ORCID Profile
0000-0001-5099-8495
Current Organisation
University of Aberdeen
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Publisher: Elsevier BV
Date: 07-2015
Publisher: Public Library of Science (PLoS)
Date: 02-07-2201
Publisher: Wiley
Date: 07-12-2017
Abstract: Ruminococcus bromii is a dominant member of the human colonic microbiota that plays a ‘keystone’ role in degrading dietary resistant starch. Recent evidence from one strain has uncovered a unique cell surface ‘amylosome’ complex that organizes starch‐degrading enzymes. New genome analysis presented here reveals further features of this complex and shows remarkable conservation of amylosome components between human colonic strains from three different continents and a R. bromii strain from the rumen of Australian cattle. These R. bromii strains encode a narrow spectrum of carbohydrate active enzymes (CAZymes) that reflect extreme specialization in starch utilization. Starch hydrolysis products are taken up mainly as oligosaccharides, with only one strain able to grow on glucose. The human strains, but not the rumen strain, also possess transporters that allow growth on galactose and fructose. R. bromii strains possess a full complement of sporulation and spore germination genes and we demonstrate the ability to form spores that survive exposure to air. Spore formation is likely to be a critical factor in the ecology of this nutritionally highly specialized bacterium, which was previously regarded as ‘non‐sporing’, helping to explain its widespread occurrence in the gut microbiota through the ability to transmit between hosts.
Publisher: American Society for Microbiology
Date: 08-2014
DOI: 10.1128/JCM.00764-14
Abstract: Spontaneously expectorated sputum is traditionally used as the s ling method for the investigation of lower airway infections. While guidelines exist for the handling of these s les for culture-based diagnostic microbiology, there is no comparable consensus on their handling prior to culture-independent analysis. The increasing incorporation of culture-independent approaches in diagnostic microbiology means that it is of critical importance to assess potential biases. The aim of this study was to assess the impact of delayed freezing on culture-independent microbiological analyses and to identify acceptable parameters for s le handling. Sputum s les from eight adult cystic fibrosis (CF) patients were collected and aliquoted into sterile Bijou bottles. Aliquots were stored at room temperature before being frozen at −80°C for increasing intervals, up to a 72-h period. S les were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions. Substantial variation was observed in s les with high- ersity bacterial communities over time, whereas little variation was observed in low- ersity communities dominated by recognized CF pathogens, regardless of time to freezing. Partitioning into common and rare species demonstrated that the rare species drove changes in similarity. The percentage abundance of anaerobes over the study significantly decreased after 12 h at room temperature ( P = 0.008). Failure to stabilize s les at −80°C within 12 h of collection results in significant changes in the detected community composition.
Publisher: Springer Science and Business Media LLC
Date: 09-12-2010
Publisher: Informa UK Limited
Date: 03-2010
DOI: 10.1586/ERM.09.81
Abstract: Lower respiratory tract bacterial infections, such as those associated with cystic fibrosis lung disease, represent a major healthcare burden. Treatment strategies are currently informed by culture-based routine diagnostics whose limitations, including an inability to isolate all potentially clinically significant bacterial species present in a s le, are well documented. Some advances have resulted from the introduction of culture-independent molecular assays for the detection of specific pathogens. However, the application of bacterial community profiling techniques to the characterization of these infections has revealed much higher levels of microbial ersity than previously recognized. These findings are leading to a fundamental shift in the way such infections are considered. Increasingly, polymicrobial infections are being viewed as complex communities of interacting organisms, with dynamic processes key to their pathogenicity. Such a model requires an analytical strategy that provides insight into the interactions of all members of the infective community. The rapid advance in sequencing technology, along with protocols that limit analysis to viable bacterial cells, are for the first time providing an opportunity to gain such insight.
Publisher: Informa UK Limited
Date: 03-2010
Publisher: Wiley
Date: 06-12-2006
DOI: 10.1111/J.1462-2920.2006.01186.X
Abstract: Insoluble plant polysaccharides and endogenous mucin are important energy sources for human colonic microorganisms. The object of this study was to determine whether or not specific communities colonize these substrates. Using faecal s les from four in iduals as inocula for an anaerobic in vitro continuous flow system, the colonization of wheat bran, high amylose starch and porcine gastric mucin was examined. Recovered substrates were extensively washed and the remaining tightly attached bacterial communities were identified using polymerase chain reaction- lified 16S rRNA gene sequences and fluorescent in situ hybridization. The substrate had a major influence on the species of attached bacteria detected. Sequences retrieved from bran were dominated by clostridial cluster XIVa bacteria, including uncultured relatives of Clostridium hathewayi, Eubacterium rectale and Roseburia species. Bacteroides species were also detected. The most abundant sequences recovered from starch were related to the cultured species Ruminococcus bromii, Bifidobacterium adolescentis, Bifidobacterium breve and E. rectale. The most commonly recovered sequences from mucin were from Bifidobacterium bifidum and uncultured bacteria related to Ruminococcus lactaris. This study suggests that a specific subset of bacteria is likely to be the primary colonizers of particular insoluble colonic substrates. For a given substrate, however, the primary colonizing species may vary between host in iduals.
Publisher: Springer Science and Business Media LLC
Date: 10-11-2015
Publisher: Elsevier BV
Date: 11-2015
Publisher: Oxford University Press (OUP)
Date: 16-02-2018
DOI: 10.1093/IBD/IZX061
Publisher: American Society for Microbiology
Date: 07-2005
DOI: 10.1128/AEM.71.7.3692-3700.2005
Abstract: The effects of changes in the gut environment upon the human colonic microbiota are poorly understood. The response of human fecal microbial communities from two donors to alterations in pH (5.5 or 6.5) and peptides (0.6 or 0.1%) was studied here in anaerobic continuous cultures supplied with a mixed carbohydrate source. Final butyrate concentrations were markedly higher at pH 5.5 (0.6% peptide mean, 24.9 mM 0.1% peptide mean, 13.8 mM) than at pH 6.5 (0.6% peptide mean, 5.3 mM 0.1% peptide mean, 7.6 mM). At pH 5.5 and 0.6% peptide input, a high butyrate production coincided with decreasing acetate concentrations. The highest propionate concentrations (mean, 20.6 mM) occurred at pH 6.5 and 0.6% peptide input. In parallel, major bacterial groups were monitored by using fluorescence in situ hybridization with a panel of specific 16S rRNA probes. Bacteroides levels increased from ca. 20 to 75% of total eubacteria after a shift from pH 5.5 to 6.5, at 0.6% peptide, coinciding with high propionate formation. Conversely, populations of the butyrate-producing Roseburia group were highest (11 to 19%) at pH 5.5 but fell at pH 6.5, a finding that correlates with butyrate formation. When tested in batch culture, three Bacteroides species grew well at pH 6.7 but poorly at pH 5.5, which is consistent with the behavior observed for the mixed community. Two Roseburia isolates grew equally well at pH 6.7 and 5.5. These findings suggest that a lowering of pH resulting from substrate fermentation in the colon may boost butyrate production and populations of butyrate-producing bacteria, while at the same time curtailing the growth of Bacteroides spp.
Publisher: Public Library of Science (PLoS)
Date: 24-02-2014
Publisher: Springer Science and Business Media LLC
Date: 17-02-2013
DOI: 10.1038/NG.2536
Publisher: Elsevier BV
Date: 08-2015
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Alan Walker.