Search

The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.

Background: Crohn's disease (CD) and ulcerative colitis (UC) diagnosis requires comprehensive examination of the patient. Faecalibacterium prausnitzii and Escherichia coli have been reported as representatives of Inflammatory Bowel Disease (IBD) dysbiosis. The aim was to determine whether or not quantification of these species can be used as a complementary tool either for diagnostic or prognostic purposes. Methods: Mucosa-associated F. prausnitzii and E. coli abundance was determined in 28 controls (H), 45 CD, 28 UC patients and 10 irritable bowel syndrome (IBS) subjects by quantitative polymerase chain reaction (qPCR) and the F. prausnitzii E. coli index (F-E index) was calculated. Species abundances were normalized to total bacteria and human cells. Data was analyzed taking into account patients' phenotype and most relevant clinical characteristics. Results: IBD patients had lower F. prausnitzii abundance than H and IBS (P.

During screening of human gut isolates in search of novel antimicrobials, the butyrate-producing strain Roseburia faecis M72/1 was found to produce an inhibitory substance active against Bacillus subtilis. Partial purification of the antimicrobial was achieved and activity found to be heat labile. Our findings suggest that R. faecis M72/1 produces a proteinaceous inhibitor whose production may be triggered by trypsin in the gastrointestinal tract.

Diet is a major factor driving the composition and metabolism of the colonic microbiota. The amount, type and balance of the main dietary macronutrients (carbohydrates, proteins and fats) have a great impact on the large intestinal microbiota. The human colon contains a dense population of bacterial cells that outnumber host cells 10-fold. Bacteroidetes, Firmicutes and Actinobacteria are the three major phyla that inhabit the human large intestine and these bacteria possess a fascinating array of enzymes that can degrade complex dietary substrates. Certain colonic bacteria are able to metabolise a remarkable variety of substrates whilst other species carry out more specialised activities, including primary degradation of plant cell walls. Microbial metabolism of dietary carbohydrates results mainly in the formation of short chain fatty acids and gases. The major bacterial fermentation products are acetate, propionate and butyrate; and the production of these tends to lower the colonic pH. These weak acids influence the microbial composition and directly affect host health, with butyrate the preferred energy source for the colonocytes. Certain bacterial species in the colon survive by cross-feeding, using either the breakdown products of complex carbohydrate degradation or fermentation products such as lactic acid for growth. Microbial protein metabolism results in additional fermentation products, some of which are potentially harmful to host health. The current 'omic era promises rapid progress towards understanding how diet can be used to modulate the composition and metabolism of the gut microbiota, allowing researchers to provide informed advice, that should improve long-term health status.

Recent molecular analyses suggest that bacteria related to strains SS2/1 and SSC/2, previously reported to be distantly related to Anaerostipes caccae NCIMB 13811T, represent one of the ten most abundant phylotypes detected in adult human faecal samples. These two strains were isolated as d -lactate-utilizing bacteria from faecal samples of a healthy individual. We show here that they share >99.9% similarity in 16S rRNA gene sequence with a new butyrate-producing isolate recovered from a colonic biopsy of a Crohn's disease patient, and also with the sequence reported recently for Eubacterium hadrum ATCC 29173T. Biochemical profiling using API Rapid ID 32A and API ZYM test systems confirmed a close phenotypic similarity to E. hadrum ATCC 29173T, but also indicated that the description of this species should be expanded to include the ability to produce butyrate from d -lactate and acetate. Phylogenetic analysis confirmed an affinity between E. hadrum and members of the genus Anaerostipes (92.3–94.2% sequence similarity) belonging to the family Lachnospiraceae (formerly Clostridium cluster XIVa). Based on phylogenetic, phenotypic and chemotaxonomic evidence it is proposed that E. hadrum be transferred to the genus Anaerostipes with the name Anaerostipes hadrus comb. nov. The type strain of A. hadrus comb. nov. is =ATCC 29173T (=DSM 3319T = VP 82-52T).

Strains of the rumen cellulolytic bacterium Ruminococcus flavefaciens vary in their ability to utilise isolated plant xylans for growth. Here an 11.5 kb fragment of genomic DNA from the xylan-utilizing R. flavefaciens strain 17 that contains the xynD gene, which encodes an extracellular xylanase/ β -(1,3-1,4)-glucanase, was analysed. Sequencing revealed five consecutive open reading frames downstream from xynD on the same strand, preceded by the divergently transcribed ORF3. These include the following genes likely to be involved in utilisation of xylan breakdown products: xylA , encoding a β -(1,4)-xylosidase, xsi , encoding a xylose isomerase and ORF8 encoding part of an ABC-type sugar transporter. The products of ORF3 and of a partial ORF1 found upstream of xynD , show significant sequence similarity to AraC-type regulatory proteins while ORF4 and ORF7 show no close relationship to other known proteins. Homologues of the xylA and xsi genes, and inducible β -xylosidase activity, were readily detectable in three xylan-utilizing R. flavefaciens strains 17, B1a and C94 but not in two xylan non-utilizing strains, C1a and B34b, suggesting that this cluster may be absent from xylan non-utilizing strains.

Various proposals have been made for the enhancement of fibre degradation in the rumen through genetic manipulation of both cellulolytic and non-cellulolytic members of the rumen bacterial flora. Progress is now being made in developing methods for gene transfer based on plasmids or temperate phage in prominent rumen species such as Bacteroides ruminicola and Selenomonas ruminantium, but the complexity of the rumen ecosystem makes the likely effects of proposed strain manipulations difficult to predict. Similar work in rumen cellulolytic bacteria could make a valuable contribution to the molecular analysis of their fibre degrading activities.

Introduction Determining faecal sample bacterial community structure through sequence analysis of DNA has become a very important facet of inflammatory bowel disease (IBD) research. The possible impact of different commercially available DNA extraction kits and the influence of different lab environments on the data generated has however received relatively little attention. The study compared bacterial communities in faecal samples extracted using commercial DNA kits in established gastrointestinal research laboratories. Methods Faecal samples from 2 healthy volunteers and 2 IBD patients with relapse were investigated. DNA extraction was undertaken using MoBio and Fastprep DNA extraction kits in two established labs. Two protocols were followed for processing samples using the Fastprep kit. Each DNA sample was then split and an aliquot transferred to the other lab. Pyrosequencing PCR of bacterial 16S rRNA genes was performed in both labs on all samples. Quantitative PCR analysis (q-PCR) to validate sequencing data was also performed. Hierarchical clustering was done using the Jaccard and Theta Yue & Clayton similarity coefficients on the pyrosequencing data. Results DNA extracted using methods FastPrep1, FastPrep2 and the MoBio kit yielded median DNA concentrations of 476 (interquartile range 290–518), 453 (IQR 228–689) and 22 (IQR 9–36) ng/µL respectively. Those obtained with MoBio were significantly lower than FastPrep (p Ruminococcaceae and Bacteroidetes were significantly increased in MoBio extracted samples, while Lachnospiraceae and Enterobacteriaceae were significantly reduced (p Enterobacteriaceae , Bacteroides , Ruminococcaceae and Lachnospiraceae respectively. Conclusion This study demonstrates significant differences in DNA yield and bacterial DNA composition seen when comparing DNA extracted from the same faecal sample with different extraction kits. This highlights the importance of ensuring that all samples to be analysed together are prepared with the same DNA extraction method, and the need for caution when comparing studies that have used different methods. Disclosure of Interest None Declared

Background: Exposure to Helicobacter hepaticus, common enterohepatic bacteria, increases the incidence of experimental colitis and promotes colonic tumorigenesis. However, the role of H. hepaticus in pathogenesis of necrotizing enterocolitis (NEC) is not known. Neonatal NEC is a devastating disease of prematurely born babies. The cause of NEC is not clear, but inappropriate bacterial colonization plays an important role in NEC pathogenesis. Autophagy protects organisms against diverse pathologies, such as bacterial infections. However, uncontrolled activation of autophagy may lead to cellular injury. Aim: To test the effect of H. hepaticus on development of intestinal injury and expression of inflammatory and autophagic regulators in the rat model of NEC. Methods: Pregnant rats and newborn pups were kept either in H. hepaticus-free or in the H. hepaticus-contaminated environment. Prematurely born rat pups were hand-fed with formula and exposed to asphyxia/cold stress to develop NEC. After 96 hours, all animals were sacrificed and ileal tissue was collected. Incidence of NEC injury, expression of inflammatory cytokines (IL-6, IL-8, IL-18 & TNF-α) and protein levels of autophagy regulators (Beclin 1, LC3II & p62) were evaluated in the ileum. Results: Results: The incidence of NEC was significantly increased to 71% (25/35) in rats exposed to H. hepaticus compared with the H. hepaticus-free group with NEC incidence of 33% (13/39; p < 0.001). The survival rates were not affected by H. hepaticus. The presence of H. hepaticus was detected in the GI tract of the H. hepaticus group. IL-8 and IL-18 gene expression was significantly altered in the H. hepaticus group, whereas IL-6 and TNF-α levels were not changed. Protein levels of Beclin 1 and LC3II were markedly increased, whereas p62 levels were significantly decreased in the ileum from the H. hepaticus group. Conclusions: Helicobacter hepaticus exacerbates intestinal injury and induces intestinal inflammation in the rat NEC model. Exposure to H. hepaticus is also associated with a strong induction of the autophagy pathway in the site of injury the terminal ileum. Inappropriate activation of intestinal autophagy by bacterial insult may facilitate massive cell death, leading to severe mucosal injury. Supported by the NIH Grant HD-39657 (to B.D.)