs, contact lenses and contact lens cases that had previously shown to be resistant to several antibiotics and multipurpose contact lenses disinfectant solutions. Morphological analysis by transmission electron microscopy placed the phage into the Myoviridae family. Its genome size was 161,350 bp with a G + C content of 54.2%, containing 276 putative protein-encoding genes and 24 tRNAs. A detailed comparative genomic analysis positioned vB_SmaM_Ps15 as a new species of the Menderavirus genus, which currently contains six very similar globally distributed members. It was confirmed as a virulent phage, free of known lysogenic and pathogenicity determinants, which supports its potential use for the treatment of S. maltophilia eye infections

Effect of ginger root powder on gastrointestinal bacteria composition, gastrointestinal symptoms, mental health, fatigue, and quality of life: A double-blind placebo-controlled trial

Background: Despite compositional alterations in gastrointestinal microbiota being purported to underpin some of the therapeutic effects of ginger, the effect of a standardized ginger supplement on gut microbiota has not been tested in humans. Objectives: To determine the effect of a standardized ginger (Zingiber officinale) root powder, compared to placebo, on gastrointestinal bacteria and associated outcomes in healthy adults. Methods: A randomized double-blind placebo-controlled trial allocated participants aged 18 to 30 y to ginger or microcrystalline cellulose (MCC) placebo. The intervention comprised 1.2 g/d of ginger (4 capsules per day totaling 84 mg/d of active gingerols/shogaols) for 14 d following a 1-wk run-in period. Primary outcomes were gastrointestinal community composition, alpha and beta diversity, and differential abundance, measured using 16S rRNA gene sequencing of fecal samples. Secondary outcomes were gastrointestinal symptoms, bowel function, depression, anxiety, stress, fatigue, quality of life, and adverse events. Results: Fifty-one participants were enrolled and analyzed (71% female; mean age 25 ± 3 y; ginger: n = 29, placebo: n = 22). There was a greater increase in relative abundance of phylum, Actinobacteria, observed following ginger supplementation compared to placebo (U: 145.0; z: −2.1; P = 0.033). Ginger was associated with a greater abundance of the genera Parabacteroides, Bacillus, Ruminococcaceae incertae sedis, unclassified Bacilli, families Defluviitaleaceae, Morganellaceae, and Bacillaceae as well as lower abundance of the genus Blautia and family Sphingomonadaceae (P < 0.05). An improvement in indigestion symptoms was observed with ginger supplementation (U: 196.0; z: −2.4; P = 0.015). No differences between ginger and placebo groups were found for alpha and beta diversity or other secondary outcomes. No moderate or severe adverse events were reported. Conclusions: Supplementation with ginger root powder was safe and altered aspects of gastrointestinal bacteria composition; however, it did not change alpha- or beta diversity, bowel function, gastrointestinal symptoms, mood, or quality of life in healthy adults. These results provide further understanding regarding the mechanisms of action of ginger supplementation. This trial was registered in the Australia New Zealand Clinical Trials Registry as ACTRN12620000302954p and the Therapeutic Goods Administration as CT-2020-CTN-00380-1.</p

OTUreporter: a modular automated pipeline for the analysis and report of amplicon data

While 16S rRNA gene amplicon sequencing is not considered a state-of-the-art technique any more, it is now considered a well-matured technique for the routine screening of samples of microbiological interest. The maturity of the technique with the lower costs, have provided an increased demand even in areas foreign to typical research.<br> <br> OTUreporter was developed aiming to bridge the gap between a sequencing service provider without dedicated bioinformatics personnel, and a non-expert customer. OTUreporter was also designed keeping in mind customers with limited computing resources for the initial stages of the amplicon data analysis.<br> <br> Unlike many automated 16S rRNA gene amplicon tools such those made available by sequencing companies (e.g. Illumina's "16S Metagenomics" tool), OTUreporter is not a "black box" and uses software that it is actually used in research context for this matters.<br> <br> OTUreporter accesses BaseSpace directly to gather amplicon data and sequencing run details, avoiding any need for the manual download. The main program used in the background is mothur. OTUreporter uses a slightly modified version of the MiSeqSOP protocol for processing the amplicon data.<br> <br> The final output of OTUreporter is a report. The report summarises the details, not only of the analysis, but also of the sequencing jobs themselves. The report, based on a RMarkdown template, creates two different outputs of the same report: a slimmer printer-friendly pdf document, and an extended html output with interactive content.<br> <br><div> OTUreporter is currently in beta testing at the Ramaciotti Centre for Genomics.</div><div><br></div><div>If you use OTUreporter or reuse any of its contents, please cite the repository at Bitbucket (https://bitbucket.org/xvazquezc/otureporter) or this poster as: <br></div><div>Vázquez-Campos, X., Chilton, A., Koval, J., Tree, J. J., & Wilkins, M. R. OTUreporter: a modular automated pipeline for the analysis and report of amplicon data. Sydney Bioinformatics Research Symposium 2018. 15 Jun 2018. Sydney, NSW, Australia. DOI: <a rel="noreferrer noopener" target="_blank">10.6084/m9.figshare.6521171.</a><br><br></div