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How colon resist to bile

How colon resist to bile


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There is a disease called bile reflux which can make damage to the stomach. I just don't know how the stomach can be damaged by bile but the colon (small intestine) can resist with it?


Intestinal Sulfation Is Essential to Protect Against Colitis and Colonic Carcinogenesis

Background & aims: Sulfation is a conjugation reaction essential for numerous biochemical and cellular functions in mammals. The 3'-phosphoadenosine 5'-phosphosulfate (PAPS) synthase 2 (PAPSS2) is the key enzyme to generate PAPS, which is the universal sulfonate donor for all sulfation reactions. The goal of this study was to determine whether and how PAPSS2 plays a role in colitis and colonic carcinogenesis.

Methods: Tissue arrays of human colon cancer specimens, gene expression data, and clinical features of cancer patients were analyzed. Intestinal-specific Papss2 knockout mice (Papss2 ΔIE ) were created and subjected to dextran sodium sulfate-induced colitis and colonic carcinogenesis induced by a combined treatment of azoxymethane and dextran sodium sulfate or azoxymethane alone.

Results: The expression of PAPSS2 is decreased in the colon cancers of mice and humans. The lower expression of PAPSS2 in colon cancer patients is correlated with worse survival. Papss2 ΔIE mice showed heightened sensitivity to colitis and colon cancer by damaging the intestinal mucosal barrier, increasing intestinal permeability and bacteria infiltration, and worsening the intestinal tumor microenvironment. Mechanistically, the Papss2 ΔIE mice exhibited reduced intestinal sulfomucin content. Metabolomic analyses revealed the accumulation of bile acids, including the Farnesoid X receptor antagonist bile acid tauro-β-muricholic acid, and deficiency in the formation of bile acid sulfates in the colon of Papss2 ΔIE mice.

Conclusions: We have uncovered an important role of PAPSS2-mediated sulfation in colitis and colonic carcinogenesis. Intestinal sulfation may represent a potential diagnostic marker and PAPSS2 may serve as a potential therapeutic target for inflammatory bowel disease and colon cancer.

Keywords: Colitis Colon Cancer PAPSS2 Sulfation Sulfomucin.

Copyright © 2021 AGA Institute. Published by Elsevier Inc. All rights reserved.


Colon Conditions

  • Colitis: Inflammation of the colon. Inflammatory bowel disease or infections are the most common causes. : Small weak areas in the colon's muscular wall allow the colon's lining to protrude through, forming tiny pouches called diverticuli. Diverticuli usually cause no problems, but can bleed or become inflamed or infected. : When diverticuli become inflamed or infected, diverticulitis results. Abdominal pain, fever, and constipation are common symptoms. (hemorrhage): Multiple potential colon problems can cause bleeding. Rapid bleeding is visible in the stool, but very slow bleeding might not be. : A name for either Crohn's disease or ulcerative colitis. Both conditions can cause colon inflammation (colitis). : An inflammatory condition that usually affects the colon and intestines. Abdominal pain and diarrhea (which may be bloody) are symptoms. : An inflammatory condition that usually affects the colon and rectum. Like Crohn's disease, bloody diarrhea is a common symptom of ulcerative colitis. : Stools that are frequent, loose, or watery are commonly called diarrhea. Most diarrhea is due to self-limited, mild infections of the colon or small intestine. : The bacteria Salmonella can contaminate food and infect the intestine. Salmonella causes diarrhea and stomach cramps, which usually resolve without treatment. : The bacteria Shigella can contaminate food and invade the colon. Symptoms include fever, stomach cramps, and diarrhea, which may be bloody. : Many different bacteria commonly contaminate water or food in developing countries. Loose stools, sometimes with nausea and fever, are symptoms. : Polyps are small growths. Some of these develop into cancer, but it takes a long time. Removing them can prevent many colon cancers. : Cancer of the colon affects more than 100,000 Americans each year. Most colon cancer is preventable through regular screening.

Results and discussion

Two distinct classes of 5hmC enrichment profiles are observed at active genes in normal human colon

We first set out to identify genes marked by 5hmC in colon by hmeDIP-seq in order to ultimately follow their methylation fate in cancer. Initial hmeDIP-seq on five DNA samples from normal mucosa of affected patients showed 5hmC enrichment at promoters, absent at the transcription start site (TSS), abundant within the body of genes and underrepresented within intergenic regions (Figure 1a and b).

5hmC promoter profiles and their association with active genes in normal colon. (a) hmeDIP-seq profile for all genes around the TSS in normal colon tissue (n = 5). (b) Quantification of 5hmC enrichments in genomic features. (c) Two distinct promoter profiles were identified. Left panel: high 5hmC within a promoter window (-1 kb to +0.5 kb) with a ‘narrow’ promoter profile. Right panel: high 5hmC within gene bodies (from the TSS to the TTS) with a ‘broad’ promoter profile. Below are examples of each type of profile. (d) 5hmC and CpG content in the promoter. High, intermediate and low CpG content (HCP, ICP and LCP, respectively). Inset numbers represent the number of promoters for each category (LCP numbers not shown). (e) 5hmC content at promoter CpG islands. The levels represent an average of the population for each promoter type, thus individual loci may not necessarily display the full profile. Additional file 2 shows further examples. (f) Expression levels (log2 microarray intensity) of genes associated with 5hmC promoter profiles (P values were obtained by a Wilcox test).

From the profiling of 5hmC content across genes we identified two types of enrichments at gene promoters (Figure 1c). A ‘narrow’ type was observed after ranking 5hmC read content inside a window of -1 kb to +0.5 kb of the TSS and a ‘broad’ type after ranking by 5hmC read content in the gene body (from TSS to the TTS). We identified 2,156 unique ‘narrow’ and 2,199 unique ‘broad’ promoters (listed in Additional file 1).

The ‘narrow’ and ‘broad’ profiles were distinct in terms of promoter CpG content (Figure 1d) and in distribution of 5hmC around promoter CpG islands (Figure 1e). Promoters with the ‘narrow’ profile were enriched for intermediate CpG content promoters (ICP) whereas the ‘broad’ promoters where mostly high in CpG content (Figure 1d). Both promoter types showed that 5hmC is enriched within the shores of promoter CpG islands, more so within the upstream shore, and a higher overall content of 5hmC for the ‘narrow’ type (Figure 1e). Note, however, that the enrichment of 5hmC in the downstream shore of ACTN2 is lower than that for AGAP1. The levels measured over the islands represent an average of the population for each type of promoter, and thus individual loci may not necessarily display the full enrichment profile across the associated promoter CpG island. Additional file 2 shows further examples to illustrate this. Interestingly, comparison of the 5hmC profiles with Illumina expression array data from four normal cases showed that ‘narrow’ promoter genes are less active than the ‘broad’ type (Figure 1f), in accordance with previous correlations made for higher 5hmC content at promoters and reduced gene activity in mouse and human ES cells [41,42]. Biological processes also typified the 5hmC promoters gene ontology categories indicative of gut function were enriched for the ‘narrow’ type whereas cell differentiation and development where enriched for the ‘broad’ type (Additional file 2).

Together these data show that the content and distribution of 5hmC within promoters and gene bodies correlates with gene activities involved in normal gut epithelial function and differentiation.

5hmC enrichment is similar to 5mC enrichment at genic regions

Next we examined DNA methylation content with respect to the 5hmC profiles by comparing our hmeDIP-seq data to published meDIP-seq data for normal colon tissue [43] (Additional file 3). We generated heatmaps for 5hmC and 5mC enrichment profiles from -3 kb to +20 kb around the TSS (Additional file 3a). Ten clusters were generated based on the distribution of 5hmC and 5mC within this window. Overall we found that where 5hmC-specific enrichment is observed, the enrichment profiles are similar for 5mC (Additional file 3a). The exception was cluster 2 where there was more DNA methylation near the TSS than 5 hmC. Further comparison of 5hmC and 5mC profiles closer to the TSS (-3 kb to +3 kb) of all loci suggest that the differences in enrichment patterns for 5hmC and 5mC occur near the TSS and upstream promoter region (Additional file 3b). This suggests that several gene promoters may have DNA methylation without 5 hmC.

The heatmaps also identified the ‘narrow’ promoters as typified by clusters 3 and 8 whereas the ‘broad’ promoters fell within clusters 5, 6, 7 and 9 (Additional file 3c). With the exception of clusters 2 and 3 that showed an enrichment for LCP promoters, most of the 5hmC/5mC clusters fell with promoters of an intermediate or high CpG content (Additional file 3e).

We then compared the meDIP-seq methylation clusters to the methylation levels assessed by the Infinium27k arrays in 17 normal samples from our patient cohort (Additional file 3e). For the loci plotted in the heatmap the maximal distance of the Infinium probes to the TSS is 1499 bp. The highest methylation levels for these probes were around the promoters grouped within clusters 1 and 2, which correspond to the meDIP-seq data where the highest methylation enrichment was observed (Additional file 3a and e). Similarly clusters 4 to 9 which all reported low amounts of DNA methylation around the TSS by meDIP-seq also had lower levels of DNA methylation at the corresponding Infinium probes (Additional file 3a and e).

Thus in our normal colon tissues, the Infinium arrays concur with meDIP-seq enrichment patterns proximal to the TSS of genes.

Reduced levels of 5hmC in colon tumours do not correlate with changes in TET transcript levels

Having established profiles for 5hmC and 5mC in normal colon we next analysed their behaviour in neoplasia. Our colon cancer cohort is composed of 47 normal tissues, 36 adenomas and 31 adenocarcinomas (Additional file 1). We confirmed that 5hmC and 5mC are globally reduced during colon cancer progression using liquid chromatography mass spectrometry (LCMS) and immunofluorescence (IF) (Figure 2a and b). The IF also shows that 5hmC is concentrated in the differentiated colon epithelium and is low in the base of the crypts and tumours consistent with previous reports [21]. Importantly, we observed TET1, TET2 and TET3 were consistently transcribed in normal and tumour tissue and that the absolute levels of TET1 were low relative to TET2 and TET3 by Sybr-Green qRT-PCR (Figure 2c). Further analysis of TET expression in normal-tumour matched cases by Taqman qRT-PCR showed no correlation with the changes in global levels of 5hmC (Additional file 4). Moreover, mining of recently published data sets [31,44] indicates that TETs are present in normal crypt and differentiated epithelium and tumours.

Reduced 5hmC in tumours without global changes in TET s transcripts. (a) Global content of 5hmC and 5mC in normal (N), adenoma (Ad) and adenocarcinoma (T) DNA by mass spectrometry (P values were obtained by a Wilcox test). (b) Representative images from a colon cancer tissue microarray immunofluorescence. Arrows indicate the epithelium, arrowheads the stroma. (c) Absolute levels of TETs (standard curve method) in selected cases from our colon cancer cohort. Orange vertical bands represent the median. Negative values indicate TETs transcripts are less abundant than B2M transcripts. There was no significant change in levels across tissues but considerable variation within tissues.

Mutation at the Fe2 and a-KG binding pockets could account for a lack of TET activity [30] but these were specifically excluded in our sample set through targeted exonic sequencing (Additional file 5a and Additional methods). We identified non-synonymous mutations elsewhere in the catalytic domains of TETs but their presence did not correlate with the changes in global 5hmC levels (Additional file 5b). Reduction of 5hmC in tumours may also be due to inhibition of TETs by metabolites that accumulate through mutation of IDH1/2, Fumarate hydratase (FH) or Succinate dehydrogenase (SDH) [39,45]. In our study IDH1/2 mutations were excluded in a subset of samples (not shown) and recent larger studies have shown IDH1/2, FH or SDH mutation is rare or absent in colon cancer [31,40].

We do not have TET protein data associated with our sample set and therefore we cannot exclude that the global reduction in 5hmC could be due to post-transcriptional events with an impact on variations in the stability or activity of TETs. However, the detection of mRNA at levels similar to the normal tissues suggests that the reduced levels of 5hmC that we uncover in all our colon tumours is unlikely to be due to an absence or mutation of TETs or an inhibition by currently recognised onco-metabolites.

5hmC is reduced across the genome of tumours with a small effect on gene transcription

We profiled 5hmC in four matching adenocarcinomas. The hmeDIP-seq read content in tumours showed an overall similar distribution to the normal tissue but with markedly reduced 5hmC levels across the genome as assessed by 5hmC content within repetitive elements (Additional file 6) and within genes (Additional file 7a and b). The reduced level of 5hmC in tumours compared to normal was confirmed at selected loci by a glycosylase-restriction enzyme sensitive assay (gluc-MS-qPCR - Additional file 7c) indicating that genes continue to be marked by a reduced amount of 5hmC in tumours.

Illumina expression array data generated from four normals and 14 tumours showed a small but statistically significant reduction in gene activity for genes with ‘broad’ 5hmC promoters (Additional file 7d). Thus, although 5hmC associates with active gene transcription, the reduction of 5hmC in tumours were accompanied by very small expression level changes. These results indicate that genes that acquire 5hmC in normal colon are transcriptionally active in tumours and suggest that low levels of 5hmC do not hinder transcription.

Loci marked by 5hmC in normal have an innate resistance to DNA hypermethylation in cancer

To ascertain whether promoters normally marked by 5hmC undergo DNA methylation changes in colon cancer, we assessed DNA methylation in 17 tumours matched to the normal tissues using Infinium methylation arrays. The Infinium27k arrays are a robust platform for quantitative measurement of the DNA methylation status of 27,578 CpG sites located at the promoter regions of 14,495 protein-coding genes [43,46]. Infinium technology is based on bisulfite conversion that does not distinguish between 5mC and 5hmC. However, 5hmC only makes up a small percentage of modified cytosines in normal colon and an even smaller percentage in colon cancer tissue. Based on the median levels of 5hmC detected by LCMS (Figure 2), only about 2.4% of 5mC reported in the Infinium data is likely to be undistinguishable from 5hmC in normal cells, and about 0.7% in tumours.

Methylation changes in our patient cohort showed both gain and loss of promoter DNA methylation (Figure 3a). To refine our analysis of 5hmC content to changes in DNA methylation at the promoters assessed by the Infinium platform, we counted the hmeDIP-seq reads from normals in 200 bp windows around the Infinium probes (Figure 3b). After ranking by read content we identified the top 3,000 5hmC enriched loci (5hmC-high) as well as 3,000 loci where 5hmC was low or undetected (5hmC-low). Interestingly, by this measurement of read counts around the Infinium probes, we observed that promoters with high 5hmC in normal are either resistant to methylation change or are prone to methylation loss (79% loss vs. 21% gain from 676 probes with significant change out of 3,000) and that 5hmC marked promoters more frequently associate with a range of intermediate levels of methylation in normal (Figure 3c left panel and d). 5hmC low promoters more frequently associated with low levels of methylation in normal and showed an increased propensity to methylation gain, albeit methylation loss was also observed (56% gain vs. 44% loss from 379 probes with significant change out of 3,000) (Figure 3c right panel and d). We also find that the methylation-prone genes that lack 5hmC in normal have a low level of expression in the normal tissue (Figure 3d, right panel), in agreement with a recent report where propensity to methylation gain in tumours is frequent at promoters of genes with low expression in the normal tissue [47].

Promoters marked by 5hmC in normal colon resist DNA methylation gain in tumours. (a) DNA methylation changes in adenocarcinoma (n = 17) relative to matched normal tissues (n = 17) (Infinium arrays). Each dot represents a CpG (grey dots are changes with P <0.01). (b) 5hmC read content measured in windows around the Infinium probes (black bars). CpG island (CpGi) as orange bar. (c) Overlay of 5hmC high or 5hmC low promoters on the methylation states. (d) Left panel: 5hmC content around the Infinium probes of promoters with a significant change in methylation. High 5hmC promoters are prone to loss of DNA methylation in tumours whereas low 5hmC promoters are prone to methylation gain in tumours (limma geneSetTest). Middle panel: 5hmC content in normal and levels of DNA methylation in normal to show that methylation gain or loss occurs across a range of methylation levels in normal (P values from a Wilcox test). Right panel: 5hmC content in normal and expression levels in normal. DNA methylation prone genes (5hmC low) have low expression in the normal tissue (P values from a Wilcox test). (e) Heatmap comparing 5hmC and 5mC levels in normal to the 5mC changes in tumours at selected loci.

Importantly, the reciprocal pattern of high/low 5hmC in normal with loss/gain of methylation in adenocarcinoma was already present at the adenoma stages (Additional file 8a and b) and observed at CpG islands and island shores (Additional file 8c). This reciprocal pattern was also present at previously identified colon cancer-specific small regions of differential DNA methylation (sDMRs) [8] (Additional file 8d) and clearly observed and verified in a number of colon cancer relevant gene promoters (Figure 3e and Additional file 9).

Together these results indicate that gene promoters marked with 5hmC in normal rarely become hypermethylated when 5hmC is reduced in tumours. Indeed these promoters have a tendency to lose DNA methylation in cancer. We also identified 117 promoters where 5hmC was still detected in adenocarcinomas, albeit at very low levels, and found that these where three times more likely to have lost methylation rather than gain (27% vs. 8.5%, respectively) (Additional file 10). These results may suggest that DNA demethylation at a subset of proximal promoters could be mediated via hydroxymethylation and/or that the presence of 5hmC helps to repel DNA methylating complexes as previously suggested [48,49].

There is strong evidence from cell labelling experiments that colon cancer can originate from the stem cell/progenitor compartment [50]. Our data, and that of others [21], showing that global 5hmC levels are low in the stem cell compartment and in cancer tissues may suggest that 5hmC is not lost in colon cancer. Rather, 5hmC may not accumulate due to an aberrant progenitor-like proliferative state. One explanation for why the loci that would accumulate 5hmC upon terminal differentiation are seemingly more resistant to gain of DNA methylation in cancer, in contrast with loci that do not accumulate 5hmC, could be that the TETs in cancer cells are bound to their target promoters to prevent de novo DNA methylation.

TET2 marks promoters in cancer cells that resist DNA methylation gain in primary tumours but is not required to maintain a demethylated state

In order to examine whether TETs are bound to DNA in cancer cells we turned to the colorectal cancer cell line HCT116. This cell line shows low global levels of 5hmC and TET2 and TET3 transcript levels comparable to that observed in normal and adenocarcinoma tissue (Additional file 11a to c). Despite the extremely low global content of 5hmC in these cells, lower than that seen in the primary tissues, TET2 and TET3 proteins can be detected in the nuclear fraction (Additional file 11d) albeit a sizeable amount of TET2 is present in the cytoplasm (Additional file 11d and e). A similar subcellular distribution of TET2 is observed in normal colon crypts and tumours by immunohistochemistry (Additional file 12).

Chromatin immunoprecipitation sequencing (ChIP-seq) revealed that TET2 preferentially binds to gene promoters within 1 kb of the TSS (Figure 4a and b). Overall 3,144 promoters were identified as TET2 targets (Additional file 1) of which the large majority were CpG island-containing promoters of the HCP type (Figure 4c and d). CpG islands bound by TET2 were largely unmethylated as measured by Infinium450k arrays (from GSE29290) and CpG island shores showed lower methylation levels at the TET2 bound sites relative to those not bound by TET2 (Figure 4e). We validated a number of loci identified in the TET2 ChIP-seq by ChIP-qPCR (Additional file 13). Interestingly, presence of TET2 associated with active genes measured by expression arrays (GSE36133) or evidenced by a considerable overlap with RNA Pol2 binding sites (ENCODE Pol2 ChIP-seq) (Figure 4f and g).

TET2 binds promoters of active genes in cancer cells. (a) Example of TET2 binding profile in HCT116 colorectal cancer cells. (b) TET2 binds close to TSSs and (c, d) primarily at CpG islands within HCP promoters. (e) TET2 bound islands are largely unmethylated and (f, g) associate with active genes.

If the TETs bind to DNA and protect against hypermethylation in tumours, then it would be expected that promoters susceptible to DNA methylation gain in colon tumours would form a distinct group with a minimal overlap with TET target promoters. We therefore examined whether loci that gained DNA methylation in our primary tumours (1,597 probes for 1,077 promoters) were likely TET2 target promoters (4,201 probes for 3,144 promoters). This analysis showed less than 1% overlap between loci that gain DNA methylation in tumours and the TET2 bound promoters (Figure 5a). These results could suggest that TET2 might be part of a mechanism that protects promoters from de novo DNA methylation. To examine this we depleted TET2 in HCT116 cells by stable transfection of shRNAs (Figure 5b and c). In one instance we used shRNA against TET2 alone (TET2C) and in the other shRNA against TET2 and TET3 (TET2 + 3 where TET3 mRNA was not affected and therefore treat this sample as a TET2 only knockdown) (Figure 5c). LCMS after TET2 depletion showed a marked reduction in the global level of 5hmC (Figure 5d), confirming TET2 oxygenase activity in HCT116, without changes in global levels of 5mC (Figure 5d) but this could be due to the small contribution of promoter methylation to the methylome. Infinium arrays identified several loci with changes in DNA methylation (Figure 5e) that were for the most part low in magnitude (median of change was 10.4% not shown). Similar changes in levels of DNA methylation were recently observed after TET1 depletion in differentiated cells [51]. However in our study, methylation levels at TET2 bound CpG islands were largely unaffected after TET2 depletion (less than 1%, Figure 5e), suggesting that these promoters do not require high levels of TET2 to maintain the methylation free state and are intrinsically resistant to methylation changes.

Pervasive maintenance of a methylation-free state at TET2 bound promoters. (a) DNA methylation gain in primary tumours was remarkably scarce at the TET2 bound promoters identified in HCT116 cells (P <0.0001, binomial test). (b) Western blot for TET2 and beta TUBULIN from whole cell extracts of HCT116 cells stably transfected with a non-targeting shRNA control (shCtrl.) or with shRNA to TET2 (TET2C) or to TET2 and TET3 (TET2 + 3). Fold change in the knockdown was calculated relative to the shCtrl. (c) qRT-PCR for TET2 and TET3. (d) Global levels of 5hmC and 5mC by LCMS. (e) DNA methylation changes by Infinium arrays after depletion of TET2.

Survival outcomes estimated from publicly available colorectal cancer datasets [52,53] further indicate that TET2 expression levels do not significantly associate with patient survival, which is consistent with the small effect that we see in these in vitro TET2 studies. TET2 therefore seems to play a moderate role in controlling cytosine modifications during gut tumourigenesis.

Promoters with high levels of 5hmC in normal colon overlap with bivalently marked promoters in human embryonic stem cells that do not become methylated in colon cancer

If tumours arise from intestinal cells in the crypt and if 5hmC is a mark of terminally differentiated cells, then how do we explain the resistance of 5hmC promoters to methylation gain in tumours prior to their accumulating 5hmC in normal tissue? TET2 depletion only has a moderate effect on DNA methylation in cancer cells, suggesting that the protective mechanism is unlikely to be due to continuous TET2 binding at target promoters. Although TET2 may not be involved in maintaining the unmethylated state of its target promoters, we cannot exclude that other proteins within a TET-complex may be involved. However there may be alternative explanations, one of which is that 5hmC promoters are epigenetically marked during early development to make them intrinsically unlikely to develop characteristics such as H3K27me3 in the soma that predispose to DNA methylation gain.

Precedents for early epigenetic marking include genomic imprinting and X-inactivation, but may also include the recently described instructive process for gain of methylation in cancer which occurs at promoters containing histone H3K4 and H3K27 tri-methylation (so-called bivalent promoters) in human embryonic stem cells (hESC) [54-58]. ESCs unlike most other proliferating cells already have high levels of 5hmC. In mouse ESCs Tet1 is found either at the TSS of bivalent promoters together with silencing complexes independent of 5hmC or downstream of the TSS together with 5hmC and the PRC2 complex [59,60]. In human ESC 5hmC has been found more at active gene promoters and enhancers than at poised (bivalent) enhancers [61].

A comparison of our dataset of 5hmC marked promoters to a published dataset of hESC bivalent promoters [57] confirmed that approximately 65% of promoters that gain methylation in our colon cancer cohort are also bivalently marked in hESC (Figure 6a and b). Consequently we also examined the extent to which promoters marked by 5hmC in normal colon overlap with bivalently marked promoters in hESCs. We found that 30% of all 5hmC promoters overlapped with bivalent genes in hESCs (Figure 6a and b). Interestingly, these mostly coincided with bivalent promoters that do not become hypermethylated in colorectal cancer. This observation indicates that bivalent promoters can be broadly separated into discrete instructive categories: one for silencing after tissue differentiation and susceptible to methylation gain in cancer and another for poised activation and acquisition of 5hmC with resistance to methylation gain in cancer. If 5hmC is acquired as an end point of instructive activation, this would fit with our data where we see 5hmC accumulating in terminally differentiated cells at genes that are active in both cancer and normal tissue.

5hmC marked promoters are not subject to histone-bivalency-mediated methylation gain. Venn diagrams to illustrate a high incidence of promoter methylation gain in our cohort at promoters with H3K4me3/K27me3 bivalency in human embryonic stem cells (hESCbiv). The incidence of methylation gain is low at hESCbiv promoters marked by 5hmC in normal colon. (a) For narrow and (b) broad 5hmC promoters.


Pancreas

Intestinal glands

These are formed by modification of surface epithelium of small intestine. The two main intestinal glands are Brunner’s gland and Crypts of Lieberkühn.

  1. Brunner’s glands are found only in first few centimetres of duodenum. They secrete large amount of alkaline mucus to protect the duodenal wall from highly acidic gastric juice and to neutralize hydrochloric acid.
  2. Crypt of Lieberkühns are small pits located all over the entire surface of the small intestine, lies between the intestinal villi. They are covered by epithelium composed of two types of cells. 1) Goblet cells: secrete mucus. 2) Enterocytes: secrete water and electrolyte, also reabsorb the water and electrolyte along with the end product of digestion over the surface of adjacent villi. At the base of these crypts, panethcells and argentaffin cells are present. Paneth cells found mainly in duodenum are rich in zinc and contain acidophilic granules. Argentaffin cells synthesize secretin hormone and 5-hydroxytryptamine.

EnzymeSubstrateSite of action
Ptyalin (salivary amylase) Starch Mouth
Pepsin
Gastric Lipase
Renin
Proteins
Little amount of fats
Casein
Stomach
Child’s stomach
Pancreatic amylase
Trypsin
Chymotrypsin
Elastase
Carboxypeptidase
Pancreatic lipase
Nuclease
Enterokinase
Aminopeptidase
Dipeptidase
Disaccharidase
Intestinal lipase
Nucleotidase
Nucleosidase
Starch
Proteins
Proteins
Protein (Elastin)
Large peptides
Fats (Triglycerides)
Nucleic acids (DNA, RNA)
Trypsinogen
Large peptides
Dipeptides
Disaccharide
Fats
Nucleotide
Nucleoside
Small Intestine


Author information

Affiliations

Department of Medicine, Infectious Diseases Service, Memorial Sloan Kettering Cancer Center, New York, 10065, New York, USA

Charlie G. Buffie, Peter T. McKenney, Melissa Kinnebrew, Ying Taur & Eric G. Pamer

Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, 10065, New York, USA

Charlie G. Buffie, Peter T. McKenney, Lilan Ling, Asia Gobourne, Daniel No, Melissa Kinnebrew, Eric Littmann, Ying Taur, Nora C. Toussaint, Joao B. Xavier & Eric G. Pamer

Computational Biology Program, Sloan-Kettering Institute, New York, 10065, New York, USA

Vanni Bucci, Richard R. Stein, Chris Sander, Nora C. Toussaint & Joao B. Xavier

Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, 02747, Massachusetts, USA

Donald B. and Catherine C. Marron Cancer Metabolism Center, Sloan-Kettering Institute, New York, 10065, New York, USA

Genomics Core Laboratory, Sloan-Kettering Institute, New York, 10065, New York, USA

Department of Medicine, Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, 10065, New York, USA

Marcel R. M. van den Brink & Robert R. Jenq

Immunology Program, Sloan-Kettering Institute, New York, 10065, New York, USA

Marcel R. M. van den Brink & Eric G. Pamer

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Contributions

C.G.B. and E.G.P. designed the experiments and wrote the manuscript with input from co-authors. C.G.B. performed animal experiments and most analyses. V.B., R.R.S., J.B.X., C.S. and C.G.B. performed microbiota time-series inference modelling and analysis. P.T.M. and C.G.B designed and performed ex vivo experiments. L.L., A.G., A.V. D.N. and M.K. performed 16S amplicon quantification and multiparallel sequencing (454, MiSeq) and contributed to data analysis. M.R.M.v.d.B., R.R.J., Y.T., E.L., C.G.B. and E.G.P. assessed clinical parameters and supervised patient cohort analysis. N.C.T. and C.G.B. performed metagenomic shotgun sequencing analysis. J.R.C. and H.L. developed the metabolomics analysis platform and performed quantification of bile acid species.

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Immunohistochemistry and Colon Cancer

Immunohistochemical applications surrounding colon cancer are seen at several levels such as: characterization of the tumor (endocrine or epithelial type), hereditary disposition, and for prognostic purposes (MSI testing). MSI testing has been discussed previously and thus will not be discussed, in detail, here other than to say that the Bethesda protocol is rapidly gaining acceptance regarding this testing. The more prevalent use of IHC is in the presence of possible or suspected metastatic disease in which the colon is a possible primary. The common locations for metastases from colon cancers are the liver and lung both organs of which can produce cancer morphology essentially identical to metastases from the colon.


Scientists uncover how high-fat diet drives colorectal cancer growth

As cancer death rates drop overall, doctors have noted a frightening anomaly: deaths from colorectal cancer in people under 55 appear to be creeping up. According to the American Cancer Society, deaths in this younger group increased by 1 percent between 2007 and 2016.

A new study led by Salk Institute scientists suggests that high-fat diets fuel colorectal cancer growth by upsetting the balance of bile acids in the intestine and triggering a hormonal signal that lets potentially cancerous cells thrive. The findings, which appeared in Cell on February 21, 2019, could explain why colorectal cancer, which can take decades to develop, is being seen in younger people growing up at a time when higher-fat diets are common.

"This study provides a new way to lower inflammation, restore intestinal health and to dramatically reduced tumor progression," says Professor Ronald Evans, director of the Gene Expression Laboratory, Howard Hughes Medical Institute investigator and holder of Salk's March of Dimes Chair in Molecular and Developmental Biology.

The research, conducted in a mouse model, suggests how lifestyle and genetics converge. The researchers found that animals with an APC mutation, the most common genetic mutation found in humans with colorectal cancer, developed cancer faster when fed a high-fat diet.

"It could be that when you're genetically prone to get colon cancer, something like a high-fat diet is the second hit," says study co-author Ruth Yu, a staff researcher in the Gene Expression Laboratory at Salk.

The intestine and colon (commonly lumped together as the "gut") are hard-working organs. As you eat, your gut needs to constantly regenerate its lining to undo the damage done by digestive acids. To do this, the gut houses a population of stem cells that can replenish lining cells when needed.

Scientists have found that colorectal cancers often originate from mutations in these stem cells. The most common colorectal cancer-linked mutation is in a gene called APC, which normally acts as a "tumor suppressor" gene because it controls how often cells divide. Mutations in the APC gene can remove that control and allow cells to divide rapidly and become cancerous.

Over the last four decades, Evans and his colleagues have investigated the roles of bile acids. (30 types of bile acids float around in the gut to help digest food and absorb cholesterol, fats and fat-soluble nutrients.) Among the lab's discoveries was the revelation that bile acids send hormonal signals to intestinal stem cells through a protein called the Farnesoid X receptor (FXR). For the new study, the researchers uncovered how high-fat diets affect that hormonal signaling.

Study first author Ting Fu, a postdoctoral fellow at Salk, began by following a clue in a mouse model with an APC mutation. These mice develop early signs of colorectal cancer, so she decided to monitor bile acid levels in the mice at the same time. She discovered that types of bile acids known to interact with FXR increased at the same time as cancer initiation -- and that the presence of additional bile acids accelerated cancer progression.

"We saw a very dramatic increase in cancer growth correlated to bile acid," says Michael Downes, a senior staff scientist at Salk and co-corresponding author of the study. "Our experiments showed that maintaining a balance of bile acids is key to reducing cancer growth."

The researchers showed that feeding these mice a high-fat diet was like adding fuel to a fire: high-fat diets increased levels of two specific bile acids that dampen the activity of FXR. The gut wants to repair itself, and FXR keeps the process slow, steady and safe. When bile acids inhibit FXR, a group of stem cells starts growing rapidly and accumulating DNA damage.

"We knew that high-fat diets and bile acids were both risk factors for cancer, but we weren't expecting to find they were both affecting FXR in intestinal stem cells," says Annette Atkins, a staff researcher at Salk and co-author of the study.

The mice with APC mutations developed benign growths called adenomas. In humans, adenomas are common in the intestine and are routinely removed during colonoscopies. These growths normally take decades to turn into malignant adenocarcinomas. Yet the adenomas in these mice quickly turned cancerous when given high-fat diets.

At last, the researchers had found a possible cellular mechanism to explain the rise in colorectal cancer deaths in younger people. Their theory is that as high-fat diets have become more common in the United States, more people with an APC mutation are accelerating their cancer growth through these diets.

Next, the researchers decided to test a new cancer-fighting weapon. They used a molecule called FexD, developed at Salk, to activate FXR in intestinal stem cells. FexD appeared to counteract the damage done by unbalanced bile acids in both mouse organ models and human colon cancer cell lines.

While more experiments need to be done before FexD is tested in humans, the team says the drug candidate has some promising qualities: it can reach the colon and it only acts on FXR, so it should produce fewer side effects than other drugs.

"While colon cancer is considered 'incurable,' Ting's work opens up an entirely new frontier in the understanding and treatment of the disease," says Evans.


Gastrointestinal Microbiology in the Normal Host

Molecular Studies of the Microflora of the Colon

Molecular studies of colonic flora give a better picture of the true flora than cultural studies. Molecular identification of isolates also gives greater accuracy and speed than phenotypic identification. Both types of studies, used together, give more accurate identification of certain taxa and studies of additional genes (beyond 16S rDNA) are needed for certain organisms (viz., streptococci and staphylococci). Various molecular approaches to the study of the colonic microflora have been used. Included are denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis when these approaches are combined with cloning and sequencing, the results are improved. Group-specific primers have been used for detection and identification of predominant groups of bacteria in feces. This approach, combined with FISH, is effective but only small portions of the total bacteria have been detected in some fecal samples in some studies. The study of emergent bowel resection, mentioned above in the section on ileal flora, found that there were no significant differences in overall numbers of bacteria in different parts of the colon. Real-time PCR showed that bifidobacteria counts were significantly higher in the large bowel than in the terminal ileum, Eubacterium rectale and F. prausnitzii were dominant in the ascending and descending colons, and lactobacilli were more prominent in the distal large bowel. Benno’s group has had good results with T-RFLP studies of bowel flora, using a data base that they have developed for this purpose. The use of group-specific probes with real-time PCR is a very good technique which provides a good snapshot of the bowel flora with quantitation if one uses an extensive set of appropriate primer-probes. This approach has been used to compare the microbiota of different groups of individuals such as infants and elderly people with the general population. Detection limits with real-time PCR are as low as 10 1 or fewer organisms of a particular phylotype per sample. With the newly available real-time PCR equipment, extremely high throughput is now available included are trays with 384 wells so that if one develops all the appropriate primer-probes, it is now feasible to study a large number of individual genera and/or species rather than groups or clusters of organisms. DNA microarray analysis cannot be used effectively by most smaller laboratories unless reliable commercially available kits are available but one study showed good results with a microarray of 40 species commonly encountered in the gut. A problem with several of these techniques such as FISH, real-time PCR, and microarrays is that one can only find the organisms or groups that one has specific primer-probes for and there is still a considerable portion of the bowel flora that remains uncharacterized.

A tedious and time-consuming study of clone libraries, and one not suitable for high throughput at this time, is nonetheless an excellent procedure for detailed analysis of colonic or other diverse and complicated microfloras. Newly available pyrosequencing machines, when fully developed, will greatly assist in this type of analysis. The clone library approach has been used effectively by a number of investigators and has provided outstanding data from the study of small numbers of individuals. For this procedure, DNA is recovered from the sample to be studied, it is enriched and amplified for the 16S rDNA using broad-range primers, and then the PCR products are cloned into Escherichia coli by established procedures. The 16S rDNA nucleotide sequences of the clone inserts are determined by cycle sequencing and trimmed to remove vector sequence, chimeras, and sequences of poor quality. Sequences are grouped into phylotypes so that the least similar pair within the phylotype has 99% similarity (some use 98% as the cutoff). In an elegant study of the diversity of the human intestinal flora, both fecal samples and mucosal biopsies from six different colonic sites were obtained from three healthy adults. In all, these workers performed phylogenetic analyses on a total of 11 831 bacterial and 1524 archaeal near-full-length 16S rDNA sequences ( Figures 2 and 3 ). From this, they identified 395 bacterial phylotypes and a single archaeal phylotype (Methanobrevibacter smithii). Most of the bacteria were members of the Firmicutes and Bacteroidetes phyla. Within the Firmicutes phylum, there were 301 phylotypes, 191 of which were novel 95% of the Firmicutes sequences were members of the class Clostridia. Known butyrate-producing bacteria represented 2454 sequences and 42 phylotypes, all belonging to clostridial clusters IV, XIVa, and XVI. There were 65 Bacteroidetes phylotypes, with large variations between the three study subjects. Bacteroides thetaiotaomicron was present in all three individuals. Relatively few sequences were associated with the Proteobacteria, Actinobacteria, Fusobacteria, and Verrucomicrobia phyla. Both the observed and estimated richness of the flora increased in parallel fashion with additional sampling the authors estimate that one unique phylotype would be expected for every 100 additional clones sequenced ( Figure 4 ). There was relatively little variability between the six mucosal sites studied. The greatest amount of variability overall was related to differences between the three subjects whose specimens were analyzed ( Figure 5 ) with the next greatest variability related to differences between feces and mucosal analyses. Overall, a majority of the bacterial sequences encountered belonged to uncultivated species and novel bacteria. The authors of this study point out that the limited sensitivity of broad-range PCR may hinder detection of rare phylotypes and that their methods did not distinguish between living and dead microorganisms. Studies by various groups proceeded beyond the above approach to analyze the metagenomics (metabolic function analysis) of the bowel flora.

Figure 2 . Phylogenetic tree based on the combined human intestinal 16S rDNA sequence data set. The label for each clade includes, in order, the total number of recovered sequences, phylotypes, and novel phylotypes (in parentheses). The angle where each triangle joins the tree represents the relative abundance of sequences, and the lengths of the two adjacent sides indicate the range of branching depths within that clade. Six of the seven phyla represented by sequences recovered in this study are shown in red the unclassified clade near cyanobacteria is not pictured in the inset. Reproduced with permission from Eckburg PB, Bik EM, Bernstein CN, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635–1638.

Figure 3 . Relative abundance of sequences from stool and pooled mucosal samples per subject. The sequence frequencies are grouped according to phylum, colored according to Figure 2 . ‘Other’ represents the fusobacteria, actinobacteria, and unclassified near cyanobacteria phyla, each containing less than 0.2% of the total sequences. ‘M’ denotes pooled mucosal sequences per subject and ‘S’ refers to stool sample. Reproduced with permission from Eckburg PB, Bik EM, Bernstein CN, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635–1638.

Figure 4 . Individual-based rarefaction curves for combined sequences at multiple operational taxonomic unit (OTU) cutoff levels. The slopes of the curves decrease as the OTU definitions relax toward 95%. The curves seem to plateau at OTU cutoffs 90% for example, at the 90% cutoff, the last 430 clones sampled do not change the final richness value of 90 phylotypes. Every clone sampled has been seen more than once at the 83% OTU cutoff. The total numbers of OTUs per definition are listed in the inset, as calculated by dissimilarity matrices and DOTUR. Reproduced with permission from Eckburg PB, Bik EM, Bernstein CN, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635–1638.

Figure 5 . Individual-based rarefaction curves for sequences from each anatomic site per subject. Phylotypes were defined using the 99% operational taxonomic unit (OTU) cutoff. Reproduced with permission from Eckburg PB, Bik EM, Bernstein CN, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635–1638.

One group recently proposed a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups they used direct comparisons of microbial communities from the human GI tract in an absolute evolutionary coordinate space.


Best Foods for Colon Cancer Prevention

A low-fiber diet is a key driver of microbiome depletion, the disappearance of diversity in our good gut flora.

Transcript

Below is an approximation of this video’s audio content. To see any graphs, charts, graphics, images, and quotes to which Dr. Greger may be referring, watch the above video.

We have � trillion micro-organisms” residing in our gut, give or take a few trillion, but “the spread of the Western lifestyle has been accompanied by microbial changes,” which may be contributing to our epidemics of chronic disease. The problem is that we’re eating these meat-sweet diets, characterized by “a high intake of animal products and sugars, [processed foods], and a low intake of [whole plant foods].”

Contrary to the fermentation of the carbohydrates that make it down to our colon—the fiber and resistant starch that benefit us “through the generation of [these magical] short-chain fatty acids” like butyrate—”microbial protein fermentation [when excess protein is consumed…that] generates potentially toxic and pro-carcinogenic metabolites involved in [colorectal cancer].” And so, what we eat can cause an imbalance in our gut microbiome, and potentially create “a ‘recipe’ for colorectal cancer,” where a high-fat, high-meat, high-processed food diet tips the scale towards dysbiosis and colorectal cancer, whereas a high-fiber and -starch, lower-meat diet can pull you back into symbiosis with your friendly flora, and away from cancer.

We now have evidence from interventional studies suggesting that “adopting a plant-based, minimally processed high-fiber diet may rapidly reverse the effects of meat-based diets on the gut microbiome.” So, what may be “a new form of personalised…microbiome…medicine for chronic disease”? It’s called food, which can “rapidly and reproducibly alter…the human gut microbiome.” Switch people between a whole food plant-based diet and more of an animal food-based diet, and you can see dramatic shifts within two days, which can result in toxic metabolites. Switch people to an animal food-based diet, and levels of deoxycholic acid go up, which is “a secondary bile acid known to promote DNA damage” and liver cancers. Why do levels go up? Because the bad bacteria producing the stuff triple—in just two days.

And, over time, the richness of the microbial diversity in our gut is disappearing. Here’s our bacterial tree of life that’s getting depleted. Why is this happening? The “fiber gap.” “A low-fiber diet is a key driver of microbiome depletion.” Yeah, there’s antibiotics, and Caesarean sections, and indoor plumbing, but “the only factor that has been empirically demonstrated to be important is a diet low in…MACs’ (not Big Macs), “microbiota-accessible carbohydrates,” which is just a fancy name for fiber found in a whole plant foods and resistant starch, found mostly in beans, peas, lentils, and whole grains.

Our “intake of dietary fiber,” our intake of whole plant foods, “is negligibly low in the Western world” when compared to what we evolved to eat over millions of years. “Such a low-fiber diet provides insufficient nutrients for [our] gut microbes, leading not only to the loss of [bacterial diversity and richness], but also to a reduction in the production of [those beneficial] fermentation end products…” that they make with the fiber. We are, in effect, “starving our microbial self.”

What are we going to do about “the deleterious consequences of a diet deficient in” whole plant foods? Create new-fangled “functional foods,” of course, and supplements, and drugs—prebiotics, probiotics, synbiotics. Think how much money there is to be made! Or, we could just eat the way our bodies were meant to eat. What kind of value is that going to get your stockholders, though? Don’t you know probiotic pills may be “the next big source” of Big Pharma billions?

Why eat healthy though, when you can just have someone else eat healthy for you, and then get a fecal transplant from a vegan! Researchers compared the microbiomes of vegans versus omnivores, and found the vegan’s friendly flora were churning out more of the good stuff, showing that a plant-based diet may result in more beneficial metabolites in the bloodstream and less of the bad stuff like TMAO. But while the impact of a vegan diet on what the bacteria were making was “large,” the “effect on the composition of the gut microbiome [was] surprisingly modest.” They “only [found] slight differences between the gut microbiomes of omnivores [versus] vegans”? That was a shocker to the researchers this “very modest difference…juxtaposed against the significantly enhanced dietary consumption of fermentable plant-based foods.” The vegans were eating nearly twice the fiber. Anyone see the problem here? The vegans just barely made the minimum daily intake of fiber. Why? Because Oreos are vegan, Cocoa Pebbles are vegan, french fries, Coke, potato chips there are vegan Doritos and Pop-Tarts. You can eat a terrible vegan diet.

Burkitt showed that you need to get at least 50 grams a day (of fiber) for colon cancer prevention. And that’s only half of what our bodies were designed to get. We evolved getting about 100 grams a day. And that’s what you see in modern populations that are immune to epidemic colorectal cancer. So, what if instead of feeding people a vegan diet, you just fed people that kind of diet, a diet centered around whole plant foods? We’ll find out, next.

Please consider volunteering to help out on the site.

Sources

  • Gagnière J, Raisch J, Veziant J, et al. Gut microbiota imbalance and colorectal cancer. World J Gastroenterol. 201622(2):501-18.
  • Derrien M, Veiga P. Rethinking Diet to Aid Human-Microbe Symbiosis. Trends Microbiol. 201725(2):100-112.
  • Vipperla K, O'keefe SJ. Diet, microbiota, and dysbiosis: a 'recipe' for colorectal cancer. Food Funct. 20167(4):1731-40.
  • Pallister T, Spector TD. Food: a new form of personalised (gut microbiome) medicine for chronic diseases?. J R Soc Med. 2016109(9):331-6.
  • David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014505(7484):559-63.
  • Segata N. Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity. Curr Biol. 201525(14):R611-3.
  • O'Keefe SJ, Li JV, Lahti L, et al. Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun. 20156:6342.
  • Deehan EC, Walter J. The Fiber Gap and the Disappearing Gut Microbiome: Implications for Human Nutrition. Trends Endocrinol Metab. 201627(5):239-242.
  • Sonnenburg ED, Sonnenburg JL. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab. 201420(5):779-786.
  • Arkan MC. The intricate connection between diet, microbiota, and cancer: A jigsaw puzzle. Semin Immunol. 201732:35-42.
  • Wu GD, Compher C, Chen EZ, et al. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut. 201665(1):63-72.
  • Jew S, Abumweis SS, Jones PJ. Evolution of the human diet: linking our ancestral diet to modern functional foods as a means of chronic disease prevention. J Med Food. 200912(5):925-34.

Acknowledgements

Image credit: Kristina DeMuth. Image has been modified.

Topics

Below is an approximation of this video’s audio content. To see any graphs, charts, graphics, images, and quotes to which Dr. Greger may be referring, watch the above video.

We have � trillion micro-organisms” residing in our gut, give or take a few trillion, but “the spread of the Western lifestyle has been accompanied by microbial changes,” which may be contributing to our epidemics of chronic disease. The problem is that we’re eating these meat-sweet diets, characterized by “a high intake of animal products and sugars, [processed foods], and a low intake of [whole plant foods].”

Contrary to the fermentation of the carbohydrates that make it down to our colon—the fiber and resistant starch that benefit us “through the generation of [these magical] short-chain fatty acids” like butyrate—”microbial protein fermentation [when excess protein is consumed…that] generates potentially toxic and pro-carcinogenic metabolites involved in [colorectal cancer].” And so, what we eat can cause an imbalance in our gut microbiome, and potentially create “a ‘recipe’ for colorectal cancer,” where a high-fat, high-meat, high-processed food diet tips the scale towards dysbiosis and colorectal cancer, whereas a high-fiber and -starch, lower-meat diet can pull you back into symbiosis with your friendly flora, and away from cancer.

We now have evidence from interventional studies suggesting that “adopting a plant-based, minimally processed high-fiber diet may rapidly reverse the effects of meat-based diets on the gut microbiome.” So, what may be “a new form of personalised…microbiome…medicine for chronic disease”? It’s called food, which can “rapidly and reproducibly alter…the human gut microbiome.” Switch people between a whole food plant-based diet and more of an animal food-based diet, and you can see dramatic shifts within two days, which can result in toxic metabolites. Switch people to an animal food-based diet, and levels of deoxycholic acid go up, which is “a secondary bile acid known to promote DNA damage” and liver cancers. Why do levels go up? Because the bad bacteria producing the stuff triple—in just two days.

And, over time, the richness of the microbial diversity in our gut is disappearing. Here’s our bacterial tree of life that’s getting depleted. Why is this happening? The “fiber gap.” “A low-fiber diet is a key driver of microbiome depletion.” Yeah, there’s antibiotics, and Caesarean sections, and indoor plumbing, but “the only factor that has been empirically demonstrated to be important is a diet low in…MACs’ (not Big Macs), “microbiota-accessible carbohydrates,” which is just a fancy name for fiber found in a whole plant foods and resistant starch, found mostly in beans, peas, lentils, and whole grains.

Our “intake of dietary fiber,” our intake of whole plant foods, “is negligibly low in the Western world” when compared to what we evolved to eat over millions of years. “Such a low-fiber diet provides insufficient nutrients for [our] gut microbes, leading not only to the loss of [bacterial diversity and richness], but also to a reduction in the production of [those beneficial] fermentation end products…” that they make with the fiber. We are, in effect, “starving our microbial self.”

What are we going to do about “the deleterious consequences of a diet deficient in” whole plant foods? Create new-fangled “functional foods,” of course, and supplements, and drugs—prebiotics, probiotics, synbiotics. Think how much money there is to be made! Or, we could just eat the way our bodies were meant to eat. What kind of value is that going to get your stockholders, though? Don’t you know probiotic pills may be “the next big source” of Big Pharma billions?

Why eat healthy though, when you can just have someone else eat healthy for you, and then get a fecal transplant from a vegan! Researchers compared the microbiomes of vegans versus omnivores, and found the vegan’s friendly flora were churning out more of the good stuff, showing that a plant-based diet may result in more beneficial metabolites in the bloodstream and less of the bad stuff like TMAO. But while the impact of a vegan diet on what the bacteria were making was “large,” the “effect on the composition of the gut microbiome [was] surprisingly modest.” They “only [found] slight differences between the gut microbiomes of omnivores [versus] vegans”? That was a shocker to the researchers this “very modest difference…juxtaposed against the significantly enhanced dietary consumption of fermentable plant-based foods.” The vegans were eating nearly twice the fiber. Anyone see the problem here? The vegans just barely made the minimum daily intake of fiber. Why? Because Oreos are vegan, Cocoa Pebbles are vegan, french fries, Coke, potato chips there are vegan Doritos and Pop-Tarts. You can eat a terrible vegan diet.

Burkitt showed that you need to get at least 50 grams a day (of fiber) for colon cancer prevention. And that’s only half of what our bodies were designed to get. We evolved getting about 100 grams a day. And that’s what you see in modern populations that are immune to epidemic colorectal cancer. So, what if instead of feeding people a vegan diet, you just fed people that kind of diet, a diet centered around whole plant foods? We’ll find out, next.


Watch the video: Αλεξίου Γεώργιος - Χολολιθίαση (October 2022).