Microbiome

Sommer MO, Church GM, Dantas G (2010) The human microbiome harbors a diverse reservoir of antibiotic resistance genes. Virulence l(4) 299-303... 

Applications of Next-Generation Sequencing Technologies to the Study of the Human Microbiome... 

Along with the dramatic shift from culture-dependent to sequencing techniques used in analyzing, the human microbiome came a wealth of information about its role in human health and disease. It is important to note, however, that while many associations have been found between the microbiome and certain disease states, a causal direction has yet to be established for many of these relationships. 

The gut microbiome is also being investigated for its role in severe malnutrition states such as kwashiorkor (156,157). Indeed, a complex interplay exists between the gut microbiota and host metabolism, and likely has far-ranging implications on normal metabolic homeostasis as well as several disease states, the mechanisms of which we are just beginning to elucidate. 

Not surprisingly, the cutaneous microbiome has been studied for its potential role in dermatologic conditions such as psoriasis, atopic dermatitis, and acne. Psoriasis, a chronic idiopathic inflammatory disease of the skin (170), has been associated with an overrepresentation of Firmicutes and underrepresentation of Actinobacteria when compared to both the unaffected skin of psoriatic patients and the skin of normal controls (171). Additionally, Pro-teobacteria were detected less frequently in psoriatic lesions compared to skin of healthy controls (171). Subsequent studies using pyrosequencing techniques confirmed that Actinobacteria were more abundant in controls compared to patients with psoriasis however, Proteobacteria were significantly higher in trunk skin samples from psoriatic patients compared to controls (172). 

Shifts in the cutaneous microbiome have also been noted in chronic ulcer disease, such as those caused by venous stasis or diabetes (175). Patients with chronic ulcers treated with antibiotics have been shown to have an increased abundance of Pseudomonadaceae while an increase in Streptococcaceae has been noted in diabetic ulcers (175). A longitudinal shift in wound microbiota has also been shown to coincide with impaired healing in diabetic mice, and may interact with aberrantly expressed host cutaneous defense response genes leading to ulcerogenesis (176). When compared to controls, the feet of diabetic men has also been noted to have decreased populations of Staphylococcus species, a relative increase in the population of S. aureus and increased bacterial diversity, which may increase the risk for wound infections in diabetic patients (177). 

Foodomics can be an adequate strategy to investigate the complex issues related to prevention of future diseases and health promotion through the mentioned functional foods and nutraceuticals. It is now well known that health is heavily influenced by genetics. However, diet, lifestyle, and environment can have a crucial influence on the epigenome, gut microbiome and, by association, the transcriptome, proteome and, ultimately, the metabolome. When the combination of genetics and nutrition/Ufestyle/environment is not properly balanced, poor health is a result. 

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