Analysis of the intestinal lumen microbiota in an animal model of colorectal cancer

Gut microbiota and fatigue in rectal cancer patients: a cross-sectional pilot study

CONTEXT

Although microbial-mediated disturbance of intestinal mucosal homeostasis (dysbiosis) is believed to contribute to the pathogenesis of chemotherapy and radiotherapy (CRT)-related fatigue, potential differences in the gut microbial diversity and in the abundance of gut microbial taxa between fatigued and non-fatigued patients have not been adequately examined, particularly in the rectal cancer population.

PURPOSE

In this cross-sectional study, we aim to examine the differences in (a) gut microbial diversity and gut microbial abundances and (b) predicted functional pathways of the gut microbiome between rectal cancer participants with and without fatigue at the end of CRT.

METHODS

Rectal cancer patients (n = 50) provided stool samples for 16S rRNA gene sequencing and symptom ratings for fatigue at the end of CRT. Gut microbiome data were analyzed using QIIME2, LEfSe, and the R statistical package.

RESULTS

Fatigued (n = 35) participants showed enriched bacterial abundances of Eubacterium, Streptococcus, Adlercreutzia, and Actinomyces, as well as enriched abundances of the microbial sucrose degradation pathway, compared to non-fatigued patients at the end of CRT (n = 15).

CONCLUSIONS

Differentially abundant microbial taxa were identified in fatigued and non-fatigued rectal cancer participants at the end of CRT. However, the exact role of these taxa (and identification of species) in the biology of CRT-related fatigue remains to be examined.

Tostes M, Costa NM. The Potential Prebiotic Effects of Yacon (Smallanthus sonchifolius) in Colorectal Cancer

Background:

Colorectal cancer is caused by genetic predisposition and lifestyle risk factors and is associated with altered homeostasis of the intestinal microbiota. Evidence suggests that chronic infection and inflammation contribute to carcinogenic mutagenesis and promote cancer initiation and progression. Food components with prebiotic properties, such as fructooligosaccharides (FOS), promote intestinal integrity and health benefits. Yacon (Smallanthus sonchifolius) is an abundant source of FOS, which are fermented by beneficial bacteria, improving the intestinal environment affected by colorectal cancer.

Objective:

In the current review, the aim was to discuss colorectal cancer and its inflammatory process of development. Also, some general aspects concerning yacon roots and its prebiotic properties are described. Finely, the beneficial effects of yacon to reduce intestinal parameters altered due to colorectal cancer are summarized.

Conclusion:

It was verified that yacon might improve immunological parameters, intestinal barrier, intestinal microbiota, and inflammation in induced colorectal cancer in animals, especially. Researches with humans must be further investigated to prove these positive effects.

Gegen Qinlian decoction enhances immunity and protects intestinal barrier function in colorectal cancer patients via gut microbiota

BACKGROUND

We previously showed, using the Traditional Chinese Medicine System Pharmacology Database, that Gegen Qinlian decoction (GQD) had a direct antitumor effect, and was combined with programmed cell death protein (PD)-1 inhibitors to treat microsatellite stable (MSS) tumor-bearing mice. However, the effect of GQD on patients with colorectal cancer (CRC) is not clear.

AIM

To determine the therapeutic mechanism of GQD in improving immune function, reducing inflammation and protecting intestinal barrier function.

METHODS

Seventy patients with CRC were included in this study: 37 in the control group and 33 in the treatment group. The proportions of CD4⁺ T, CD8⁺ T, natural killer (NK), NKT and T regulatory cells were measured by flow cytometry. Levels of the cytokines tumor necrosis factor (TNF)-α, interferon (IFN)-γ, interleukin (IL)-2, IL-6, IL-10 and serotonin (5-hydroxytryptamine; 5-HT) in serum were assessed by enzyme-linked immunosorbent assay (ELISA). The expression of zonula occludens (ZO)-1, occludin, nuclear factor (NF)-κB and TNF-α in tumor and normal tissues was measured by immunohistochemistry. The composition of gut microbiota from patients in the treatment group was assessed using 16S rDNA analysis.

RESULTS

There were no adverse events in the treatment group. The proportion of CD4⁺ T cells and NKT cells in the post-treatment group was significantly higher than that in the pre-treatment and control groups (P < 0.05). The level of TNF-α in the post-treatment group was significantly lower than that in the pre-treatment and control groups (P < 0.05). The concentration of 5-HT in the post-treatment group was significantly lower than that in the pre-treatment group (P < 0.05). The expression of ZO-1 and occludin in tumor tissues in the treatment group was significantly higher than that in the control group (P < 0.05). The expression of ZO-1 in normal tissues of the treatment group was significantly higher than that in the control group (P = 0.010). Compared with the control group, expression of NF-κB and TNF-α in tumor tissues of the treatment group was significantly decreased (P < 0.05). Compared with the pre-treatment group, GQD decreased the relative abundance of Megamonas and Veillonella. In addition, GQD increased the relative abundance of Bacteroides, Akkermansia and Prevotella.

CONCLUSION

GQD enhances immunity and protects intestinal barrier function in patients with CRC by regulating the composition of gut microbiota.

Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota

Numerous host extrinsic and intrinsic factors affect the gut microbiota composition, but their cumulative effects do not sufficiently explain the variation in the microbiota, suggesting contributions of missing factors. The Japanese population possesses homogeneous genetic features suitable for genome-wide association study (GWAS). Here, we performed GWASs for human gut microbiota using 1068 healthy Japanese adults. To precisely evaluate genetic effects, we corrected for the impacts of numerous host extrinsic and demographic factors by introducing them as covariates, enabling us to discover five loci significantly associated with microbiome diversity measures: HS3ST4, C2CD2, 2p16.1, 10p15.1, and 18q12.2. Nevertheless, these five variants explain only a small fraction of the variation in the gut microbiota. We subsequently investigated the heritability of each of the 21 core genera and found that the abundances of six genera are heritable. We propose that the gut microbiota composition is affected by a highly polygenic architecture rather than several strongly associated variants in the Japanese population.

Effects of Polysaccharides From Auricularia auricula on the Immuno-Stimulatory Activity and Gut Microbiota in Immunosuppressed Mice Induced by Cyclophosphamide

Recently, the immuno-enhancing potential of polysaccharide from Auricularia auricula (AAP) has been an area of research interest. However, the immune-stimulatory activity and mechanisms of AAP in immunosuppressive mice treated with cyclophosphamide (CTX) are still poorly understood. This study aimed to evaluate the immuno-enhancing effects of AAP and mine its possible mechanisms. Firstly, polysaccharides were isolated from A. auricula and purified. Secondly, the immune-stimulatory activities of the first AAP fraction (AAP1) were evaluated in the CTX-treated mice. Results showed that AAP1 significantly enhanced immune organ indexes, remarkably stimulated IFN-γ, IL-2, IL-4, IL-10, and TNF-α levels in the serum, and dramatically up-regulated the mRNA levels of Claudin-1, Occludin and ZO-1. Compared to the CTX group, AAP1 administration restored the gut microbiota composition similar to that of the control group by decreasing the ratio of Firmicutes/Bacteroidetes and increasing the relative abundances of short-chain fatty acid-producing microbiota. This study provides useful information for its further application as an immune-stimulator in foods and drugs.

Preclinical Evidence of Probiotics in Colorectal Carcinogenesis: A Systematic Review

BACKGROUND

Colorectal cancer, the second major cause of cancer deaths, imposes a major health burden worldwide. There is growing evidence that supports that the use of probiotics is effective against various diseases, especially in gastrointestinal diseases, including the colorectal cancer, but the differences between the strains, dose, and frequency used are not yet clear.

AIMS

To perform a systematic review to compile the results of studies carried out in animal models and investigated the effect of probiotics on colorectal carcinogenesis.

METHODS

Studies were selected in PubMed/MEDLINE and Scopus according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Search filters were developed using three parameters: probiotics, colorectal cancer, and animal model.

RESULTS

From a structured search, we discovered 34 original articles and submitted them to a risk of bias analysis using SYRCLE's tool. The studies show a great diversity of models, most were conducted in rats (55.8%) and used 1,2 dimethylhydrazine as the drug to induce colorectal carcinogenesis (61.7%). The vast majority of trials investigated Lactobacillus (64%) and Bifidobacterium (29.4%) strains. Twenty-six (86.6%) studies found significant reduction in lesions or tumors in the animals that received probiotics. The main methodological limitation was the insufficient amount of information for the adequate reproducibility of the trials, which indicated a high risk of bias due to incomplete characterization of the experimental design.

CONCLUSIONS

The different probiotics' strains showed anti-carcinogenic effect, reduced the development of lesions and intestinal tumors, antioxidant and immunomodulatory activity, and reduced fecal bacterial enzymes.

Saccharomyces cerevisiae may serve as a probiotic in colorectal cancer by promoting cancer cell apoptosis

OBJECTIVES

Shotgun metagenomic sequencing of human fecal samples has shown that Saccharomyces cerevisiae (S. cerevisiae) is significantly suppressed in colorectal cancer (CRC) and probably plays an important role in CRC progression. However, these results need to be validated. Here we aimed to confirm the results of high-throughput sequencing and demonstrate the mechanisms mediating the effect of S. cerevisiae on progression from colorectal adenoma (CRA) to CRC.

METHODS

We used a quantitative polymerase chain reaction (qPCR) assay to examine the relative abundance of S. cerevisiae in 281 fecal samples collected from 106 healthy controls, 108 patients with CRA and 67 with CRC. C57BL/6 and APC^Min/+ mouse models and in vitro cell assays were subsequntly used for additional analyses. The mouse models were treated or not treated with broad-spectrum antibiotics and given an S. cerevisiae gavage for 8 weeks. Western blot, 16S rRNA sequencing, qPCR, immunohistochemistry, RNA sequencing, cell counting kit-8 assay, colony formation assay and flow cytometry were performed.

RESULTS

S. cerevisiae was 2.68-fold and 3.94-fold less abundant in patients with CRA and CRC, respectively, than in the controls. In vivo experiments showed that S. cerevisiae reduced colorectal tumor progression by promoting epithelial cell apoptosis and modulated gut microbial structure and intestinal immunity. S. cerevisiae downregulated nuclear factor kappa light chain enhancer of activated B cells and the mechanistic target of rapamycin signaling pathways. Cell assays confirmed the pro-apoptotic effect of S. cerevisiae.

CONCLUSIONS

S. cerevisiae may play a probiotic role in CRC by promoting cancer cell apoptosis. It can reduce CRC progression by modulating the mucosal microbial structure.

Progress in Research on Colorectal Cancer-Related Microorganisms and Metabolites

Intestinal flora is an important component in the human body, which have been reported to be involved in the occurrence and development of colorectal cancer (CRC). Indeed, changes in the intestinal flora in CRC patients compared to those in control subjects have been reported. Several bacterial species have been shown to exhibit the pro-inflammatory and pro-carcinogenic properties, which could consequently have an impact on colorectal carcinogenesis. In this review, we summarize the current knowledge on the potential links between the intestinal microbiota and CRC. We illustrated the mechanisms by which intestinal flora imbalance affects CRC, mainly focusing on inflammation, microbial metabolites, and specific bacteria species. In addition, we discuss how a diet exhibits a strong impact on microbial composition and provides risks for developing CRC. Finally, we describe the potential future directions that are based on intestinal microbiota manipulation for CRC diagnosis and treatment.

Human Microbe-Disease Association Prediction by a Novel Double-Ended Random Walk with Restart

Microorganisms in the human body play a vital role in metabolism, immune defense, nutrient absorption, cancer control, and prevention of pathogen colonization. More and more biological and clinical studies have shown that the imbalance of microbial communities is closely related to the occurrence and development of various complex human diseases. Finding potential microbial-disease associations is critical for understanding the pathology of a few diseases and thus further improving disease diagnosis and prognosis. In this study, we proposed a novel computational model to predict disease-associated microbes. Specifically, we first constructed a heterogeneous interconnection network based on known microbe-disease associations deposited in a few databases, the similarity between diseases, and the similarity between microorganisms. We then predicted novel microbe-disease associations by a new method called the double-ended restart random walk model (DRWHMDA) implemented on the interconnection network. In addition, we performed case studies of colon cancer and asthma for further evaluation. The results indicate that 10 and 9 of the top 10 microorganisms predicted to be associated with colorectal cancer and asthma were validated by relevant literatures, respectively. Our method is expected to be effective in identifying disease-related microorganisms and will help to reveal the relationship between microorganisms and complex human diseases.

Comparison of the Gut Microbiota Between Pulsatilla Decoction and Levofloxacin Hydrochloride Therapy on Escherichia coli Infection

Gut microbiota serves as a critical indicator for gut health during treatment of pathogenic bacterial infection. Both Pulsatilla Decoction (abbreviated to PD, a traditional Chinese medicine compound) and Levofloxacin Hydrochloride (LVX) were known to have therapeutic effects to intestinal infectious disease. However, the changes of gut microbiota after PD or LVX treatment remain unclear. Herein, this work aimed to investigate the changes of intestinal flora after PD or LVX therapy of Escherichia coli infection in rats. Results revealed that PD exhibited a valid therapeutic approach for E. coli infection via the intestinal protection, as well as the inhibited release of IL-8 and ICAM-1. Besides, PD was beneficial to rebuild the gut microbiota via restoring Bacteroidetes spp in the composition of the gut microbiota. Comparatively, LVX treatment promoted the infection and ravaged gut microbiota by significantly decreasing Bacteroidetes and increasing Firmicutes. These findings not only highlight the mechanism of Chinese herbal formula, but extend the application of PD as veterinary medicine, feed additive and pre-mixing agent for improving the production of animal derived foods.

Impacts of foodborne inorganic nanoparticles on the gut microbiota-immune axis: potential consequences for host health

BACKGROUND

In food toxicology, there is growing interest in studying the impacts of foodborne nanoparticles (NPs, originating from food additives, food supplements or food packaging) on the intestinal microbiome due to the important and complex physiological roles of these microbial communities in host health. Biocidal activities, as described over recent years for most inorganic and metal NPs, could favour chronic changes in the composition and/or metabolic activities of commensal bacteria (namely, intestinal dysbiosis) with consequences on immune functions. Reciprocally, direct interactions of NPs with the immune system (e.g., inflammatory responses, adjuvant or immunosuppressive properties) may in turn have effects on the gut microbiota. Many chronic diseases in humans are associated with alterations along the microbiota-immune system axis, such as inflammatory bowel diseases (IBD) (Crohn's disease and ulcerative colitis), metabolic disorders (e.g., obesity) or colorectal cancer (CRC). This raises the question of whether chronic dietary exposure to inorganic NPs may be viewed as a risk factor facilitating disease onset and/or progression. Deciphering the variety of effects along the microbiota-immune axis may aid the understanding of how daily exposure to inorganic NPs through various foodstuffs may potentially disturb the intricate dialogue between gut commensals and immunity, hence increasing the vulnerability of the host. In animal studies, dose levels and durations of oral treatment are key factors for mimicking exposure conditions to which humans are or may be exposed through the diet on a daily basis, and are needed for hazard identification and risk assessment of foodborne NPs. This review summarizes relevant studies to support the development of predictive toxicological models that account for the gut microbiota-immune axis.

CONCLUSIONS

The literature indicates that, in addition to evoking immune dysfunctions in the gut, inorganic NPs exhibit a moderate to extensive impact on intestinal microbiota composition and activity, highlighting a recurrent signature that favours colonization of the intestine by pathobionts at the expense of beneficial bacterial strains, as observed in IBD, CRC and obesity. Considering the long-term exposure via food, the effects of NPs on the gut microbiome should be considered in human health risk assessment, especially when a nanomaterial exhibits antimicrobial properties.

Auxiliary antitumor effects of fungal proteins from Hericium erinaceus by target on the gut microbiota

Cancer represents a major disease burden worldwide. Despite continuous advances obtained in medical therapies recently, resistance to standard drugs and adverse effects still represent important causes of therapeutic failure. There is growing evidence that the gut microbiota can affect the response to chemo- and immunotherapeutic drugs by modulating efficacy and/or toxicity, and diet is the most important factor affecting the gut microbiota. In this study, we assessed the auxiliary antitumor effects of immunomodulatory fungal proteins from Hericium erinaceus (HEP) administered with the chemotherapy drug 5-Fluorouracil (5-Fu), and we attempted to identify new potential prebiotic bacteria for auxiliary antitumor treatment. There were 1,455 proteins identified from H. erinaceus. In a xenografted mouse model of cancer, HEP with 5-Fu significantly suppressed tumor growth, inhibited inflammatory markers such as interferon (IFN)-γ, interleukin (IL)-1β, IL-2, IL-6, tumor necrosis factor (TNF)-α, and lipopolysaccharide (LPS), and regulated the expression of Akt, CCDN1, CKD4, FOXM1, MMP7, MYC, PPAR-α, and PPAR-γ. 16S rRNA sequencing showed that HEP ameliorated the dysbacteriosis induced by 5-Fu, as it inhibited certain aerobic and microaerobic bacteria including Parabacteroides, Flavobacteriaceae, Christensenellaceae, Anoxybacillus, Aggregatibacter, Comamonadaceae, Planococcaceae, Desulfovibrionaceae, Sporosarcina, Staphylococcus, Aerococcaceae, and Bilophila in the xenografted mice, and increase some probiotic bacteria such as Bifidobacterium, Gemellales, Blautia, Sutterella, Anaerostipes, Roseburia, Lachnobacterium, Lactobacillus, and Desulfovibrio. This demonstrates that HEP could promote the antitumor efficacy of 5-Fu by improving the microbiota composition, the immune inflammatory response, and homeostasis.

Oral and intestinal bacterial exotoxins: Potential linked to carcinogenesis

Growing evidence suggests that imbalances in resident microbes (dysbiosis) can promote chronic inflammation, immune-subversion, and production of carcinogenic metabolites, thus leading to neoplasia. Yet, evidence to support a direct link of individual bacteria species to human sporadic cancer is still limited. This chapter focuses on several emerging bacterial toxins that have recently been characterized for their potential oncogenic properties toward human orodigestive cancer and the presence of which in human tissue samples has been documented. These include cytolethal distending toxins produced by various members of gamma and epsilon Proteobacteria, Dentilisin from mammalian oral Treponema, Pasteurella multocida toxin, two Fusobacterial toxins, FadA and Fap2, Bacteroides fragilis toxin, colibactin, cytotoxic necrotizing factors and α-hemolysin from Escherichia coli, and Salmonella enterica AvrA. It was clear that these bacterial toxins have biological activities to induce several hallmarks of cancer. Some toxins directly interact with DNA or chromosomes leading to their breakdowns, causing mutations and genome instability, and others modulate cell proliferation, replication and death and facilitate immune evasion and tumor invasion, prying specific oncogene and tumor suppressor pathways, such as p53 and β-catenin/Wnt. In addition, most bacterial toxins control tumor-promoting inflammation in complex and diverse mechanisms. Despite growing laboratory evidence to support oncogenic potential of selected bacterial toxins, we need more direct evidence from human studies and mechanistic data from physiologically relevant experimental animal models, which can reflect chronic infection in vivo, as well as take bacterial-bacterial interactions among microbiome into consideration.

High Fat High Calories Diet (HFD) Increase Gut Susceptibility to Carcinogens by Altering the Gut Microbial Community

Objective: To investigate the risk of colorectal cancer and its relationship with colonic flora and microenvironment under high-fat and high-calorie diet. Methods: Wistar rats were used to study, and they were given normal diet, high-fat diet, and dimethyl hydrazine (DMH) to induce the occurrence of colorectal cancer. Then observe the difference in tumor formation and the relationship among microbial community, inflammatory factors and metabolism. Results: No tumors were found in the normal diet group (G1) and the high-fat diet group (G3). Four nodules were found in the four rats in the normal diet + DMH group (G2) and 8 cancerous nodules were formed in 7 rats (70%) from high-fat diet + DMH group (G4). Cholesterol and TNF-α increased, IL-1, IL-6 and LEP decreased in the high-fat diet group. The difference was statistically significant. In the cancer-inducing group, only the difference in cholesterol was statistically significant. Compared with the normal diet group (G1) and the high-fat diet group (G3), the rat's gut bacterial abundance was not significantly different, but the gut flora structure was significantly changed. The content of Candida in the intestinal tract of rats in the high-fat diet group was reduced (P = 0.015), while the content of Verrucomicrobia increased (P = 0.035); In the comparison of genus content, Ruminococcus, Candida, Saccharibacteria genera incertae sedis, Enterobacter, Clostridium IV, Enterococcus, Enterorhabdus, Acetivibrio, Adlercreutzia, Lactococcus, etc., decreased significantly, while Akkermansia, Warthococcus, Staphylococcus, Butyricimonas, Clostridium XVIII, etc. increased significantly.

Conclusion: This study found that high-fat, high-calorie diet can increase the susceptibility of the intestine to carcinogenic factors. The reason may be that the high-fat diet causes the body to appear inflammatory states and microbial community imbalance, especially rumenococcus, candida, Saccharomyces, Enterobacter, Clostridium IV, Enterococcus, Enterobacter, Vibrioaceticus and other genus reduction are important links. Exploring ways to improve these floras is an important factor to improve the resistance of the intestinal tract to cancer-inducing agents.

Traditional Processed Meat Products Re-designed Towards Inulin-rich Functional Foods Reduce Polyps in Two Colorectal Cancer Animal Models

Inulin-rich foods exert a prebiotic effect, as this polysaccharide is able to enhance beneficial colon microbiota populations, giving rise to the in situ production of short-chain fatty acids (SCFAs) such as propionic and butyric acids. These SCFAs are potent preventive agents against colorectal cancer due to their histone deacetylases inhibitory properties, which induce apoptosis in tumor colonocytes. As colorectal cancer is the fourth most common neoplasia in Europe with 28.2 new cases per 100,000 inhabitants, a cost-effective preventive strategy has been tested in this work by redesigning common porcine meat products (chorizo sausages and cooked ham) consumed by a substantial proportion of the population towards potential colorectal cancer preventive functional foods. In order to test the preventive effect of these inulin-rich meat products against colorectal cancer, an animal model (Rattus norvegicus F344) was used, involving two doses of azoxymethane (10 mg/kg) and two treatments with dextran sodium sulfate (DSS) during a 20-week assay period. Control feed, control sausages, functional sausages (15.7% inulin), control cooked ham and functional cooked ham (10% inulin) were used to feed the corresponding animal cohorts. Then, the animals were sacrificed and their digestive tract tissues were analyzed. The results showed a statistically significant 49% reduction in the number of colon polyps in the functional meat products cohorts with respect to the control meat products animals, as well as an increase in the cecum weight (an indicator of a diet rich in prebiotic fiber), a 51.8% increase in colon propionate production, a 39.1% increase in colon butyrate concentrations, and a reduction in the number of hyperplastic Peyer's patches. Metagenomics studies also demonstrated colon microbiota differences, revealing a significant increase in Bacteroidetes populations in the functional meat products (mainly due to an increase in Bacteroidaceae and Prevotellaceae families, which include prominent propionate producers), together with a reduction in Firmicutes (especially due to lower Lachnospiraceae populations). However, functional meat products showed a remarkable increase in the anti-inflammatory and fiber-fermentative Blautia genus, which belongs to this Lachnospiraceae family. The functional meat products cohorts also presented a reduction in important pro-inflammatory bacterial populations, such as those of the genus Desulfovibrio and Bilophila. These results were corroborated in a genetic animal model of CRC (F344/NSlc-Apc1588/kyo) that produced similar results. Therefore, processed meat products can be redesigned towards functional prebiotic foods of interest as a cost-effective dietary strategy for preventing colorectal cancer in human populations.

Gut microbiota, dietary phytochemicals and benefits to human health

Purpose of the review

In this review, we discuss the roles of the gut microbiota, dietary phytochemicals in improving human health. Recent studies have reported that the human gut microbiota can be altered by dietary phytochemicals including phenolics, carotenoids, and dietary fibers. In addition, both pathogenic and nonpathogenic bacteria show regulatory effects with phytochemicals, suggesting potential synergistic effects in the improvement of human gut health and prevention of chronic diseases.

Recent findings

Numerous studies have been conducted on gut microbial alterations induced by phytochemicals, such as phenolics and carotenoids. Butyrate, a short-chain fatty acid produced via bacterial fermentation in the colon, also shows a significantly beneficial effect in the maintenance of gut microbial homeostasis. However, the molecular mechanisms underlying the effects of diets and the interactions of the gut microorganisms remain poorly understood. The gut microbiome profile changes have been observed in chronic inflammation-induced diseases including colitis, Crohn's disease, immune dysfunction, colon cancer, obesity and diabetes. The anti-inflammatory effects of dietary phytochemicals against these diseases may be partially mediated by regulation of microbial profiles. Latest advances in biomedical technology such as the next-generation sequencing (NGS), and continuous cost reduction associated with these technologies, enabled researchers to perform ever-increasing number of large-scale, high-throughput computational analyses to elucidate the potential mechanism of phytochemical-microbiome interactions.

Summary

Information obtained from these studies may provide valuable insights to guide future clinical research for the development of therapeutics, botanicals and drug efficacy testing, many of which will be discussed in this review.

Supplementation of triple viable probiotics combined with dietary intervention is associated with gut microbial improvement in humans on a high-fat diet

Numerous animal studies have demonstrated that oral probiotics may have a beneficial role in preventing obesity, inflammatory bowel disease and even colorectal cancer, which are all associated with a high-fat diet (HFD). However, the underlying beneficial effects of combined probiotic and dietary intervention on the gut microbiota of 'non-patient' individuals previously on an HFD have yet to be fully elucidated. In the present study, fecal samples were obtained from 36 volunteers on a high-fat diet and after dietary intervention for 4 months, and 16S rDNA sequencing was applied to identify how probiotics and dietary intervention had altered the composition of the microbiota. The results demonstrated that probiotics treatment and dietary intervention in combination raised the diversity of lumen microbes compared with their individual applications. A markedly separated distribution (β-diversity) was observed, confirming the difference in gut microbiota composition among the treatment groups. Bacterial taxonomic analysis demonstrated that the relative abundance of 30 species was altered among the groups following dietary intervention and/or probiotic supplementation. The majority of the species that exhibited a population increase belonged to two butyrate-producing families, Ruminococcaceae and Lachnospiraceae, whereas the species with reduced populations mainly belonged to the Bacteroidaceae family. Collectively, these results suggest that combined probiotic and dietary intervention is able to improve the gut microbiota composition of human subjects on an HFD.

Altered intestinal microbiota associated with colorectal cancer

The gut microbiota plays an important role in the development and progression of colorectal cancer (CRC). To learn more about the dysbiosis of carcinogenesis, we assessed alterations in gut microbiota in patients with CRC. A total of 23 subjects were enrolled in this study: 9 had CRC (CRC group) and 14 had normal colons (normal group). The microbiome of the mucosal-luminal interface of each subject was sampled and analyzed using 16S rRNA gene amplicon sequencing. We also used Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to predict microbial functional profiles. The microbial composition of the mucosal lumen differed between the groups, and the presence of specific bacteria may serve as a potential biomarker for colorectal carcinogenesis. We identified a significant reduction in Eubacterium, which is a butyrate-producing genera of bacteria, and a significant increase in Devosia in the gut microbiota of CRC patients. Different levels of gut microflora in healthy and CRC samples were identified. The observed abundance of bacterial species belonging to Eubacterium and Devosia may serve as a promising biomarker for the early detection of CRC.

Intervention with α-Ketoglutarate Ameliorates Colitis-Related Colorectal Carcinoma via Modulation of the Gut Microbiome

The intestinal microbiome plays a crucial role in promoting intestinal health, and perturbations to its constitution may result in chronic intestinal inflammation and lead to colorectal cancer (CRC). α-Ketoglutarate is an important intermediary in the NF-κB-mediated inflammatory pathway that maintains intestinal homeostasis and prevents initiation of intestinal inflammation, a known precursor to carcinoma development. The objective of this study was to assess the potential protective effects of α-ketoglutarate intervention against CRC development, which may arise due to its known anti-inflammatory and antitumour effects. CRC was induced in C57BL/6 mice using azoxymethane (AOM) and dextran sulfate sodium (DSS). Tumour frequency, histological rating, and colonic microbiota were assessed in colonic samples. The findings demonstrated that α-ketoglutarate offered significant protection against CRC development in mice. Furthermore, α-ketoglutarate also exhibited immunomodulatory effects mediated via downregulation of interleukin (IL)-6, IL-22, tumour necrosis factor (TNF)-α, and IL-1β cytokines. Finally, intervention with α-ketoglutarate tended to minimise the frequency of opportunistic pathogens (Escherichia and Enterococcus) while increasing the populations of Akkermansia, Butyricicoccus, Clostridium, and Ruminococcus. Taken together, our findings show that dietary α-ketoglutarate intervention may protect against inflammation-related CRC.

Microbiome and colorectal cancer: Roles in carcinogenesis and clinical potential

The gastrointestinal tract harbors most of the microbiota associated with humans. In recent years, there has been a surge of interest in assessing the relationships between the gut microbiota and several gut alterations, including colorectal cancer. Changes in the gut microbiota in patients suffering colorectal cancer suggest a possible role of host-microbe interactions in the origin and development of this malignancy and, at the same time, open the door for novel ways of preventing, diagnosing, or treating this disease. In this review we survey current knowledge on the healthy microbiome of the gut and how it is altered in colorectal cancer and other related disease conditions. In describing past studies we will critically assess technical limitations of different approaches and point to existing challenges in microbiome research. We will have a special focus on host-microbiome interaction mechanisms that may be important to explain how dysbiosis can lead to chronic inflammation and drive processes that influence carcinogenesis and tumor progression in colon cancer. Finally, we will discuss the potential of recent developments of novel microbiota-based therapeutics and diagnostic tools for colorectal cancer.

Oral administration of Lactobacillus rhamnosus GG to newborn piglets augments gut barrier function in pre-weaning piglets

To understand the effects of Lactobacillus rhamnosus GG (ATCC 53103) on intestinal barrier function in pre-weaning piglets under normal conditions, twenty-four newborn littermate piglets were randomly divided into two groups. Piglets in the control group were orally administered with 2 mL 0.1 g/mL sterilized skim milk while the treatment group was administered the same volume of sterilized skim milk with the addition of viable L. rhamnosus at the 1st, 3rd, and 5th days after birth. The feeding trial was conducted for 25 d. Results showed that piglets in the L. rhamnosus group exhibited increased weaning weight and average daily weight gain, whereas diarrhea incidence was decreased. The bacterial abundance and composition of cecal contents, especially Firmicutes, Bacteroidetes, and Fusobacteria, were altered by probiotic treatment. In addition, L. rhamnosus increased the jejunal permeability and promoted the immunologic barrier through regulating antimicrobial peptides, cytokines, and chemokines via Toll-like receptors. Our findings indicate that oral administration of L. rhamnosus GG to newborn piglets is beneficial for intestinal health of pre-weaning piglets by improving the biological, physical, and immunologic barriers of intestinal mucosa.

Characterization of the Early Life Microbiota Development and Predominant Lactobacillus Species at Distinct Gut Segments of Low- and Normal-Birth-Weight Piglets

Microbial exposure during early life plays a pivotal role in modulating the health and intestinal development of the host. Our recent study showed that the low-birth-weight (LBW) piglets harbored a different fecal microbiota compared to normal-birth-weight (NBW) piglets during early life with a lower abundance of the genus Lactobacillus. Considering the spatial variations in gut microbiota at distinct gut locations, this study was designed to further investigate the differences in the microbiota composition and predominant Lactobacillus species in the ileum and colon between LBW and NBW piglets during early life, including day 7 (D7), day 21 (D21, before weaning), and day 35 (D35, 2 weeks after weaning). Compared with the normal group, LBW piglets harbored a significantly lower proportion of short-chain fatty acids producing microbes, such as Ruminococcaceae and Prevotellaceae in the ileum on D7, Alistipes and Lachnospiraceae in the colon on D7, Blautia in the colon on D21, and Ruminiclostridium 9 in the colon on D35. The relative abundance of the phylum Bacteroidetes was also declined in both ileum and colon of LBW piglets on D7. Meanwhile, the levels of total SCFAs on D7, D21, and D35, acetate and valerate on D7 and D21, propionate on D21, and lactate on D21 and D35, were also declined in the colon of LBW piglets. Moreover, functional alterations in the gut microbiota of LBW piglets were characterized by differentially abundant microbial genes involved in multiple pathways such as amino acid metabolism, energy metabolism, replication and repair, and metabolism of cofactors and vitamins in the colon. Additionally, lower numbers of L. salivarius on D7 and L. amylovorus on D21 resided in the colon of LBW piglets compared to those in the normal ones. Collectively, LBW piglets have altered bacterial communities, microbial metabolism and gene functions in the ileum and colon during early life, especially the colonic community. This work will help to develop novel ideas in identifying the reliable biomarkers affecting the gut microbiota development in LBW piglets during early life and facilitate the development of new nutritional interventions.

A Novel Human Microbe-Disease Association Prediction Method Based on the Bidirectional Weighted Network

The survival of human beings is inseparable from microbes. More and more studies have proved that microbes can affect human physiological processes in various aspects and are closely related to some human diseases. In this paper, based on known microbe-disease associations, a bidirectional weighted network was constructed by integrating the schemes of normalized Gaussian interactions and bidirectional recommendations firstly. And then, based on the newly constructed bidirectional network, a computational model called BWNMHMDA was developed to predict potential relationships between microbes and diseases. Finally, in order to evaluate the superiority of the new prediction model BWNMHMDA, the framework of LOOCV and 5-fold cross validation were implemented, and simulation results indicated that BWNMHMDA could achieve reliable AUCs of 0.9127 and 0.8967 ± 0.0027 in these two different frameworks respectively, which is outperformed some state-of-the-art methods. Moreover, case studies of asthma, colorectal carcinoma, and chronic obstructive pulmonary disease were implemented to further estimate the performance of BWNMHMDA. Experimental results showed that there are 10, 9, and 8 out of the top 10 predicted microbes having been confirmed by related literature in these three kinds of case studies separately, which also demonstrated that our new model BWNMHMDA could achieve satisfying prediction performance.

Identification and Analysis of Human Microbe-Disease Associations by Matrix Decomposition and Label Propagation

Studies have shown that microbes exist widely in the human body and are closely related to human complex diseases. Predicting potential associations between microbes and diseases is conducive to understanding the mechanisms of complex diseases and can also facilitate the diagnosis and prevention of human diseases. In this paper, we put forward the Matrix Decomposition and Label Propagation for Human Microbe-Disease Association prediction (MDLPHMDA) on the basis of the dataset of known microbe-disease associations collected from the database of HMDAD and the Gaussian interaction profile kernel similarity for diseases and microbes, disease symptom similarity. Moreover, the performance of our model was evaluated by means of leave-one-out cross validation and five-fold cross validation, and the corresponding AUCs of 0.9034 and 0.8954 ± 0.0030 were gained, respectively. In case studies, 10, 9, 9, and 8 out of the top 10 predicted microbes for asthma, colorectal carcinoma, liver cirrhosis, and type 1 diabetes were confirmed by literatures, respectively. Overall, evaluation results showed that MDLPHMDA has good performance in potential microbe-diseasepositive free parameter, which associations prediction.

Effects of different levels of methionine on sow health and plasma metabolomics during late gestation

Fetal growth, survival, and development are benchmarks for the production performance of sows, and methionine has been shown to impact fetal protein mass and the transport of nutrients through the uteroplacental vasculature. This study evaluated the effects of dietary methionine, administered during the late gestation period, on the production performance of sows. Specifically, it measured the effect of methionine on biochemical indicators in the plasma, plasma metabolites, and fecal bacterial communities. Thirty Landrace × Large White sows at day 90 of gestation were randomly assigned to three groups and fed the following diets: (1) a basal diet containing 0.36% methionine; (2) a basal diet + 0.12% methionine (0.48% methionine); and (3) a basal diet + 0.24% methionine (0.60% methionine). The results showed that the 0.48% methionine diet significantly (P < 0.05) increased piglets' birth weight, and the 0.60% methionine diet significantly (P < 0.05) improved the survival ratio. Dietary methionine lowered the triglyceride (TG) levels (P < 0.05), total bilirubin (BILT3) (P < 0.001) concentration, and gamma-glutamyl transferase (GGT) (P < 0.05) enzyme activity in the plasma at farrowing. In the plasma metabolomics, dietary methionine increased plasma pyroglutamic acid and decreased 2-pyrrolidinone, hypotaurine, and anyl-histidine in both the 0.48% methionine and 0.60% methionine groups. In addition, the bacteria richness (Chao1 and ACE) and diversity (Shannon) were reduced in the 0.48% methionine group. For the microbiota composition, at the family level, the 0.48% methionine group had a significant increase (P < 0.05) in the relative abundance of Methanobacteriaceae compared to the other two groups, but a decrease in the relative abundance of Enterobacteriaceae, Ruminococcaceae and Erysipelotrichaceae compared to the 0.60% methionine group. In conclusion, a diet consisting of 0.48% methionine administered during the late gestation period can improve the production performance of sows and maintain their health.

A reliable method for colorectal cancer prediction based on feature selection and support vector machine

Colorectal cancer (CRC) is a common cancer responsible for approximately 600,000 deaths per year worldwide. Thus, it is very important to find the related factors and detect the cancer accurately. However, timely and accurate prediction of the disease is challenging. In this study, we build an integrated model based on logistic regression (LR) and support vector machine (SVM) to classify the CRC into cancer and normal samples. From various factors, human location, age, gender, BMI, and cancer tumor type, tumor grade, and DNA, of the cancer, we select the most significant factors (p < 0.05) using logistic regression as main features, and with these features, a grid-search SVM model is designed using different kernel types (Linear, radial basis function (RBF), Sigmoid, and Polynomial). The result of the logistic regression indicates that the Firmicutes (AUC 0.918), Bacteroidetes (AUC 0.856), body mass index (BMI) (AUC 0.777), and age (AUC 0.710) and their combined factors (AUC 0.942) are effective for CRC detection. And the best kernel type is RBF, which achieves an accuracy of 90.1% when k = 5, and 91.2% when k = 10. This study provides a new method for colorectal cancer prediction based on independent risky factors. Graphical abstract Flow chart depicting the method adopted in the study. LR (logistic regression) and ROC curve are used to select independent features as input of SVM. SVM kernel selection aims to find the best kernel function for classification by comparing Linear, RBF, Sigmoid, and Polynomial kernel types of SVM, and the result shows the best kernel is RBF. Classification performance of LR + RF, LR + NB, LR + KNN, and LR + ANNs models are compared with LR + SVM. After these steps, the cancer and healthy individuals can be classified, and the best model is selected.

Differences Between the Intestinal Lumen Microbiota of Aberrant Crypt Foci (ACF)-Bearing and Non-bearing Rats

BACKGROUND

Multiple factors including host-microbiota interaction could contribute to the conversion of healthy mucosa to sporadic precancerous lesions. An imbalance of the gut microbiota may be a cause or consequence of this process.

AIM

The goal was to investigate and analyze the composition of gut microbiota during the genesis of precancerous lesions of colorectal cancer.

METHODS

To analyze the composition of gut microbiota in the genesis of precancerous lesions, a rat model of 1, 2-dimethylhydrazine (DMH)-induced aberrant crypt foci (ACF) was established. The feces of these rats and healthy rats were collected for 16S rRNA sequencing.

RESULTS

The diversity and density of the rat intestinal microbiota were significantly different between ACF-bearing and non-bearing group. ACF were induced in rats treated with DMH and showed increased expression of the inflammatory cytokines IL-6, IL-8, and TNF-α. Firmicutes was the most predominant phylum in both ACF-bearing and non-bearing group, followed by Bacteroidetes. Interestingly, although the density of Bacteroidetes decreased from the fifth week to the 17th week in both groups, it was significantly reduced in ACF-bearing group at the 13th week (P < 0.01). At the genus level, no significant difference was observed in the most predominant genus, Lactobacillus. Instead, Bacteroides and Prevotella were significantly less abundant (P < 0.01), while Akkermansia was significantly more abundant (P < 0.05) in ACF-bearing group at the 13th week.

CONCLUSION

Imbalance of the intestinal microbiota existed between ACF-bearing and non-bearing rats, which could be used as biomarker to predict the genesis of precancerous lesions in the gut.

Carboxymethyl pachyman (CMP) reduces intestinal mucositis and regulates the intestinal microflora in 5-fluorouracil-treated CT26 tumour-bearing mice

The compound 5-fluorouracil (5-FU) is the first choice chemotherapeutic agent for the treatment of colorectal cancer (CRC), but intestinal mucositis is a primary limiting factor in anticancer therapy. There is currently no broadly effective targeted treatment to cure this side effect. Carboxymethylated pachyman (CMP) is a polysaccharide that is modified from the structure of pachyman isolated from Poria cocos (Chinese name: Fu Ling). Meanwhile, recent studies have shown that CMP exhibits immune regulatory, anti-inflammatory and antioxidant activities. Therefore, the purpose of this study was to evaluate the intestinal protective effect of CMP in 5-FU-treated CT26 tumour-bearing mice and to further explore its underlying mechanism(s) of action. Initially, a CT26 colon carcinoma xenograft mice model was established. The colon length, colon tissue injury, intestinal flora, short-chain fatty acids (SCFAs) and indicators linked to inflammation, antioxidation and apoptosis were then measured. Our results showed that CMP in combination with 5-FU reversed intestinal shortening (p < 0.01) and alleviated 5-FU-induced colon injury (p < 0.001) via suppression of ROS production; increasing the levels of CAT, GSH-Px and GSH; decreasing expression of NF-κB, p-p38 and Bax; and elevating the levels of Nrf2 and Bcl-2. More importantly, CMP had a significant impact and counteracted the intestinal microflora disorders produced by 5-FU by increasing the proportion of Bacteroidetes, lactobacilli, and butyric acid-producing and acetic acid-producing bacteria and restoring the intestinal flora diversity. Overall, this work suggested that CMP could regulate the ecological balance of the intestinal flora and reduce colon injuries induced by 5-FU in CT26 tumour-bearing mice, and the mechanism involved may be associated with the regulation of the NF-κB, Nrf2-ARE and MAPK/P38 pathways.

The Dynamic Changes of Gut Microbiota in Muc2 Deficient Mice

Gut dysbiosis is associated with colitis-associated colorectal carcinogenesis, and the genetic deficiency of the Muc2 gene causes spontaneous development of colitis and colorectal cancer. Whether there are changes of gut microbiota and a linkage between the changes of microbiota and intestinal pathology in Muc2^-/- mice are unclear. Muc2^-/- and Muc2^+/+ mice were generated by backcrossing from Muc2^+/- mice, and the fecal samples were collected at different dates (48th, 98th, 118th, 138th, and 178th day). Gut microbiota were analyzed by high-throughput sequencing with the universal 16S rRNA primers (V3⁻V5 region). All mice were sacrificed at day 178 to collect colonic tissue and epithelial cells for the analysis of histopathology and inflammatory cytokines. On the 178th day, Muc2^-/- mice developed colorectal chronic colitis, hyperplasia, adenomas and adenocarcinomas, and inflammatory cytokines (e.g., cyclooxygenase 2 (COX-2), interleukin 6 (IL-6), tumor necrosis factor-α (TNF-α), interleukin 1 β (IL-1β), i-kappa-B-kinase β (IKKβ)) were significantly increased in colonic epithelial cells of Muc2^-/- mice. In general, structural segregation of gut microbiota was observed throughout the experimental time points between the Muc2^-/- and Muc2^+/+ mice. Impressively, in Muc2^-/- mice, Alpha diversities reflected by Shannon and Chao indexes were higher, the phylum of Firmicutes was enriched and Bacteroidetes was decreased, and Desulfovibrio, Escherichia, Akkermansia, Turicibacter, and Erysipelotrichaceae were significantly increased, but Lactobacilli and Lachnospiraceae were significantly decreased. Moreover, the abundance of Ruminococcaceae and butyrate-producing bacteria was significantly higher in the Muc2^-/- mice. There were significant differences of gut microbiota between Muc2^-/- and Muc2^+/+ mice. The dynamic changes of microbiota might contribute to the development of colitis and colitis-associated colorectal carcinogenesis. Therefore, this study revealed specific functional bacteria in the development of colitis and colitis-associated colorectal carcinogenesis, which will benefit the development of preventive and therapeutic strategies for chronic inflammation and its malignant transformation.

The Effects of Berberine on the Gut Microbiota in Apc min/+ Mice Fed with a High Fat Diet

Background: Berberine (BBR) has been extensively reported to inhibit colorectal cancer (CRC) development, though its bioavailability is poor. Nowadays, an increasing number of studies have shown that BBR significantly accumulates in the intestines and could regulate gut microbiota in obesity. The purpose of this study was to further explore the effects of BBR on gut microbiota in Apc ^min/+ mice receiving a high fat diet (HFD). Methods: Apc ^min/+ mice received either HFD alone or HFD and BBR for 12 weeks. The intestinal tissues were collected to evaluate the efficiency of BBR on neoplasm development by hematoxylin and eosin staining. Meanwhile, immunohistochemistry was conducted to investigate the effects of BBR on cyclin D1 and β-catenin in colon tissues. Fecal samples were subjected to 16S rRNA sequencing. Results: BBR significantly reduced intestinal tumor development and altered the structure of gut microbiota in Apc ^min/+ mice fed with an HFD. At the phylum level, it was able to significantly inhibit the increase in Verrucomicrobia. At the genus level, it was able to suppress Akkermansia and elevate some short chain fat acid (SCFA)-producing bacteria. Conclusions: BBR significantly alleviated the development of CRC in Apc ^min/+ mice fed with HFD and restored the enteric microbiome community.

Colorectal carcinogenesis: an archetype of gut microbiota-host interaction

Sporadic colorectal cancer (CRC) remains a major cause of worldwide mortality. Epidemiological evidence of markedly increased risk in populations that migrate to Western countries, or adopt their lifestyle, suggests that CRC is a disease whose aetiology is defined primarily by interactions between the host and his environment. The gut microbiome sits directly at this interface and is now increasingly recognised as a modulator of colorectal carcinogenesis. Bacteria such as Fusobacterium nucleatum and Escherichia coli (E. Coli) are found in abundance in patients with CRC and have been shown in experimental studies to promote neoplasia. A whole armamentarium of bacteria-derived oncogenic mechanisms has been defined, including the subversion of apoptosis and the production of genotoxins and pro-inflammatory factors. But the microbiota may also be protective: for example, they are implicated in the metabolism of dietary fibre to produce butyrate, a short chain fatty acid, which is anti-inflammatory and anti-carcinogenic. Indeed, although our understanding of this immensely complex, highly individualised and multi-faceted relationship is expanding rapidly, many questions remain: Can we define friends and foes, and drivers and passengers? What are the critical functions of the microbiota in the context of colorectal neoplasia?

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment

Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues. We found statistically significant associations between loss-of-function mutations in tumor genes and shifts in the abundances of specific sets of bacterial taxa, suggestive of potential functional interaction. This correlation allows us to statistically predict interactions between loss-of-function tumor mutations in cancer-related genes and pathways, including MAPK and Wnt signaling, solely based on the composition of the microbiome. In conclusion, our study shows that CRC microbiomes are correlated with tumor mutational profiles, pointing towards possible mechanisms of molecular interaction.

Effects of the intestinal microbial metabolite butyrate on the development of colorectal cancer

Colorectal cancer (CRC) is one of the major health threats in developed countries. Changes in dietary components, such as more protein and lipid intake, can increase the risk of CRC. Diet affects CRC in many ways. They regulate the composition and function of gut microbiota, which have an amazing metabolic capacity and can produce short chain fatty acids (SCFAs), such as propionate, acetate, and butyrate. Butyrate is a principal energy source for colonic epithelial cells and plays an important role in maintaining the stability of gut microbiota and the integrity of intestinal epithelium. However, there are few studies reviewing the anti-CRC potentials of butyrate. This review summarizes the recent research progresses in the effect of gut microbiota imbalance and the decrease in intestinal microbial metabolite butyrate caused by unbalanced diet on CRC development, and discusses the mechanisms of butyrate-induced anti-CRC activities, which may guide people to prevent CRC by improving diet structures.

Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus)

Gut microbiota plays a crucial importance in their host. Disturbance of the microbial structure and function is known to be associated with inflammatory intestinal disorders. Enteritis is a significant cause of high mortality in fish species, including grass carp (Ctenopharyngodon idellus). Study regarding the association between microbial alternations and enteritis in grass carp is still absent. In this study, changes in the gut microbiota of grass carp suffering from enteritis were investigated using NGS-based 16S rRNA sequencing. Six healthy and ten abnormal fish (showing reddening anus, red odiferous fluid accumulating in the abdominal capacity, and flatulence and haemorrhage in the intestine) were collected from a fish farm in Huanggang Fisheries Institute (Hubei, China). Our results revealed that the diversity, structure, and function of gut microbiota were significantly different between diseased and healthy fish (P < 0.05). Particularly, members of the genera Dechloromonas, Methylocaldum, Planctomyces, Rhodobacter, Caulobacter, Flavobacterium, and Pseudomonas were significantly increased in diseased fish compared with that in healthy fish (P < 0.05). Predicted function indicated that microbiota significantly changed the specific metabolic pathways (related to amino acid metabolism, xenobiotics biodegradation and metabolism, and carbohydrate metabolism) in diseased fish (P < 0.05). Taken together, our findings point out the association between changes of the gut microbiota and enteritis in grass carp, which provide basic information useful for diagnoses, prevention, and treatment of intestinal diseases occurring in cultured fish.

Both the intratumoral immune and microbial microenvironment are linked to recurrence in human colon cancer: results from a prospective, multicenter nodal ultrastaging trial

Colon cancer (CC) is the third most common cancer diagnosed in the United States and the incidence has been rising among young adults. We and others have shown a relationship between the immune infiltrate and prognosis, with improved disease-free survival (DFS) being associated with a higher expression of CD8⁺ T cells. We hypothesized that a microbial signature might be associated with intratumoral immune cells as well as DFS. We found that the relative abundance of one Operational Taxonomic Unit (OTU), OTU_104, was significantly associated with recurrence even after applying false discovery correction (HR 1.21, CI 1.08 to 1.36). The final multivariable model showed that DFS was influenced by three parameters: N-stage, CD8⁺ labeling, as well as this OTU_104 belonging to the order Clostridiales. Not only were CD8⁺ labeling and OTU_104 significant contributors in the final DFS model, but they were also inversely correlated to each other (p=0.022). Interestingly, CD8⁺ was also significantly associated with the microbiota composition in the tumor: CD8⁺ T cells was inversely correlated with alpha diversity (p=0.027) and significantly associated with the beta diversity. This study is the first to demonstrate an association among the intratumoral microbiome, CD8⁺ T cells, and recurrence in CC. An increased relative abundance of a specific OTU_104 was inversely associated with CD8⁺ T cells and directly associated with CC recurrence. The link between this microbe, CD8⁺ T cells, and DFS has not been previously shown.

A Method to Define the Effects of Environmental Enrichment on Colon Microbiome Biodiversity in a Mouse Colon Tumor Model

Several recent studies have illustrated the beneficial effects of living in an enriched environment on improving human disease. In mice, environmental enrichment (EE) reduces tumorigenesis by activating the mouse immune system, or affects tumor bearing animal survival by stimulating the wound repair response, including improved microbiome diversity, in the tumor microenvironment. Provided here is a detailed procedure to assess the effects of environmental enrichment on the biodiversity of the microbiome in a mouse colon tumor model. Precautions regarding animal breeding and considerations for animal genotype and mouse colony integration are described, all of which ultimately affect microbial biodiversity. Heeding these precautions may allow more uniform microbiome transmission, and consequently will alleviate non-treatment dependent effects that can confound study findings. Further, in this procedure, microbiota changes are characterized using 16S rDNA sequencing of DNA isolated from stool collected from the distal colon following long-term environmental enrichment. Gut microbiota imbalance is associated with the pathogenesis of inflammatory bowel disease and colon cancer, but also of obesity and diabetes among others. Importantly, this protocol for EE and microbiome analysis can be utilized to study the role of microbiome pathogenesis across a variety of diseases where robust mouse models exist that can recapitulate human disease.

Isoliquiritigenin decreases the incidence of colitis-associated colorectal cancer by modulating the intestinal microbiota

Imbalances in intestinal bacteria correlate with colitis-associated colorectal cancer (CAC). Traditional Chinese medicines have been used to adjust the gut microbiota, and isoliquiritigenin (ISL), a flavonoid extracted from licorice, has shown antitumor efficacy. In this study, the effects of ISL on CAC development and the gut microbiota were evaluated using an azoxymethane and dextran sulphate sodium (AOM/DSS)-induced mouse model of CAC (CACM). Histopathological analysis suggested that ISL reduced tumor incidence in vivo. Moreover, high-throughput sequencing and terminal restriction fragment length polymorphism (T-RFLP) studies of the bacterial 16S rRNA gene revealed that the structure of the gut microbial community shifted significantly following AOM/DSS treatment, and that effect was alleviated by treatment with high-dose ISL (150 mg/kg). Compared to the microbiota in the control mice (CK), the levels of Bacteroidetes decreased and the levels of Firmicutes increased during CAC development. ISL reversed the imbalance at the phylum level and altered the familial constituents of the gut microbiota. Specifically, the abundance of Helicobacteraceae increased after treatment with high-dose ISL, while the abundance of Lachnospiraceae and Rikenellaceae decreased. At the genus level, ISL reduced the abundance of opportunistic pathogens (Escherichia and Enterococcus), and increased the levels of probiotics, particularly butyrate-producing bacteria (Butyricicoccus, Clostridium, and Ruminococcus). Thus, ISL protects mice from AOM/DSS-induced CAC, and ISL and the gut microbiota may have synergistic anti-cancer effects.

Evolutionary biologic changes of gut microbiota in an 'adenoma-carcinoma sequence' mouse colorectal cancer model induced by 1, 2-Dimethylhydrazine

The molecular biological mechanisms underlying the evolutionary biologic changes leading to carcinogenesis remain unclear. The main objective of our study was to explore the evolution of the microbiota community and molecules related with CRC in the dynamic transition from normal colon epithelium to premalignant adenoma with the aid of an 'adenoma-carcinoma sequence' mouse CRC model induced by DMH. We generated a modified mouse CRC model induced by DMH for DNA sequences, and characterized the molecular networks. Data from 454 pyrosequencing of the V3- V5 region of the 16S rDNA gene and immunohistochemical detection of APC, P53, K-RAS and BRAF genes were assessed with Principal coordinates, UniFrac, and Kruskal-Wallis rank sum test. The inflammatory group showed enrichment of Bacteroidetes and Porphyromonadaceae (P < 0.01). OTUs affiliated with Firmicutes were enriched in the hyperproliferative group (P < 0.01). Rikenellaceae and Ruminococcaceae showed an increasing trend during the CRC process while the opposite pattern was observed for Prevotellaceaeand Enterobacteriaceae. OTUs related to Alistipes finegoldii were significantly increased during CRC development, P53, K-RAS and BRAF, were gradually increased (P < 0.05). Conversely, expression of APC was decreased during the course of development of CRC. Our results demonstrate that the biological evolutionary shift of gut microbiota, characterized by a gradual decrease in 'driver' bacteria and an increase in DNA damage-causing bacteria, is accompanied by tumor development in the CRC model. The synergistic actions of microbiota dysbiosis and effects of bacterial metabolites on related molecular events are proposed to contribute to the progression of CRC tumorigenesis.

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis

Epidemiological studies propose a protective role for dietary fiber in colon cancer (CRC). One possible mechanism of fiber is its fermentation property in the gut and ability to change microbiota composition and function. Here, we investigate the role of a dietary fiber mixture in polyposis and elucidate potential mechanisms using TS4Cre × cAPC^l°^x468 mice. Stool microbiota profiling was performed, while functional prediction was done using PICRUSt. Stool short-chain fatty acid (SCFA) metabolites were measured. Histone acetylation and expression of SCFA butyrate receptor were assessed. We found that SCFA-producing bacteria were lower in the polyposis mice, suggesting a decline in the fermentation product of dietary fibers with polyposis. Next, a high fiber diet was given to polyposis mice, which significantly increased SCFA-producing bacteria as well as SCFA levels. This was associated with an increase in SCFA butyrate receptor and a significant decrease in polyposis. In conclusion, we found polyposis to be associated with dysbiotic microbiota characterized by a decline in SCFA-producing bacteria, which was targetable by high fiber treatment, leading to an increase in SCFA levels and amelioration of polyposis. The prebiotic activity of fiber, promoting beneficial bacteria, could be the key mechanism for the protective effects of fiber on colon carcinogenesis. SCFA-promoting fermentable fibers are a promising dietary intervention to prevent CRC.

Longitudinal Analysis of Fecal Microbiome and Pathologic Processes in a Rotenone Induced Mice Model of Parkinson's Disease

Recent studies reported an association between gut microbiota composition and Parkinson’s disease (PD). However, we know little about the relationship between microbiome dysbiosis and the pathogenesis of PD. The objective of this study was to describe the evolution of fecal microbiota using an oral rotenone model of PD from a longitudinal study over a period of 4 weeks. Gastrointestinal function was assessed by measuring fecal pellet output, motor functions was assessed by open-field and pole tests every week. α-synuclein pathology, inflammation and tyrosine hydroxylase (TH) neuron loss from the middle brain were also analyzed. Fecal samples were collected every week followed by 16S rRNA sequencing and bioinformatics analysis. We reported that chronically oral administered rotenone caused gastrointestinal dysfunction and microbiome dysbiosis prior to motor dysfunction and central nervous system (CNS) pathology. 16S rRNA sequencing of fecal microbiome showed rotenone-treated mice exhibited fecal microbiota dysbiosis characterized by an overall decrease in bacterial diversity and a significant change of microbiota composition, notably members of the phyla Firmicutes and Bacteroidetes, with an increase in Firmicutes/Bacteroidetes ratio after 3 weeks of rotenone treatment. Moreover, rotenone-induced gastrointestinal and motor dysfunctions were observed to be robustly correlated with changes in the composition of fecal microbiota. Our results demonstrated that gut microbiome perturbation might contribute to rotenone toxicity in the initiation of PD and brought a new insight in the pathogenesis of PD. Novel therapeutic options aimed at modifying the gut microbiota composition might postpone the onset and following cascade of neurodegeneration.

Fusobacterium's link to colorectal neoplasia sequenced: A systematic review and future insights

AIM

To critically evaluate previous scientific evidence on Fusobacterium's role in colorectal neoplasia development.

METHODS

Two independent investigators systematically reviewed all original scientific articles published between January, 2000, and July, 2017, using PubMed, EMBASE, and MEDLINE. A total of 355 articles were screened at the abstract level. Of these, only original scientific human, animal, and in vitro studies investigating Fusobacterium and its relationship with colorectal cancer (CRC) were included in the analysis. Abstracts, review articles, studies investigating other colonic diseases, and studies written in other languages than English were excluded from our analysis. Ninety articles were included after removing duplicates, resolving disagreements between the two reviewers, and applying the above criteria.

RESULTS

Studies have consistently identified positive associations between Fusobacterium, especially Fusobacterium nucleatum (F. nucleatum), and CRC. Stronger associations were seen in CRCs proximal to the splenic flexure and CpG island methylator phenotype (CIMP)-high CRCs. There was evidence of temporality and a biological gradient, with increased F. nucleatum DNA detection and quantity along the traditional adenoma-carcinoma sequence and in CIMP-high CRC precursors. Diet may have a differential impact on colonic F. nucleatum enrichment; evidence suggests that high fiber diet may reduce the risk of a subset of CRCs that are F. nucleatum DNA-positive. Data also suggest shorter CRC and disease-specific survival with increased amount of F. nucleatum DNA in CRC tissue. The pathophysiology of enrichment of F. nucleatum and other Fusobacterium species in colonic tissue is unclear; however, the virulence factors and changes to the local colonic environment with disruption of the protective mucus layer may contribute. The presence of a host lectin (Gal-GalNAc) in the colonic epithelium may also mediate F. nucleatum attachment to CRC and precursors through interaction with an F. nucleatum protein, fibroblast activation protein 2 (FAP2). The clinical significance of detection or enrichment of Fusobacterium in colorectal neoplasia is ambiguous, but data suggest a procarcinogenic effect of F. nucleatum, likely due to activation of oncogenic and inflammatory pathways and modulation of the tumor immune environment. This is hypothesized to be mediated by certain F. nucleatum strains carrying invasive properties and virulence factors such as FadA and FAP.

CONCLUSION

Evidence suggests a potential active role of Fusobacterium, specifically F. nucleatum, in CRC. Future prospective and experimental human studies would fill an important gap in this literature.

Small molecules related to adrenomedullin reduce tumor burden in a mouse model of colitis-associated colon cancer

To investigate the contribution of adrenomedullin (AM) and its gene-related peptide, proadrenomedullin N-terminal 20 peptide (PAMP), to the progression and potential treatment of colon cancer we studied the effects of four small molecules (SM) related to AM and PAMP on a mouse model of colon cancer. For each SM, four experimental groups of male mice were used: (i) Control group; (ii) SM group; (iii) DSS group (injected with azoxymethane [AOM] and drank dextran sulfate sodium [DSS]); and (iv) DSS + SM group (treated with AOM, DSS, and the SM). None of the mice in groups i and ii developed tumors, whereas all mice in groups iii and iv developed colon neoplasias. No significant differences were found among mice treated with PAMP modulators (87877 and 106221). Mice that received the AM negative modulator, 16311, had worse colitis symptoms than their control counterparts, whereas mice injected with the AM positive modulator, 145425, had a lower number of tumors than their controls. SM 145425 regulated the expression of proliferation marker Lgr5 and had an impact on microbiota, preventing the DSS-elicited increase of the Bacteroides/Prevotella ratio. These results suggest that treatment with AM or with positive modulator SMs may represent a novel strategy for colon cancer.

Clinical significance of Fusobacterium nucleatum, epithelial-mesenchymal transition, and cancer stem cell markers in stage III/IV colorectal cancer patients

Colorectal cancer (CRC) is a common digestive malignancy and emerging studies have closely linked its initiation and development with gut microbiota changes. Fusobacterium nucleatum (Fn) has been recently identified as a pathogenic bacteria for CRC; however, its prognostic significance for patients is poorly investigated and is less for patients within late stage. Therefore, in this study, we made efforts to analyze its level and prognostic significance in a retrospective cohort of 280 stage III/IV CRC patients. We found that the Fn level was abnormally high in tumor tissues and correlated with tumor invasion, lymph node metastasis status, and distant metastasis. We also identified it as an independent adverse prognostic factor for cancer-specific survival (CSS) and disease-free survival (DFS). The following subgroup analysis indicated that Fn level could stratify CSS and DFS in stage IIIB/C and IV patients but failed in stage IIIA patients. In addition, stage III/IV patients with low Fn level were found to benefit more from adjuvant chemotherapy than those with high Fn level, in terms of DFS. Finally, we analyzed the expression and clinical significance of epithelial-to-mesenchymal transition (EMT) markers (E-cadherin and N-cadherin) and cancer stem cell (CSC) markers (Nanog, Oct-4, and Sox-2) in CRC tissues. The results indicated that N-cadherin, Nanog, Oct-4, and Sox-2 were adverse prognostic factors in these patients, while the opposite was true for E-cadherin. More importantly, expression of E-cadherin, N-cadherin, and Nanog was significantly correlated with Fn level in tumor tissues, suggesting the potential involvement of Fn in EMT-CSC cross talk during CRC progression. Taken together, these findings indicate that Fn is a novel predictive biomarker for clinical management in stage III/IV patients, and targeting Fn may be an effective adjuvant approach for preventing CRC metastasis and chemotherapy resistance.

Fecal microbiome in dogs with inflammatory bowel disease and intestinal lymphoma

Although alteration of commensal microbiota is associated with chronic gastrointestinal (GI) diseases such as inflammatory bowel disease (IBD) in dogs, the microbiota composition in intestinal lymphoma, an important differential diagnosis of canine IBD, has not been investigated. The objective of this study was to compare the fecal microbiota in dogs with IBD, dogs with intestinal lymphoma, and healthy dogs. Eight dogs with IBD, eight dogs with intestinal lymphoma, and fifteen healthy dogs were included in the study. Fecal samples were analyzed by 16S rRNA gene next-generation sequencing. Rarefaction analysis failed to reveal any difference in bacterial diversity among healthy dogs and diseased dogs. Based on PCoA plots of unweighted UniFrac distances, the bacterial composition in dogs with intestinal lymphoma was different from those observed in dogs with IBD and healthy dogs. When compared with healthy dogs, intestinal lymphoma subjects showed significant increases in organisms belonging to the Eubacteriaceae family. The proportion of the family Paraprevotellaceae and the genus Porphyromonas was significantly higher in dogs with IBD compared to healthy dogs. These observations suggest that dysbiosis is associated with intestinal lymphoma as well as IBD in dogs.

Dietary Broccoli Impacts Microbial Community Structure and Attenuates Chemically Induced Colitis in Mice in an Ah receptor dependent manner

Consumption of broccoli mediates numerous chemo-protective benefits through the intake of phytochemicals, some of which modulate aryl hydrocarbon receptor (AHR) activity. Whether AHR activation is a critical aspect of the therapeutic potential of dietary broccoli is not known. Here we administered isocaloric diets, with or without supplementation of whole broccoli (15% w/w), to congenic mice expressing the high-affinity Ahrb/b or low-affinity Ahrd/d alleles, for 24 days and examined the effects on AHR activity, intestinal microbial community structure, inflammatory status, and response to chemically induced colitis. Cecal microbial community structure and metabolic potential were segregated according to host dietary and AHR status. Dietary broccoli associated with heightened intestinal AHR activity, decreased microbial abundance of the family Erysipelotrichaceae, and attenuation of colitis. In summary, broccoli consumption elicited an enhanced response in ligand-sensitive Ahrb/b mice, demonstrating that in part the beneficial aspects of dietary broccoli upon intestinal health are associated with heightened AHR activity.

Secretome of Intestinal Bacilli: A Natural Guard against Pathologies

Current studies of human gut microbiome usually do not consider the special functional role of transient microbiota, although some of its members remain in the host for a long time and produce broad spectrum of biologically active substances. Getting into the gastrointestinal tract (GIT) with food, water and probiotic preparations, two representatives of Bacilli class, genera Bacillus and Lactobacillus, colonize epithelium blurring the boundaries between resident and transient microbiota. Despite their minor proportion in the microbiome composition, these bacteria can significantly affect both the intestinal microbiota and the entire body thanks to a wide range of secreted compounds. Recently, insufficiency and limitations of pure genome-based analysis of gut microbiota became known. Thus, the need for intense functional studies is evident. This review aims to characterize the Bacillus and Lactobacillus in GIT, as well as the functional roles of the components released by these members of microbial intestinal community. Complex of their secreted compounds is referred by us as the "bacillary secretome." The composition of the bacillary secretome, its biological effects in GIT and role in counteraction to infectious diseases and oncological pathologies in human organism is the subject of the review.

Roseburia spp.: a marker of health?

The genus Roseburia consists of obligate Gram-positive anaerobic bacteria that are slightly curved, rod-shaped and motile by means of multiple subterminal flagella. It includes five species: Roseburia intestinalis, R. hominis, R. inulinivorans, R. faecis and R. cecicola. Gut Roseburia spp. metabolize dietary components that stimulate their proliferation and metabolic activities. They are part of commensal bacteria producing short-chain fatty acids, especially butyrate, affecting colonic motility, immunity maintenance and anti-inflammatory properties. Modification in Roseburia spp. representation may affect various metabolic pathways and is associated with several diseases (including irritable bowel syndrome, obesity, Type 2 diabetes, nervous system conditions and allergies). Roseburia spp. could also serve as biomarkers for symptomatic pathologies (e.g., gallstone formation) or as probiotics for restoration of beneficial flora.

Microbiota, Inflammation and Colorectal Cancer

Colorectal cancer, the fourth leading cause of cancer-related death worldwide, is a multifactorial disease involving genetic, environmental and lifestyle risk factors. In addition, increased evidence has established a role for the intestinal microbiota in the development of colorectal cancer. Indeed, changes in the intestinal microbiota composition in colorectal cancer patients compared to control subjects have been reported. Several bacterial species have been shown to exhibit the pro-inflammatory and pro-carcinogenic properties, which could consequently have an impact on colorectal carcinogenesis. This review will summarize the current knowledge about the potential links between the intestinal microbiota and colorectal cancer, with a focus on the pro-carcinogenic properties of bacterial microbiota such as induction of inflammation, the biosynthesis of genotoxins that interfere with cell cycle regulation and the production of toxic metabolites. Finally, we will describe the potential therapeutic strategies based on intestinal microbiota manipulation for colorectal cancer treatment.

Keratin 8 reduces colonic permeability and maintains gut microbiota homeostasis, protecting against colitis and colitis-associated tumorigenesis

Keratin 8 (CK8) is the major component of the intermediate filaments of simple or single-layered epithelia. Gene targeting mice model suggest that CK8 is involved in colonic active ion transport, colorectal hyperplasia and inflammation. In the present study, we found that CK8 is downregulated in the colon during DSS-induced colitis and AOM/DSS-induced colitis-associated colorectal cancer (CAC) development. In human patients with colon cancer, CK8 is downregulated. Using CK8 heterozygous knockout mice (CK8^+/-), we found that CK8^+/- mice are highly susceptible to DSS-induced colitis and more prone to AOM/DSS-induced CAC than wild type (WT) mice. The colonic permeability is increased with DSS or AOM/DSS treatment, leading to alteration of gut microbiota in CK8^+/- mice with CAC. Metagenomic analysis of fecal microbiota suggests Firmicutes and Proteobacteria are increased in CK8^+/- mice with CAC, while Bacteroidetes and Verrucomicrobia are decreased. Antibiotic treatment decreases the incidence of colorectal cancer tumorigenesis and TLR4 inhibitor attenuates the susceptibility of CK8^+/- mice to DSS-induced colitis. These data suggest CK8 protects mice from colitis and colitis-associated colorectal cancer by modulating colonic permeability and gut microbiota composition homeostasis.