New Research In Microbiome
Research No-1
Colorectal Carcinogenesis from Gut-associated Lymphoid Tissue Clinical and Experimental Documentation
Aims: The conventional (tubular or villous) adenoma-carcinoma pathway and the serrated adenoma-carcinoma pathway evolve in the vast colorectal mucosa built with crypts lined with mucus producing goblet cells and columnar cells. In contrast, few carcinomas developing in the tiny, spotty gut-associated-lymphoid-tissue (GALT) mucosal domain have been reported.
Place and Duration of Study: Department of Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden. The experiments in rats were carried out during four years.
Methodology: All publications on human colorectal GALT-carcinomas were reviewed. Archival sections from previous experiments in carcinogen-treated rats exhibiting colonic GALT follicles, were re-evaluated.
Results: Only 21 GALT-carcinomas found in 18 patients are in record. Four had ulcerative colitis, two were members of a Lynch syndrome family, two of a CRC family, one of a FAP family, two abdominal pain, two rectal bleedings, one diverticular disease, one a submucosal rectal tumor, one protracted constipation, and two had no symptoms or ground diseases. Conversely, 53% of 276 carcinogen-treated rats had developed GALT-carcinomas.
Conclusions: It is generally recognized that the vast majority of the CRCs in humans evolve via the conventional adenoma-carcinoma pathway or the serrated adenoma-carcinoma pathway in the GALT-free colorectal mucosal domain. Less frequently CRCs in humans develop in the tiny, spotty GALT mucosal domain. Whereas natural exposures to dietary/environmental factors, genome differences, obesity, type 2 diabetes, and the colonic microbiome are important for the development of CRC in the GALT-free colorectal mucosa in humans, no factors have been advanced to explain the development of carcinomas in colorectal GALT domains in humans. On the other hand, more than 50% of the SD rats injected with DMH developed colonic GALT-carcinomas. Although the cause(s) for the difference in frequency of GALT carcinomas in the two species remains mute, the results strongly suggest that the carcinogen DMH was the most important single factor for the induction of colonic GALT carcinoma in SD male rats. More research is necessary to unveil the factor(s) responsible for the development of GALT carcinomas in the human colorectal mucosa.
Research No-2
Effects of High and Low Dose Iron-Containing Micronutrient Powders for In-Home Fortification of Complementary Foods on the Gut Microbiome and Gut Inflammation in Kenyan Infants
Objectives: Primary outcome was change in composition of gut microbiome, after 3 weeks and 4 months. Secondary outcomes were changes in faecal calprotectin, treated diarrhoea, anaemia, iron status and systemic inflammation.
Methods: We performed two randomized controlled trials in 6-month-old Kenyan infants consuming home-fortified maize porridge daily for four months. 1) infants received an MNP containing 2.5 mg iron as NaFeEDTA (+2.5 mgFeMNP) or the identical MNP without iron (-2.5 mgFeMNP). 2) a different MNP containing 12.5 mg iron as ferrous fumarate (+12.5 mgFeMNP) or the identical MNP without iron (-12.5 mgFeMNP).
Results: We enrolled 117 infants, and 101 infants completed the studies between March 2010 and September 2012. Baseline prevalence of anaemia and systemic inflammation were 67.3% and 29.7%, respectively. At baseline, 63% of the total microbial 16S rRNA could be assigned to Bifidobacteriaceae; using qPCR, Salmonella was detected in 22.8% of infants, B. cereus in 38.6%, S. aureus in 71.3%, C. difficile in 53.5%, and C. perfringens in 86.1%. Body iron stores increased in the +12.5 mgFeMNP (p=0.001), but not in the +2.5 mgFeMNP. Using pyrosequencing, +FeMNPs increased enterobacteria, especially Escherichia/Shigella (p=0.048), the enterobacteria/ bifidobacteria ratio (p=0.020), and Clostridium (p=0.03) compared to -FeMNPs; +FeMNPs also increased faecal calprotectin (p=0.002). Most of these effects were confirmed using qPCR, and many were statistically stronger in ±12.5 mgFeMNP study than in ±2.5 mgFeMNP study. During the trial, 27.3% of infants in the +12.5 mgFeMNP group required treatment for diarrhoea vs. 8.3% in the -12.5 mgFeMNP group (p=0.092).
Conclusions: In rural Africa where infectious disease burden is high, provision of iron-containing MNPs to infants increases gut inflammation and modifies the gut microbiome toward a potentially more pathogenic profile.
Research No-3
Comparison of DNA Extraction Methods for Human Oral Microbiome Research
The oral micro biome is highly diverse and its composition is associated with oral disease and potentially diseases at other sites. Our objective is to evaluate DNA extraction methods potentially suitable for population-based investigations on the oral human microbiome and disease risk. Six commonly used microbial DNA extraction kits, employing either enzymatic methods or mechanical bead beating for cell lysis, were evaluated for the following aspects total DNA yield and quality and 16s rRNA DNA product and representation of microbial diversity. All analyses were carried out using a pooled and homogenized sample from one study subject. 16s rRNA gene sequence data were processed using the QIIME pipeline. One way ANOVA and Kruskal-Wallis tests were used to compare the different DNA extraction methods. We found that enzymatic extraction kits produced higher human genomic DNA, compared with mechanical extraction kits, however, phylogenic diversity in oral microbiome community structure from 16s rRNA gene sequence reads revealed no important differences between kit types. Enzymatic and mechanical bead beating kits provide alternative approaches for DNA extraction of oral microbiome DNA from oral wash samples. Greater total DNA yields are found in enzymatic approaches but microbial diversity can be similarly well characterized by either enzymatic or mechanical bead beating approaches
Research No-4
The role of the microbiome for human health: from basic science to clinical applications
The 2017 annual symposium organized by the University Medical Center Groningen in The Netherlands focused on the role of the gut microbiome in human health and disease. Experts from academia and industry examined interactions of prebiotics, probiotics, or vitamins with the gut microbiome in health and disease, the development of the microbiome in early-life and the role of the microbiome on the gut–brain axis. The gut microbiota changes dramatically during pregnancy and intrinsic factors (such as stress), in addition to extrinsic factors (such as diet, and drugs) influence the composition and activity of the gut microbiome throughout life. Microbial metabolites, e.g. short-chain fatty acids affect gut–brain signaling and the immune response. The gut microbiota has a regulatory role on anxiety, mood, cognition and pain which is exerted via the gut–brain axis. Ingestion of prebiotics or probiotics has been used to treat a range of conditions including constipation, allergic reactions and infections in infancy, and IBS. Fecal microbiota transplantation (FMT) highly effective for treating recurrent Clostridium difficile infections. The gut microbiome affects virtually all aspects of human health, but the degree of scientific evidence, the models and technologies and the understanding of mechanisms of action vary considerably from one benefit area to the other. For a clinical practice to be broadly accepted, the mode of action, the therapeutic window, and potential side effects need to thoroughly be investigated. This calls for further coordinated state-of-the art research to better understand and document the human gut microbiome’s effects on human health.
Research No-5
Why does the microbiome affect behaviour?
Growing evidence indicates that the mammalian microbiome can affect behaviour, and several symbionts even produce neurotransmitters. One common explanation for these observations is that symbionts have evolved to manipulate host behaviour for their benefit. Here, we evaluate the manipulation hypothesis by applying evolutionary theory to recent work on the gut–brain axis. Although the theory predicts manipulation by symbionts under certain conditions, these appear rarely satisfied by the genetically diverse communities of the mammalian microbiome. Specifically, any symbiont investing its resources to manipulate host behaviour is expected to be outcompeted within the microbiome by strains that do not manipulate and redirect their resources into growth and survival. Moreover, current data provide no clear evidence for manipulation. Instead, we show how behavioural effects can readily arise as a by-product of natural selection on microorganisms to grow within the host and natural selection on hosts to depend upon their symbionts. We argue that understanding why the microbiome influences behaviour requires a focus on microbial ecology and local effects within the host.