Biology subjects

Williams, R. B. H.

Publications and source records attributed to Williams, R. B. H..

6 recordsLinked to original sources

bioRxiv2018

Apparent oxygen half saturation constant for nitrifiers: genus specific, inherent physiological property, or artefact of colony morphology?

We report that a single Nitrospira sublineage I OTU performs nitrite oxidation in several full-scale domestic wastewater treatment plants (WWTPs) in the tropics (29-31 {degrees}C). Contrary to the prevailing theory for the relationship between nitrite oxidizing bacteria (NOB) and ammonia oxidizing bacteria (AOB), members of the Nitrospira sublineage I OTU had an apparent half saturation coefficient, Ks(app) lower than that of the full-scale domestic activated sludge cohabitant AOB (0.09 {+/-} 0.02 g O2 m-3 versus 0.3 {+/-} 0.03 g O2 m-3). Paradoxically, NOB may thus thrive under conditions of low oxygen supply. Low dissolved oxygen (DO) conditions could enrich for and high aeration inhibit the NOB in a long-term lab-scale reactor. The relative abundance of Nitrospira gradually decreased with increasing DO until it was washed out. Nitritation was sustained even after the DO was lowered subsequently. Based on 3D-fluorescence in situ hybridization (FISH) image analysis, the morphologies of AOB and NOB microcolonies responded to DO levels in accordance with their apparent oxygen half saturation constant Ks(app). When exposed to the same oxygenation level, NOB formed densely packed spherical clusters with a low surface area-to-volume ratio compared to the Nitrosomonas-like AOB clusters, which maintained a porous and non-spherical morphology. Microcolony morphology is thus a way for AOB and NOB to regulate oxygen exposure and sustain the mutualistic interaction. However, short-term high DO exposure can select for AOB and against NOB in full-scale domestic WWTPs and such population dynamics depend on which specific AOB and NOB species predominate under given environmental conditions.

systems biology↗

bioRxiv2017

MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

BackgroundThere are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing and there is a need to adapt short read tools to long read datasets.\n\nMethodsWe describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods.\n\nResultsAll presented methods are implemented in the open source edition of MEGAN and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community.

bioinformatics↗

bioRxiv2017

Enterococcus faecalis Promotes Innate Immune Suppression And Polymicrobial Catheter-Associated Urinary Tract Infection

Enterococcus faecalis, a member of the human gastrointestinal microbiota, is an opportunistic pathogen associated with hospital-acquired wound, bloodstream, and urinary tract infections. E. faecalis can subvert or evade immune-mediated clearance, although the mechanisms are poorly understood. In this study, we examined E. faecalis-mediated subversion of macrophage activation. We observed that E. faecalis actively prevents NF-{kappa}B signaling in mouse RAW264.7 macrophages in the presence of Toll-like receptor agonists and during polymicrobial infection with Escherichia coli. E. faecalis and E. coli co-infection in a mouse model of catheter-associated urinary tract infection (CAUTI) resulted in a suppressed macrophage transcriptional response in the bladder compared to E. coli infection alone. Finally, we demonstrated that co-inoculation of E. faecalis with E. coli into catheterized bladders significantly augmented E. coli CAUTI. Taken together, these results support that E. faecalis suppression of NF-{kappa}B-driven responses in macrophages promotes polymicrobial CAUTI pathogenesis.\n\nAuthor SummarySynergistic polymicrobial infections can contribute to both disease severity and persistence. Enterococcus faecalis and Escherichia coli are frequently co-isolated from polymicrobial urinary tract infections. Immunomodulation by co-infecting microbes can result in a more permissive environment for pathogens to establish infection. Presently, we do not yet understand how these microbes overcome host immunity to establish polymicrobial infections. To address this, we investigated how the immunosuppressive function of E. faecalis can contribute to acute infection. We defined that E. faecalis is able to suppress macrophages in vitro, despite the presence of E. coli. We also demonstrated E. faecalis ability to augment E. coli titers in vivo to establish kidney infection. Our findings raise the prospect that E. faecalis can alter host immunity to increase susceptibility to other uropathogens.

microbiology↗

bioRxiv2017

Draft Genome Sequence Of A Candidatus Brocadia Bacterium Enriched From Tropical-Climate Activated Sludge

We present the draft genome of an anaerobic ammonium-oxidizing (anammox) bacterium, cluster III Candidatus Brocadia, which was enriched in an anammox reactor. A 3.2 Mb genome sequence comprising 168 contigs was assembled, in which 2,765 gene-coding regions, 47 tRNAs, and 5S, 16S and 23S ribosomal RNAs were annotated. No evidence for the presence of a nitric oxide-forming nitrite reductase was found.

microbiology↗

bioRxiv2017

Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism

Enterococci are important human commensals and significant opportunistic pathogens associated with endocarditis, urinary tract infections, wound and surgical site infections, and medical device associated infections. These infections often become chronic upon the formation of biofilm. The biofilm matrix establishes properties that distinguish this state from free-living bacterial cells and increase tolerance to antimicrobial interventions. The metabolic versatility of the Enterococci is reflected in the diversity and complexity of environments and communities in which they thrive. Understanding metabolic factors governing colonization and persistence in different host niches can reveal factors influencing the transition from commensal to opportunistic pathogen. Here, we report a new form of iron-dependent metabolism for Enterococcus faecalis where, in the absence of heme, respiration components can be utilised for extracellular electron transfer (EET). Iron augments E. faecalis biofilm growth and generates alterations in biofilm matrix, cell spatial distribution, and biofilm matrix properties. We identify the genes involved in iron-augmented biofilm growth and show that it occurs by promoting EET to iron within biofilm.\n\nSignificanceBacterial metabolic versatility is often key in dictating the outcome of host-pathogen interactions, yet determinants of metabolic shifts are difficult to resolve. The bacterial biofilm matrix provides the structural and functional support that distinguishes this state from free-living bacterial cells. Here, we show that the biofilm matrix provides access to resources necessary for metabolism and growth which are otherwise inaccessible in the planktonic state. Our data shows that in the absence of heme, components of Enterococcus faecalis respiration (l-lactate dehydrogenase and acetaldehyde dehydrogenase) may function as initiators of EET through the cytoplasmic membrane quinone pool and utilize matrix-associated iron to carry out EET. The presence of iron resources within the biofilm matrix leads to enhanced biofilm growth.

microbiology↗

bioRxiv2016

The detection of covariation of mRNA levels of large sets of genes across multiple human populations

In this study, we analyse RNA-Seq data from panels of human lymphoblastoid cell lines (LCLs) to identify covariation in the mRNA levels of large numbers of genes. Such large scale covariation may have biological origin or be due to technical variation in analysis (generally referred to as batch effects). We show that batch effects cannot explain this covariation by demonstrating reproducibility across different human populations and across different methods of analysis. This view is also supported by enrichment of single and combinations of transcription factors (TFs) binding to cognate promoter regions, enrichment of genes shown to be sensitive to the knockdown of individual TFs, enrichment of functional pathways, and finally enrichment of protein-protein interactions in proteins encoded by groups of covarying genes. The properties of the groups of covarying genes are therefore most readily explained by the influence of cumulative variations in the effectors of gene expression that act in trans on cognate genes. We suggest that covariation has functional outcomes by showing that covariation of 83 genes involved in the spliceosome pathway accounts for 8-16% of the variation in the alternative splicing patterns of genes expressed in human LCLs.

genetics↗