This paper describes the ways in which the major rock-forming primary minerals (olivine, pyroxenes, amphiboles, feldspars, micas and chlorites) break down during weathering, the products that develop during this breakdown and the rates at which this breakdown occurs. The perspective chosen to illustrate this vast topic is that of the residual soil weathering profile. Different physical and chemical conditions characterize the various parts of such a profile. Thus, in the slightly weathered rock at the base of the profile, mineral weathering will take place in microfissures and narrow solution channels and the capillary water in such spatially restricted volumes may be expected to be close to equilibrium with the primary mineral. In these circumstances, the weathering product formed may be closely related to the primary mineral both compositionally and structurally. The saprolite higher up in the weathering profile may or may not retain the fabric and structure of the original parent rock, but in either case the close relationship observed between primary mineral and weathering product in the slightly weathered rock may be lost. This part of the profile will usually be affected by freely flowing drainage waters, the composition of which will be far from equilibrium with specific primary minerals. Weathering products which do form are likely to reflect the interaction between bulk water and bulk parent material. In the soil profile, the situation will be further complicated by organic ligands derived from decomposing organic matter or from the direct activities of soil microbes or plant roots. Thus, biological weathering will assume a much greater significance in this part of the profile compared with the mainly inorganic processes dominating in the saprolite and the slightly weathered rock. The general nature of any particular weathering profile will reflect the interactions between climate, topography, parent material, soil biota and time and superimposed upon this complexity, when considering how individual primary minerals break down in detail, will be factors related to the nature of the mineral itself. Particularly important in this respect is the inherent susceptibility of the mineral to weathering, which is related to overall chemical composition and structure, as well as the distribution and density of defects, dislocations and exsolution features, which often control the progress of the weathering reaction.

The origin and formation of soil clay minerals, namely micas, vermiculites, smectites, chlorites and interlayered minerals, interstratified minerals and kaolin minerals, are broadly reviewed in the context of research over the past half century. In particular, the pioneer overviews of Millot, Pedro and Duchaufour in France and of Jackson in the USA, are considered in the light of selected examples from the huge volume of work that has since taken place on this topic. It is concluded that these early overviews may still be regarded as being generally valid, although it may be that too much emphasis has been placed upon transformation mechanisms and not enough upon neoformation processes. This review also highlights some of the many problems pertaining to the origin and formation of soil clays that remain to be resolved.

Chronic leg and foot wounds represent an increasing burden to healthcare systems as the age of the population increases. The deep dermal tissues of all chronic wounds harbour microorganisms, however, the precise interaction between microbes in the wounds and impaired healing is unknown. With regard to antibiotic therapy, there is a lack of evidence concerning its effectiveness, optimal regimens or clinical indications for treatment. Despite this lack of evidence, antibiotics are frequently a feature of the management of chronic wounds and these patients receive significantly more antibiotic prescriptions (both systemic and topical) than age and sex-matched patients. Current guidelines for antibiotic prescribing for such wounds are often based on expert opinion rather than scientific fact and may present difficulties in interpretation and implementation to the clinician. Although the increasing prevalence of antibiotic resistance is widely recognized, the relationships between antibiotic resistance, chronic wound microbiology and rationales for antibiotic therapy have yet to be determined. This review discusses the role of microbes in chronic wounds from a clinical perspective with particular focus on the occurrence of bacteria and their impact on such wounds. The evidence and role of antibiotics in the treatment of such wounds are outlined and current practice of antibiotic usage for chronic wounds in the primary care setting described. The implications of antibiotic usage with regard to antibiotic resistance are also considered.

The majority of cases of oral cancer have been related to tobacco use and heavy alcohol consumption. However, the incidence of oral cavity carcinoma appears to be increasing in many parts of the world in a manner that it is difficult to explain with traditional risk factors alone. Meanwhile, interest in the possible relationships between microorganisms and the different stages of cancer development has been rising and numerous mechanisms by which bacteria and yeast may initiate or promote carcinogenesis are currently under investigation. In particular, a persuasive body of evidence suggests a possible etiological role involving the metabolism and production of carcinogenic products, such as acetaldehyde. Other suggested mechanisms include the induction of chronic inflammation and direct interference with eukaryotic cell cycle and signaling pathways. This review aims to summarize the known associations between microbial infection and cancer and draw attention to how they may relate to oral carcinoma.

This study determined whether comprehensive microbiological analysis offered real predictive value in terms of healing outcome, and assessed the clinical usefulness of surface swabs vs. tissue biopsies for clinically noninfected leg wounds. The wound microflora of 70 patients with chronic venous leg ulcers was quantified after sampling by swabbing and biopsy. A highly significant association between wound surface area at 4 weeks and eventual healing at 6 months was found (p<0.001), although initial wound size, sex, height, and weight were not significant predictors of outcome (p>0.1). A significant association between healing and bacterial diversity in the wound as assessed by swab (p=0.023) was demonstrated. Furthermore, the bacterial density of wound surface area by swab (CFU/mL; p=0.018) or biopsy (CFU/g tissue; p=0.038) were shown to be independent predictors of nonhealing. Logistic regression showed that microbiological analysis of biopsies provided no additional prognostic information when compared with analysis of the surface microflora (p=0.27). Hence, if biopsies do not contribute significantly to patient management, their use should be discouraged in clinically noninfected wounds. Furthermore, independent predictors of healing, such as wound surface microbial diversity and density, could identify patients likely to have an unfavorable outcome and to whom resources should be targeted.

The bacterial microfloras of 8 healing and 10 nonhealing chronic venous leg ulcers were compared by using a combination of cultural analysis and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene products. Cultural analysis of the microflora revealed that the majority of both wound types carried the aerobes Staphylococcus and Pseudomonas spp. (89 and 80%, respectively). Sequencing of 16S ribosomal DNAs selected on the basis of DGGE profiling allowed the identification of strains not detected by cultural means. Of considerable interest was the finding that more than 40% of the sequences represented organisms not cultured from the wound from which they were amplified. DGGE profiles also revealed that all of the wounds possessed one apparently common band, identified by sequencing as Pseudomonas sp. The intensity of this PCR signal suggested that the bacterial load of nonhealing wounds was much higher for pseudomonads compared to healing wounds and that it may have been significantly underestimated by cultural analysis. Hence, the present study shows that DGGE could give valuable additional information about chronic wound microflora that is not apparent from cultural analysis alone.

In order to characterize the bacterial microbiota present within oral cancerous lesions, tumorous and non-tumorous mucosal tissue specimens (approx. 1 cm 3 ) were harvested from ten oral squamous cell carcinoma (OSCC) patients at the time of surgery. Any microbial contamination on the surface of the specimens was eliminated by immersion in Betadine and washing with PBS. Bacteria were visualized within sections of the OSCC by performing fluorescent in situ hybridization with the universal oligonucleotide probe, EUB338. DNA was extracted from each aseptically macerated tissue specimen using a commercial kit. This was then used as template for PCR with three sets of primers, targeting the 16S rRNA genes of Spirochaetes, Bacteroidetes and the domain Bacteria. PCR products were differentiated by TA cloning and bacterial species were identified by partial sequencing of the 16S rRNA gene fragments. A total of 70 distinct taxa was detected: 52 different phylotypes isolated from the tumorous tissues, and 37 taxa from within the non-tumorous specimens. Differences between the composition of the microbiotas within the tumorous and non-tumorous mucosae were apparent, possibly indicating selective growth of bacteria within carcinoma tissue. Most taxa isolated from within the tumour tissue represented saccharolytic and aciduric species. Whether the presence of these bacteria within the mucosa has any bearing on the carcinogenic process is a concept worthy of further investigation.

Despite increasing interest in the possible relationships between bacteria and the different stages of cancer development, the association of bacteria with cancer of the oral cavity has yet to be adequately examined. With that in mind, the primary objective of this study was to identify any bacterial species within oral squamous cell carcinoma tissue using a standard microbiological culture approach. At the time of surgery, a 1-cm 3 portion of tissue was harvested from deep within the tumor mass using a fresh blade for each cut. Whenever possible, "superficial" portions from the mucosa overlying the tumor and nontumorous control specimens from at least 5 cm away from the primary tumor site were also obtained. Surface contamination was eliminated by immersion in Betadine and washing with phosphate-buffered saline. Each specimen was aseptically macerated and cultured on nonselective media under both aerobic and anaerobic conditions. Isolates were identified by 16S rRNA gene sequencing. Twenty deep-tissue specimens, 19 with corresponding superficial tissues and 12 with control tissues, were successfully processed. A diversity of bacterial taxa were isolated and identified, including several putatively novel species. Most isolates were found to be saccharolytic and acid-tolerant species. Notably, some species were isolated only from either the tumorous or nontumorous tissue type, indicating a degree of restriction. Successful surface decontamination of the specimens indicates that the bacteria detected were from within the tissue. A diversity of bacterial groups have been isolated from within oral squamous cell carcinoma tissue. The significance of these bacteria within the tumor warrants further study.