Turnbaugh, P. J. et al. A core microbiome in obese and lean twins. Nature 457, 480-484

Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA.
Nature (Impact Factor: 41.46). 12/2008; 457(7228):480-4. DOI: 10.1038/nature07540
Source: PubMed


The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person's gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).

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    • "He showed that the microbial environment and the genes they expressed changed within one day after switching from a low fat, plant polysaccharide-rich diet to a high-fat/high-sugar " Western " diet (Turnbaugh et al., 2009b). There is also a profound effect of nutrition on the genes expressed and the concentration of certain bacteria in the gut microbiome of distinct human populations and even those of different body mass indexes (BMIs) (De Filippo et al., 2010; Muegge et al., 2011; Turnbaugh et al., 2009a). The study demonstrated that bacterial ingestion could affect the lateral gene transfer of genes from one bacterium to another, affecting the gene expression of the microbiome. "
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    ABSTRACT: Utilization of environmental stimuli for growth is the main factor contributing to the evolution of prokaryotes and eukaryotes, independently and mutualistically. Epigenetics describes an organism's ability to vary expression of certain genes based on their environmental stimuli. The diverse degree of dose-dependent responses based on their variances in expressed genetic profiles makes it difficult to ascertain whether hormesis or oncogenesis has or is occurring. In the medical field this is shown where survival curves used in determining radiotherapeutic doses have substantial uncertainties, some as large as 50% (Barendsen, 1990). Many in-vitro radiobiological studies have been limited by not taking into consideration the innate presence of microbes in biological systems, which have either grown symbiotically or pathogenically. Present in-vitro studies neglect to take into consideration the varied responses that commensal and opportunistic pathogens will have when exposed to the same stimuli and how such responses could act as stimuli for their macro/microenvironment. As a result many theories such as radiation carcinogenesis explain microscopic events but fail to describe macroscopic events (Cohen, 1995). As such, this review shows how microorganisms have the ability to perturb risks of cancer and enhance hormesis after irradiation. It will also look at bacterial significance in the microenvironment of the tumor before and during treatment. In addition, bacterial systemic communication after irradiation and the host's immune responses to infection could explain many of the phenomena associated with bystander effects. Therefore, the present literature review considers the paradigms of hormesis and oncogenesis in order to find a rationale that ties them all together. This relationship was thus characterized to be the microbiome. Copyright © 2015 Elsevier Inc. All rights reserved.
    Environmental Research 07/2015; 142:239-256. DOI:10.1016/j.envres.2015.06.026 · 4.37 Impact Factor
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    • "A study with germ-free mice demonstrated that the colonisation with Methanobrevibacter smithiii induces Bacteroidetes thetaiotaomicron to ferment dietary fructans to acetate and butyrate, resulting in an increase of host adiposity (Samuel and Gordon, 2006). In addition, the gut microbiome of obese mice is enriched in genes encoding carbohydrate metabolism enzymes and has been demonstrated to have a greater capacity to extract energy from the diet and to generate short-chain fatty acids (SCFA) (Turnbaugh et al., 2006, 2009a). SCFAs are essential for the microbial community and play a role in regulation of energy balance, inflammatory processes, health, and obesity (Delzenne and Cani, 2011). "
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    ABSTRACT: Genetics, lifestyle, and dietary habits contribute to metabolic syndrome, but also an altered gut microbiota has been identified. Based on this knowledge it is suggested that host bacterial composition tends to change in response to dietary factors and weight loss. The aim of this study was to identify bacteria affecting host metabolism in obesity during weight loss and to correlate them with changes of the body composition obtained from bioelectrical impedance analysis (BIA). We recruited obese individuals receiving a dietary intervention according DACH (German, Austrian, and Swiss Society of Nutrition) reference values and guidelines for 'prevention and therapy of obesity' of DAG e.V., DDG, DGE e.V., and DGEM e.V. over three months. Faecal microbiota and BIA measurements were conducted at three time points, before, during, and after the intervention. Gut microbiota was analysed on the basis of 16S rDNA with quantitative real time PCR. Additionally, a food frequency questionnaire with questions to nutritional behaviour, lifestyle, and physical activity was administered before intervention. After weight reduction, obese individuals showed a significant increase of total bacterial abundance. The ratio of Firmicutes/Bacteroidetes significantly decreased during intervention. Lactobacilli significantly increased between the first and the second time point. These differences also correlated with differences in weight percentage. During the intervention period Clostridium cluster IV increased significantly between the second and the third time point. In contrast Clostridium cluster XIVa showed a decreased abundance. The dominant butyrate producer, Faecalibacterium prausnitzii, significantly increased as did the abundance of the butyryl-CoA: acetate CoA-transferase gene. Archaea and Akkermansia were significantly more prevalent after weight reduction. Our results show a clear difference in the gut bacterial composition before and after dietary intervention with a rapid change in gut microbial composition after a few weeks, but also indicate that a major shift requires long term dietary treatment.
    Beneficial Microbes 01/2015; 1(-1). DOI:10.3920/BM2014.0104 · 2.61 Impact Factor
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    • "Thus, increased relative abundances of Roseburia in the gut may provide metabolic benefits for growing juvenile howlers. Likewise, the higher Firmicutes to Bacteroidetes ratio in adult females compared with adult males and juveniles suggests higher fermentation efficiency and increased production of VFAs (Turnbaugh et al., 2006; Schleifer, 2009) helpful for meeting higher energy requirements. Another microbe, Lactococcus, that occurs in relatively high amounts in black howler females is associated with folate (vitamin B-9) biosynthesis in humans (Yatsunenko et al., 2012). "
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    ABSTRACT: In all mammals, growth, development, pregnancy, and lactation increase nutritional demands. Although primate field studies tend to focus on shifts in activity and diet as mechanisms to compensate for these demands, differences in digestive efficiency also are likely to be important. Because the gut microbiota can impact host digestive efficiency, we examined differences in activity budget, diet, and the gut microbial community among adult male (N = 4), adult female (N = 4), and juvenile (N = 5) wild black howler monkeys (Alouatta pigra) across a ten-month period in Palenque National Park, Mexico to determine how adult females and juveniles compensate for increased nutritional demands. Results indicate that adult females and juveniles consumed more protein and energy than adult males. Adult males, adult females, and juveniles also possessed distinct gut microbial communities, unrelated to diet. Juveniles exhibited a gut microbiota characterized by bacteria from the phylum Firmicutes, such as Roseburia and Ruminococcus, and demonstrated high fecal volatile fatty acid content, suggesting increased microbial contributions to host energy balances. Adult females possessed a higher Firmicutes to Bacteroidetes ratio, also suggesting increased energy production, and their gut microbiota was characterized by Lactococcus, which has been associated with folate biosynthesis. On the basis of these patterns, it appears that the gut microbiota differentially contributes to howler monkey nutrition during reproduction and growth. Determining the nutritional and energetic importance of shifts in activity, diet, and the gut microbiota in other nonhuman primate taxa, as well as humans, will transform our understanding of these life history processes and the role of host-microbe relationships in primate evolution. Am J Phys Anthropol, 2014. © 2014 Wiley Periodicals, Inc.
    American Journal of Physical Anthropology 12/2014; 155(4). DOI:10.1002/ajpa.22621 · 2.38 Impact Factor
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