Culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal cancer and polypectomized individuals

"Does the Gut microbiome influence disc health and disease?-the interplay between dysbiosis, pathobionts, and disc inflammation: a Pilot Study"

BACKGROUND CONTEXT

Gut microbiome alterations resulting in inflammatory responses have been implicated in many distant effects on different organs. However, its influence on disc health is still not fully investigated.

PURPOSE

Our objective was to document the gut biome in healthy volunteers and patients with disc degeneration and to understand the role of gut dysbiosis on human disc health.

STUDY DESIGN

Experimental case-control study.

PATIENT SAMPLE

We included 40 patients with disc degeneration (DG) and 20 healthy volunteers (HV). HV comprised of age groups 30 to 60 years with no known record of back pain and no clinical comorbidities, with normal MRI. Diseased group (DG) were patients in the same age group undergoing surgery for disc disease (disc herniation-25; discogenic stenosis-15) and without instability (with Modic-20; and non-Modic-20).

OUTCOME MEASURES

N/A.

METHODS

We analyzed 16S V3-V4 rDNA gut metagenome from 20 healthy volunteers (HV) and compared the top signature genera from 40 patients with disc degeneration (DG) across Modic and non-Modic groups. Norgen Stool DNA Kit was used for DNA extraction from ∼200 mg of each faecal sample collected using the Norgen Stool Collection Kit.16S V3-V4 rDNA amplicons were generated with universal bacterial primers 341F and 806R and amplified with Q5 High-Fidelity DNA Polymerase. Libraries were sequenced with 250×2 PE to an average of 0.1 million raw reads per sample (Illumina Novaseq 6000). Demultiplexed raw data was assessed with FastQC, and adapter trimmed reads >Q30 reads were processed in the QIME2 pipeline. Serum C-reactive protein (CRP) was measured by the immunoturbimetry method and Fatty acid-binding protein 5 (FABP5) was measured in albumin-globulin-depleted plasma through global proteome analysis.

RESULTS

We observed significant gut dysbiosis between HV and DG and also between the Modic and non-Modic groups. In the Modic group, commensals Bifidobacterium and Ruminococcus were significantly depleted, while pathobionts Streptococcus, Prevotella, and Butryvibrio were enriched. Firmicutes/Bacteroidetes ratio was decreased in DG (Modic-0.62, non-Modic-0.43) compared to HV (0.70). Bacteria-producing beneficial short-chain fatty acids were also depleted in DG. Elevated serum CRP and increased FABP5 were observed in DG.

CONCLUSION

The study revealed gut dysbiosis, an altered Firmicutes/Bacteroidetes ratio, reduced SCFA-producing bacteria, and increased systemic and local inflammation in association with disc disease, especially in Modic changes. The findings have considerable importance for our understanding and prevention of disc degeneration.

Sex-specific differences in intestinal microbiota associated with cardiovascular diseases

BACKGROUND

Cardiovascular diseases (CVD), including coronary heart disease (CHD), display a higher prevalence in men than women. This study aims to evaluate the variations in the intestinal microbiota between men and women afflicted with CHD and delineate these against a non-CVD control group for each sex.

METHODS

Our research was conducted in the framework of the CORDIOPREV study, a clinical trial which involved 837 men and 165 women with CHD. We contrasted our findings with a reference group of 375 individuals (270 men, 105 women) without CVD. The intestinal microbiota was examined through 16S metagenomics on the Illumina MiSeq platform and the data processed with Quiime2 software.

RESULTS

Our results showed a sex-specific variation (beta diversity) in the intestinal microbiota, while alpha-biodiversity remained consistent across both sexes. Linear discriminant analysis effect size (LEfSe) analysis revealed sex-centric alterations in the intestinal microbiota linked to CVD. Moreover, using random forest (RF) methodology, we identified seven bacterial taxa-g_UBA1819 (Ruminococcaceae), g_Bilophila, g_Subdoligranulum, g_Phascolarctobacterium, f_Barnesiellaceae, g_Ruminococcus, and an unknown genus from the Ruminococcaceae family (Ruminococcaceae incertae sedis)-as key discriminators between men and women diagnosed with CHD. The same taxa also emerged as critical discriminators between CHD-afflicted and non-CVD individuals, when analyzed separately by sex.

CONCLUSION

Our findings suggest a sex-specific dysbiosis in the intestinal microbiota linked to CHD, potentially contributing to the sex disparity observed in CVD incidence. Trial registration Clinical Trials.gov.Identifier NCT00924937.

A Novel Multi-Strain E3 Probiotic Formula Improved the Gastrointestinal Symptoms and Quality of Life in Chinese Psoriasis Patients

Psoriasis is a chronic immune-mediated inflammatory disease affecting the skin and other systems. Gastrointestinal disease was found to be correlated with psoriasis in previous studies and it can significantly affect the quality of life of psoriasis patients. Despite the importance of the gut microbiome in gut and skin health having already been demonstrated in many research studies, the potential effect of probiotics on GI comorbidities in psoriasis patients is unclear. To investigate the effects of probiotics on functional GI comorbidities including irritable bowel syndrome, functional constipation, and functional diarrhea in psoriasis patients, we conducted a targeted 16S rRNA sequencing and comprehensive bioinformatic analysis among southern Chinese patients to compare the gut microbiome profiles of 45 psoriasis patients over an 8-week course of novel oral probiotics. All the participants were stratified into responders and non-responders according to their improvement in GI comorbidities, which were based on their Bristol Stool Form Scale (BSFS) scores after intervention. The Dermatological Life Quality Index (DLQI) score revealed a significant improvement in quality of life within the responder group (DLQI: mean 10.4 at week 0 vs. mean 15.9 at week 8, p = 0.0366). The proportion of psoriasis patients without GI comorbidity manifestation at week 8 was significantly higher than that at week 0 (week 0: Normal 53.33%, Constipation/Diarrhea 46.67%; week 8: Normal 75.56%, Constipation/Diarrhea 24.44%, p = 0.0467). In addition, a significant difference in the gut microbiome composition between the responders and non-responders was observed according to alpha and beta diversities. Differential abundance analysis revealed that the psoriasis patients exhibited (1) an elevated relative abundance of Lactobacillus acidophilus, Parabacteroides distasonis, and Ruminococcus bromii and (2) a reduced relative abundance of Oscillibacter, Bacteroides vulgatus, Escherichia sp., and Biophila wadsworthia after the 8-week intervention. The responders also exhibited a higher relative abundance of Fusicatenibacter saccharivorans when compared to the non-responders. In summary, our study discovers the potential clinical improvement effects of the novel probiotic formula in improving GI comorbidities and quality of life in psoriasis patients. We also revealed the different gut microbiome composition as well as the gut microbial signatures in the patients who responded to probiotics. These findings could provide insight into the use of probiotics in the management of psoriasis symptoms.

Fecal microbiota as a predictor of acupuncture responses in patients with postpartum depressive disorder

Background

There are several clinical and molecular predictors of responses to antidepressant therapy. However, these markers are either too subjective or complex for clinical use. The gut microbiota could provide an easily accessible set of biomarkers to predict therapeutic efficacy, but its value in predicting therapy responses to acupuncture in patients with depression is unknown. Here we analyzed the predictive value of the gut microbiota in patients with postpartum depressive disorder (PPD) treated with acupuncture.

Methods

Seventy-nine PPD patients were enrolled: 55 were treated with acupuncture and 24 did not received any treatment. The 17-item Hamilton depression rating scale (HAMD-17) was used to assess patients at baseline and after eight weeks. Patients receiving acupuncture treatment were divided into an acupuncture-responsive group or non-responsive group according to HAMD-17 scores changes. Baseline fecal samples were obtained from the patients receiving acupuncture and were analyzed by high-throughput 16S ribosomal RNA sequencing to characterize the gut microbiome.

Results

47.27% patients responded to acupuncture treatment and 12.5% patients with no treatment recovered after 8-week follow-up. There was no significant difference in α-diversity between responders and non-responders. The β-diversity of non-responders was significantly higher than responders. Paraprevotella and Desulfovibrio spp. were significantly enriched in acupuncture responders, and these organisms had an area under the curve of 0.76 and 0.66 for predicting responder patients, respectively.

Conclusions

Paraprevotella and Desulfovibrioare may be useful predictive biomarkers to predict PPD patients likely to respond to acupuncture. Larger studies and validation in independent cohorts are now needed to validate our findings.

Desulfovibrio in the Gut: The Enemy within?

Desulfovibrio (DSV) are sulfate-reducing bacteria (SRB) that are ubiquitously present in the environment and as resident commensal bacteria within the human gastrointestinal tract. Though they are minor residents of the healthy gut, DSV are opportunistic pathobionts that may overgrow in the setting of various intestinal and extra-intestinal diseases. An increasing number of studies have demonstrated a positive correlation between DSV overgrowth (bloom) and various human diseases. While the relationship between DSV bloom and disease pathology has not been clearly established, mounting evidence suggests a causal role for these bacteria in disease development. As DSV are the most predominant genera of SRB in the gut, this review summarizes current knowledge regarding the relationship between DSV and a variety of diseases. In this study, we also discuss the mechanisms by which these bacteria may contribute to disease pathology.

Gut Microbiota and Serum Metabolites in Individuals with Class III Obesity Without Type 2 Diabetes Mellitus: Pilot Analysis

Background: Gut microbial composition seems to change in association with prediabetes. The purpose of this prospective cross-sectional study was to compare the composition of gut microbiota and energy metabolites between individuals with class III obesity but without type 2 diabetes mellitus (OB) and healthy normal weight controls. Methods: The subjects of this prospective cross-sectional study were participants recruited from a previous clinical trial (No: NCT02325804), with intervention focused on weight loss. We recruited 19 OB [mean age ± standard deviation (SD) was 35.4 ± 7.0 years, mean body mass index (BMI) ± SD was 48.8 ± 6.7 kg/m²] and 23 controls (mean age ± SD was 31.7 ± 14.8 years, mean BMI ± SD was 22.2 ± 1.7 kg/m²). Their fecal microbiota was categorized using specific primers targeting the V1-V3 region of 16S rDNA, whereas serum metabolites were characterized by nuclear magnetic resonance spectroscopy. Multivariate statistical analysis and Random Forest models were applied to discriminate predictors with the highest variable importance. Results: We observed a significantly lower microbial α-diversity (P = 0.001) and relative abundance of beneficial bacterium Akkermansia (P = 0.001) and the short-chain fatty acid-producing bacteria Eubacterium hallii (P = 0.019), Butyrivibrio (P = 0.024), Marvinbryantia (P = 0.010), and Coprococcus (P = 0.050) and a higher abundance of the pathogenic bacteria Bilophila (P = 0.018) and Fusobacterium (P = 0.022) in OB compared with controls. Notably, the Random Forest machine learning analysis identified energy metabolites (citrate and acetate), HOMA-IR, and insulin as important predictors capable of discriminating between OB and controls. Conclusions: Our results suggest that changes in gut microbiota and in serum acetate and citrate are additional promising biomarkers before progression to Type 2 diabetes. The non-invasive manipulation of gut microbiota composition in OB through a healthy lifestyle, thus, offers a new approach for managing class III obesity and associated disorders. ClinicalTrials.gov identifier: NCT02325804.

Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming

Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.

Active Sulfate-Reducing Bacterial Community in the Camel Gut

The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of -15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm^-3 day^-1. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS₂), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract.

Intelligent polymeric hydrogen sulfide delivery systems for therapeutic applications

Hydrogen sulfide (H₂S) plays an important role in regulating various pathological processes such as protecting mammalian cell from harmful injuries, promoting tissue regeneration, and regulating the process of various diseases caused by physiological disorders. Studies have revealed that the physiological effects of H₂S are highly associated with its concentrations. At relatively low concentration, H₂S shows beneficial functions. However, long-time and high-dose donation of H₂S would inhibit regular biological process, resulting in cell dysfunction and apoptosis. To regulate the dosage of H₂S delivery for precision medicine, H₂S delivery systems with intelligent characteristics were developed and a variety of biocompatibility polymers have been utilized to establish intelligent polymeric H₂S delivery systems, with the abilities to specifically target the lesions, smartly respond to pathological microenvironments, as well as real-timely monitor H₂S delivery and lesion conditions by incorporating imaging-capable moieties. In this review, we focus on the design, preparation, and therapeutic applications of intelligent polymeric H₂S delivery systems in cardiovascular therapy, inflammatory therapy, tissue regenerative therapy, cancer therapy and bacteria-associated therapy. Strategies for precise H₂S therapies especially imaging-guided H₂S theranostics are highlighted. Since H₂S donors with stimuli-responsive characters are vital components for establishing intelligent H₂S delivery systems, the development of H₂S donors is also briefly introduced.

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H₂S is an endogenous gasotransmitter that plays important role in regulating various physiological and pathological pathways.

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Controlled H₂S delivery is vital since the therapeutic effects of H₂S are highly associated with its concentrations.

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Intelligent polymeric H₂S delivery systems possess specific targeting, stimuli responsive and imaging guided capabilities, representing a strategic option for next generation of therapies.

Versatile Triad Alliance: Bile Acid, Taurine and Microbiota

Taurine is the most abundant free amino acid in the body, and is mainly derived from the diet, but can also be produced endogenously from cysteine. It plays multiple essential roles in the body, including development, energy production, osmoregulation, prevention of oxidative stress, and inflammation. Taurine is also crucial as a molecule used to conjugate bile acids (BAs). In the gastrointestinal tract, BAs deconjugation by enteric bacteria results in high levels of unconjugated BAs and free taurine. Depending on conjugation status and other bacterial modifications, BAs constitute a pool of related but highly diverse molecules, each with different properties concerning solubility and toxicity, capacity to activate or inhibit receptors of BAs, and direct and indirect impact on microbiota and the host, whereas free taurine has a largely protective impact on the host, serves as a source of energy for microbiota, regulates bacterial colonization and defends from pathogens. Several remarkable examples of the interaction between taurine and gut microbiota have recently been described. This review will introduce the necessary background information and lay out the latest discoveries in the interaction of the co-reliant triad of BAs, taurine, and microbiota.

An Investigation into the Correlation of Intestinal Flora with Obesity and Gestational Diabetes Mellitus

Method

Thirty-two pregnant women aged 25-35 who were hospitalized in Shanxi Maternal and Child Health Hospital from January 2019 to December 2019 were included for evaluation, including 15 normal pregnant women (NG_NO group), 6 pregnant women with GDM alone (G_NO group), and 7 pregnant women with overweight alone (NG_O group). Stools were collected from pregnant women at 24 and 37 weeks of gestation and newborns' first meconium. The v3-v4 variable region of the gut flora 16s rRNA was double-ended sequenced and bioinformatically analyzed using the Illumina MiSeq PE300 sequencing platform.

Results

In the third trimester of pregnancy, there were significant differences in the composition of intestinal flora between the simple overweight group, simple GDM group, and normal pregnant group. From the second trimester to the third trimester, there was no significant change in the relative distribution of intestinal flora at the phyla classification level in normal pregnant women. The relative distribution of intestinal flora at the phylum level of newborns was significantly different from that of their mothers. The characteristic intestinal microbes of newborns in simple GDM group were g_Diaphorobacter, while the simple recombinant neonates were Nocardiaceae (f_Nocardioidaceae). In addition, the results showed significant differences in intestinal flora among the normal pregnant women group, simple GDM group, simple overweight group, and GDM overweight group. The results of β diversity analysis showed a significant difference in intestinal microflora species composition structure between the simple overweight group and the normal pregnant group in the second trimester of pregnancy. The species composition structure of intestinal flora was similar between the simple GDM group and the normal pregnant group. In the third trimester of pregnancy, there was no significant difference in the β diversity index among the groups, and the composition and structure of intestinal flora were similar. There were significant differences in the composition structure (β diversity) of intestinal flora between pregnant women and their newborns in each group (P < 0.05). Correlation analysis showed that the blood glucose values of oral glucose tolerance test (OGTT)_1 h and OGTT_2 h were positively correlated with Bacteroides (Bacteroides) and negatively correlated with Proteus (Prevotella), prepregnancy BMI was negatively correlated with Bacteroides, and weight gain during pregnancy was negatively correlated with Vibrio (Desulfovibrio) in Proteus. The birth weight of newborns was positively correlated with Actinomycetes (Actinomyces), Bacteroides (Faecalibacterium), and microbacilli (Dialister) and negatively correlated with Rolston (Ralstonia).

Conclusion

Gut microbiota is strongly linked to obesity and gestational diabetes.

Association between intestinal microbiota and inflammatory bowel disease

Inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC), has emerged as a global disease with high incidence, long duration, devastating clinical symptoms, and low curability (relapsing immune response and barrier function defects). Mounting studies have been performed to investigate its pathogenesis to provide an ever‐expanding arsenal of therapeutic options, while the precise etiology of IBD is not completely understood yet. Recent advances in high‐throughput sequencing methods and animal models have provided new insights into the association between intestinal microbiota and IBD. In general, dysbiosis characterized by an imbalanced microbiota has been widely recognized as a pathology of IBD. However, intestinal microbiota alterations represent the cause or result of IBD process remains unclear. Therefore, more evidences are needed to identify the precise role of intestinal microbiota in the pathogenesis of IBD. Herein, this review aims to outline the current knowledge of commonly used, chemically induced, and infectious mouse models, gut microbiota alteration and how it contributes to IBD, and dysregulated metabolite production links to IBD pathogenesis.

Effect of gut microbiota in the colorectal cancer and potential target therapy

The symbiotic interaction between gut microbiota and the digestive tract is an important factor in maintaining the intestinal environment balance. Colorectal cancer (CRC) is a complex disease involving the interaction between tumour cells and a large number of microorganisms. The microbiota is involved in the occurrence, development and prognosis of colorectal cancer. Several microbiota species have been studied, such as Fusobacterium nucleatum (F. nucleatum), Enterotoxigenic Bacteroides fragilis (ETBF), Streptococcus bovis (S. bovis), Lactobacillus, and Bifidobacterium. Studies about the interaction between microbiota and CRC were retrieved from Embase, PubMed, Ovid and Web of Science up to 21 Oct 2021. This review expounded on the effect of microbiota on CRC, especially the dysregulation of bacteria and carcinogenicity. The methods of gut microbiota modifications representing novel prognostic markers and innovative therapeutic strategies were also described.

Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer

BACKGROUND

Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut. Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H₂S) in the human colon using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates; however, the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr).

RESULTS

Here, we show that genes for microbial sulfur metabolism are more abundant and diverse than previously observed and are statistically associated with CRC. Using ~ 17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, the anaerobic sulfite reductase (asr) genes were twice as abundant as dsr, demonstrating that Asr is likely a more important contributor to sulfate reduction in the human gut than Dsr. We identified twelve potential pathways for reductive taurine metabolism and discovered novel genera harboring these pathways. Finally, the prevalence of metabolic genes for organic sulfur indicates that these understudied substrates may be the most abundant source of microbially derived H₂S.

CONCLUSIONS

Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut. We show that genes for microbial sulfur metabolism in the human gut are more prevalent than previously known, irrespective of health status (i.e., in both healthy and diseased states). Our results significantly increase the diversity of pathways and bacteria that are associated with microbial sulfur metabolism in the human gut. Overall, our results have implications for understanding the role of the human gut microbiome and its potential contributions to the pathogenesis of CRC. Video abstract.

Epidemiology and biology of early onset colorectal cancer

Colorectal cancer (CRC) is the third leading cause of cancer-related mortality in men or women in the United States. Average-risk screening that begins at age 50 years has reduced incidence and mortality of CRC in those over 50 years of age, whereas CRC incidence in those under age 50 years (early onset colorectal cancer (eoCRC)) has recently and dramatically increased. In this review, we summarize the recent literature including risk factors for eoCRC, differences in clinicopathologic presentation and outcomes in eoCRC, and emerging evidence regarding the molecular pathways that are altered in eoCRC compared to later onset CRC (loCRC). Epidemiologic studies of eoCRC show predominance in distal colon and rectum, and association with several modifiable risk factors, including diabetes, obesity, diet, sedentary time, alcohol consumption and smoking. Data regarding potential risk factors of prior antibiotic exposure and microbiome alterations or direct carcinogen exposure are still emerging. Aggressive clinicopathologic features of eoCRC at presentation may be due to delay in diagnosis or more aggressive tumor biology. EoCRC outcomes are similar to loCRC when matched for stage, but overall mortality is greater due to higher frequency of advanced disease at a younger presentation, with more life-years lost. There are only few molecular evaluations of eoCRC to date, with findings of potential increase in TP53 and CTNNB1 somatic mutation and decrease in APC, KRAS and BRAF somatic mutation, compared to loCRC. Other findings include LINE-1 hypomethylation, absence of microsatellite instability (MSI-H), presence of chromosomal instability (CIN) or microsatellite and chromosomal stability (MACS). These studies are only now emerging and have not yet identified a specific molecular signature defining eoCRC. Further research evaluating genetic and molecular differences as well as environmental triggers for eoCRCs should provide a clearer understanding to inform targeted screening for pre-symptomatic at-risk younger individuals.

Oleanolic Acid: Extraction, Characterization and Biological Activity

Oleanolic acid, a pentacyclic triterpenoid ubiquitously present in the plant kingdom, is receiving outstanding attention from the scientific community due to its biological activity against multiple diseases. Oleanolic acid is endowed with a wide range of biological activities with therapeutic potential by means of complex and multifactorial mechanisms. There is evidence suggesting that oleanolic acid might be effective against dyslipidemia, diabetes and metabolic syndrome, through enhancing insulin response, preserving the functionality and survival of β-cells and protecting against diabetes complications. In addition, several other functions have been proposed, including antiviral, anti-HIV, antibacterial, antifungal, anticarcinogenic, anti-inflammatory, hepatoprotective, gastroprotective, hypolipidemic and anti-atherosclerotic activities, as well as interfering in several stages of the development of different types of cancer; however, due to its hydrophobic nature, oleanolic acid is almost insoluble in water, which has led to a number of approaches to enhance its biopharmaceutical properties. In this scenario, the present review aimed to summarize the current knowledge and the research progress made in the last years on the extraction and characterization of oleanolic acid and its biological activities and the underlying mechanisms of action.

Metabolic Influences of Gut Microbiota Dysbiosis on Inflammatory Bowel Disease

Inflammatory bowel diseases (IBD) are chronic medical disorders characterized by recurrent gastrointestinal inflammation. While the etiology of IBD is still unknown, the pathogenesis of the disease results from perturbations in both gut microbiota and the host immune system. Gut microbiota dysbiosis in IBD is characterized by depleted diversity, reduced abundance of short chain fatty acids (SCFAs) producers and enriched proinflammatory microbes such as adherent/invasive E. coli and H₂S producers. This dysbiosis may contribute to the inflammation through affecting either the immune system or a metabolic pathway. The immune responses to gut microbiota in IBD are extensively discussed. In this review, we highlight the main metabolic pathways that regulate the host-microbiota interaction. We also discuss the reported findings indicating that the microbial dysbiosis during IBD has a potential metabolic impact on colonocytes and this may underlie the disease progression. Moreover, we present the host metabolic defectiveness that adds to the impact of symbiont dysbiosis on the disease progression. This will raise the possibility that gut microbiota dysbiosis associated with IBD results in functional perturbations of host-microbiota interactions, and consequently modulates the disease development. Finally, we shed light on the possible therapeutic approaches of IBD through targeting gut microbiome.

Hydrogen sulfide in ageing, longevity and disease

Hydrogen sulfide (H₂S) modulates many biological processes, including ageing. Initially considered a hazardous toxic gas, it is now recognised that H₂S is produced endogenously across taxa and is a key mediator of processes that promote longevity and improve late-life health. In this review, we consider the key developments in our understanding of this gaseous signalling molecule in the context of health and disease, discuss potential mechanisms through which H₂S can influence processes central to ageing and highlight the emergence of novel H₂S-based therapeutics. We also consider the major challenges that may potentially hinder the development of such therapies.

Modulation of Gut Microbiota Composition and Short-Chain Fatty Acid Synthesis by Mogroside V in an In Vitro Incubation System

Mogroside V (MV), a sweetener, is one of the major components inSiraitia grosvenorii. In our research, after in vitro incubation with MV for 24 h, the human gut microbiota diversity changed, with an enrichment of the genera Bacteroides, Lactobacillus, Prevotella, Megasphaera, and Olsenella and the inhibition of Clostridium XlVa, Dorea, and Desulfovibrio. Moreover, the synthesis of short-chain fatty acids, such as acetate, propionate, and butyrate, was increased by gut microbiota. According to ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) analysis, MV was decomposed into secondary mogrosides, such as mogroside II/I and mogrol, by gut microbiota. Enhanced antioxidant abilities of the metabolites were found in the broth. The results suggested that MV, as a potential prebiotic, could benefit human health through its interaction with gut microbiota.

The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men

INTRODUCTION

We recently described the sulfur microbial diet, a pattern of intake associated with increased gut sulfur-metabolizing bacteria and incidence of distal colorectal cancer (CRC). We assessed whether this risk differed by CRC molecular subtypes or presence of intratumoral microbes involved in CRC pathogenesis (Fusobacterium nucleatum and Bifidobacterium spp.).

METHODS

We performed Cox proportional hazards modeling to examine the association between the sulfur microbial diet and incidence of overall and distal CRC by molecular and microbial subtype in the Health Professionals Follow-Up Study (1986-2012).

RESULTS

We documented 1,264 incident CRC cases among 48,246 men, approximately 40% of whom had available tissue data. After accounting for multiple hypothesis testing, the relationship between the sulfur microbial diet and CRC incidence did not differ by subtype. However, there was a suggestion of an association by prostaglandin synthase 2 (PTGS2) status with a multivariable adjusted hazard ratio for highest vs lowest tertile of sulfur microbial diet scores of 1.31 (95% confidence interval: 0.99-1.74, Ptrend = 0.07, Pheterogeneity = 0.04) for PTGS2-high CRC. The association of the sulfur microbial diet with distal CRC seemed to differ by the presence of intratumoral Bifidobacterium spp. with an adjusted hazard ratio for highest vs lowest tertile of sulfur microbial diet scores of 1.65 (95% confidence interval: 1.14-2.39, Ptrend = 0.01, Pheterogeneity = 0.03) for Bifidobacterium-negative distal CRC. We observed no apparent heterogeneity by other tested molecular markers.

DISCUSSION

Greater long-term adherence to the sulfur microbial diet could be associated with PTGS2-high and Bifidobacterium-negative distal CRC in men. Additional studies are needed to further characterize the role of gut microbial sulfur metabolism and CRC.

Relationship between gut microbiota and markers of myocardial fibrosis in with chronic heart failure with preserved ejection fraction

Aim. To study the relationship of gut microbiota (GM) with serum myocardial fibrosis markers in patients with heart failure with preserved ejection fraction (HFpEF).

Material and methods. The composition of the gut microbiota among 42 patients with HFpEF aged 67,0 [64,0; 71,5] years (men, 57,1%) was assessed by 16S ribosomal ribonucleic acid sequencing. The quantitative determination of myocardial fibrosis markers was carried out by enzyme-linked immunosorbent assay. Correlation and multivariate regression analysis of relationships between the relative abundance of intestinal bacteria and the concentration of the procollagen type I carboxy-terminal propeptide (PICP) and N-terminal propeptide of procollagen type III (PIIINP) was carried out.

Results. The PICP and PIIINP concentrations were 918,0 [700,0; 1032,8] pg/ml and 6,2±2,7 pg/ml, respectively. Correlation analysis revealed a direct relationship between the relative abundance of Allisonella and PICP (r=0,32), as well as Blautia, Enterobаcteriaceae (unclassified) and PIIINP (r=0,37 and r=0,32), p<0,05. The inverse relationship was determined for the relative abundance of the genera Ruminococcus (r=-0,37), Ruminococcaceae (unclassified) (r=-0,31), Gemmiger (r=(-0,35) and PICP, as well as Bilophila and PIIICP (r=(-0,34). Multivariate regression found (normalized coefficient in parentheses) that the abundance of Butyricimonas (0,27) и Blautia (0,35) was directly related to the PICP levels, while the abundance of the genus Intestinimonas ((-0,23) showed an inverse association with the marker level. The abundance of most genera had an inverse relationship with PIIINP: Atopobium (-0,25), Cellulosilyticum (-0,31), Solobacterium (-0,32), Turicibacter (-0,47), Bilophila (-0,30). The directness of the association with  PIIINP concentration was demonstrated for the relative abundance of Paraprevotella (0,32) и Desulfovibrio (0,28). The p-value for all associations is <0,05.

Conclusion. The relative abundance of GM genera in patients with HFpEF is associated with fibrosis markers (PICP and PIIINP). The results obtained make it possible to deepen the understanding of the relationship between GM and pathogenesis of HFpEF, which may become a step towards understanding the GM role in the progression of left ventricular diastolic dysfunction and rationale for future studies.

Microbiota's role in health and diseases

The microbiome is a term that usually refers to the community of various microorganisms that inhabit/live inside human/animal bodies or on their skin. It forms a complex ecosystem that includes trillions of commensals, symbiotics, and even pathogenic microorganisms. The external environment, diet, and lifestyle are the major determinants influencing the microbiome's composition and vitality. Recent studies have indicated the tremendous influence of the microbiome on health and disease. Their number, constitution, variation, and viability are dynamic. All these elements are responsible for the induction, development, and treatment of many health disorders. Serious diseases such as cancer, metabolic disorders, cardiovascular diseases, and even psychological disorders such as schizophrenia are influenced directly or indirectly by microbiota. In addition, in the last few weeks, accumulating data about the link between COVID-19 and the microbiota were published. In the present work, the role of the microbiome in health and disease is discussed. A deep understanding of the exact role of microbiota in disease induction enables the prevention of diseases and the development of new therapeutic concepts for most diseases through the correction of diet and lifestyle. The present review brings together evidence from the most recent works and discusses suggested nutraceutical approaches for the management of COVID-19 pandemic.

Functional differentiation related to decomposing complex carbohydrates of intestinal microbes between two wild zokor species based on 16SrRNA sequences

BACKGROUND

The intestinal microbes in mammals play a key role in host metabolism and adaptation. As a subterranean rodent, zokor digs tunnels for foraging and mating. These digging activities of zokors increase the energy expenditure relative to their aboveground counterparts. However, relatively little is known regarding intestinal microbes of zokor and how they make full use of limited food resources underground for high energy requirements.

RESULTS

Eospalax cansus and Eospalax rothschildi had distinct intestinal microbes. Although the composition of intestinal microbes is similar in two species, the proportion of bacterium are distinctly different between them. At phylum level, 11 phyla were shared between two species. Firmicutes and Bacteroidota were two dominant microbes in both of two species, while Eospalax cansus have a significantly high proportion of Firmicutes/Bacteroidota than that of Eospalax rothschildi. At genus level, norank_f_Muribaculaceae were dominant microbes in both of two zokor species. The relative abundance of 12 genera were significantly different between two species. Some bacterium including unclassified_f__Lachnospiraceae, Lachnospiraceae_NK4A136_group, Ruminococcus and Eubacterium_siraeum_group associated with cellulose degradation were significantly enriched in Eospalax cansus. Although alpha diversity was with no significant differences between Eospalax cansus and Eospalax rothschildi, the intestinal microbes between them are significant distinct in PCoA analysis. We have found that trapping location affected the alpha diversity values, while sex and body measurements had no effect on alpha diversity values. PICRUSt metagenome predictions revealed significant enrichment of microbial genes involved in carbohydrate metabolism in Eospalax cansus rather than Eospalax rothschildi.

CONCLUSIONS

Our results demonstrate that Eospalax cansus harbor a stronger ability of fermentation for dietary plants than Eospalax rothschildi. The stronger ability of fermentation and degradation of cellulose of intestinal microbes of Eospalax cansus may be a long-time adaptation to limited food resources underground.

Desulfovibrio Bacteria Are Associated With Parkinson's Disease

Parkinson's disease (PD) is the most prevalent movement disorder known and predominantly affects the elderly. It is a progressive neurodegenerative disease wherein α-synuclein, a neuronal protein, aggregates to form toxic structures in nerve cells. The cause of Parkinson's disease (PD) remains unknown. Intestinal dysfunction and changes in the gut microbiota, common symptoms of PD, are evidently linked to the pathogenesis of PD. Although a multitude of studies have investigated microbial etiologies of PD, the microbial role in disease progression remains unclear. Here, we show that Gram-negative sulfate-reducing bacteria of the genus Desulfovibrio may play a potential role in the development of PD. Conventional and quantitative real-time PCR analysis of feces from twenty PD patients and twenty healthy controls revealed that all PD patients harbored Desulfovibrio bacteria in their gut microbiota and these bacteria were present at higher levels in PD patients than in healthy controls. Additionally, the concentration of Desulfovibrio species correlated with the severity of PD. Desulfovibrio bacteria produce hydrogen sulfide and lipopolysaccharide, and several strains synthesize magnetite, all of which likely induce the oligomerization and aggregation of α-synuclein protein. The substances originating from Desulfovibrio bacteria likely take part in pathogenesis of PD. These findings may open new avenues for the treatment of PD and the identification of people at risk for developing PD.

A clinical nomogram incorporating salivary Desulfovibrio desulfuricans level and oral hygiene index for predicting colorectal cancer

Background

Emerging evidence demonstrates that the salivary microbiome could serve as a biomarker for various diseases. To date, the oral microbiome’s role in the diagnosis of colorectal cancer (CRC) has not been fully elucidated. We aimed to illustrate the salivary microbiome’s role in diagnosing and predicting the risk of CRC.

Methods

We collected preoperational saliva from 237 patients [95 healthy controls (HCs) and 142 CRC patients] who underwent surgical resections or colorectal endoscopy in Renji Hospital from January 2018 to January 2020. Clinical demographics, comorbidities, and oral health conditions were obtained from medical records or questionnaires. Salivary microbial biomarkers were detected using quantitative polymerase chain reaction (qPCR) after DNA extraction. Multivariate logistic regression analysis was employed to analyze the risk factors for CRC. A predictive model for the risk of developing CRC was constructed based on logistic regression analysis. Predictive accuracy was internally validated by bootstrap resampling. A clinical nomogram was constructed to visualize the predictive model.

Results

Logistic regression analysis demonstrated that the risk factors associated with CRC included age at diagnosis, male sex, poor oral hygiene, and relative salivary Desulfovibrio desulfuricans abundance. The predictive model had good discriminative (0.866) and calibration abilities (0.834) after bias correction.

Conclusions

The model based on age, sex, oral hygiene index (OHI), and the salivary Desulfovibrio desulfuricans level, which is visualized by a clinical nomogram, can predict the risk of CRC. Developing good oral hygiene habits might reduce the risk of CRC.

Endocrine cross-talk between the gut microbiome and glial cells in development and disease

Glial cells make up the major cellular component of the nervous system. Glial development is usually investigated through perturbations of host genetics, although non-host-derived signalling molecules can also regulate glial cells. Indeed, gut microbiome colonisation and the presence of microbiome-derived factors in the blood coincide with glial cell development. Emerging data suggest that the gut microbiome can regulate gliogenesis, myelination and glial epigenetics. Neurodegenerative diseases are characterised by changes in the gut microbiome and glial dysfunction. This perspective discusses the ways in which microbiome-derived molecules can engage in cross-talk with glial cells during development and in dysfunctional glial diseases.

Long-term dietary intake from infancy to late adolescence is associated with gut microbiota composition in young adulthood

BACKGROUND

Gut microbiota composition as influenced by long-term diet may be associated with the risk of adult chronic diseases. Thus, establishing the relation of long-term diet, particularly starting from early life, with adult microbiota composition would be an important research advance.

OBJECTIVE

We aimed to investigate the association of long-term intake of energy, carbohydrate, fiber, protein, and fat from infancy to late adolescence with microbiota composition in adulthood.

METHODS

Within the prospective DOrtmund Nutritional and Anthropometric Longitudinally Designed (DONALD) Study, we sampled stool 1 or 2 times within 1 y from 128 adults (median age: 29 y). Microbiota composition was profiled by 16S ribosomal RNA sequencing. Annual dietary records from age 1 to 18 y were retrieved. We estimated trajectories of energy, energy-adjusted carbohydrate, fiber, protein, and fat intake with multilevel models, producing predicted intake at age 1 y and rates of change in intake. A multivariate, zero-inflated, logistic-normal model was used to model the association between intake trajectories and the composition of 158 genera in single-sampled individuals. Associations found in this model were confirmed in double-sampled individuals using a zero-inflated Beta regression model.

RESULTS

Adjusting for covariates and temporal differences in microbiota composition, long-term carbohydrate intake was associated with 3 genera. Specifically, carbohydrate intake at age 1 y was negatively associated with Phascolarctobacterium [coefficient = -4.31; false discovery rate (FDR)-adjusted P = 0.006] and positively associated with Dialister (coefficient = 3.06; FDR-adjusted P = 0.003), and the rate of change in carbohydrate intake was positively associated with Desulfovibrio (coefficient = 13.16; FDR-adjusted P = 0.00039). Energy and other macronutrients were not associated with any genus.

CONCLUSIONS

This work links long-term carbohydrate intake to microbiota composition. Considering the associations of high carbohydrate intake and microbiota composition with some diseases, these findings could inform the development of gut microbiota-targeted dietary recommendations for disease prevention.

Personalized nutrition for colorectal cancer

The substantial burden of colorectal cancer and its increasing trend in young adults highlight the importance of dietary and lifestyle modifications for improved cancer prevention and survivorship. In this chapter, we review the cutting-edge evidence for the interplay between diet/lifestyle and the gut microbiota in the incidence and prognosis of colorectal cancer. We focus on factors for which there are data supporting their importance for the gut microbiota and colorectal cancer, including excess body weight, fiber, red and processed meat, and coffee. We discuss the potential precision nutrition approaches for modifying and exploiting the gut microbiota for improved cancer prevention and survivorship.

Effects of α-glyceryl monolaurate on growth, immune function, volatile fatty acids, and gut microbiota in broiler chickens

This study was conducted to determine the effects of dietary addition of α-glyceryl monolaurate (α-GML) on growth performance, immune function, volatile fatty acids production and cecal microbiota in broiler chickens. A total of 480 1-day-old yellow-feathered broilers were randomly assigned in equal numbers to 4 dietary treatments: basal diet (NCO) or supplementations with 30 mg/kg bacitracin (ANT), 500 mg/kg α-GML, or 1,000 mg/kg α-GML (GML2). And, each treatment contained 8 replicates with 15 chickens per replicate. After supplementation with α-GML, the total BW gain and average daily weight gain of broilers increased significantly (P < 0.05) compared with the broilers on the NCO diet. Moreover, compared with the NCO group, higher levels of immune globulin M and immune globulin Y were observed in both GML groups and the ANT group. Concentrations of acetate, propionate, butyrate, valerate, and isovalerate in GML2 were significantly higher (P < 0.05) than those in the NCO group on day 28. However, acetate, propionate, valerate, and isovalerate concentrations were reduced to significantly (P < 0.05) lower than those in the NCO group on day 56. The abundance and diversity of microbiota were found to be improved in broilers that were supplemented with GML, using operational taxonomic unit and diversity analyses. Furthermore, the GML treatments increased favorable microbiota, particularly acid-producing bacteria, on day 28 and, also, reduced opportunistic pathogens, such as Alistipes tidjanibacter and Bacteroides dorei by day 56. These results suggest that α-GML supplementation modulates cecal microbiota and broiler immunity and improves volatile fatty acid levels during the early growth stages of broilers.

Modulation of gut homeostasis by exopolysaccharides from Aspergillus cristatus (MK346334), a strain of fungus isolated from Fuzhuan brick tea, contributes to immunomodulatory activity in cyclophosphamide-treated mice

In this study, the crude exopolysaccharides (CEPSs) from fungus Aspergillus cristatus (MK346334, NCBI) isolated from Fuzhuan brick tea and its main purified fraction (EPSs-2) were investigated. Using the RAW264.7 cell model, EPSs-2 exhibited an excellent immunomodulatory effect in vitro. Then, the regulating effects of EPSs on immune function and gut microbiota were evaluated using a cyclophosphamide (Cy)-induced mice model. It was found that both CEPSs and EPSs-2 improved the body weight loss, immune organ indexes as well as the levels of TNF-α, IL-1β, IFN-γ and IgA, exhibiting potent immunoregulatory activity. Moreover, CEPSs and EPSs-2 not only attenuated the intestinal tissue damage, but also promoted the production of short-chain fatty acids and modulated the microbial composition by increasing the growth of Muribaculaceae, Prevotellaceae_UCG-001, Bacteroides, Parabacteroides and Tidjanibacter, while decreasing the relative abundances of Helicobacter, Bilophila, Mucispirillum, Lachnospiraceae, Ruminococcaceae and Clostridiales. These results indicated that the EPSs, especially EPSs-2, exhibited immunomodulatory activity associated with the modulation of gut microbiota to maintain gut homeostasis, which provided evidence for the development of novel potential prebiotics and immunomodulators.

Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults

Background: Gastrointestinal (GI) health is an important aspect of general health. Gastrointestinal symptoms are of specific importance for the elderly, an increasing group globally. Hence, promoting the elderly’s health and especially gastrointestinal health is important. Gut microbiota can influence gastrointestinal health by modulation of the immune system and the gut–brain axis. Diverse gut microbiota have been shown to be beneficial; however, for the elderly, the gut microbiota is often less diverse. Nutrition and physical activity, in particular, are two components that have been suggested to influence composition or diversity. Materials and Methods: In this study, we compared gut microbiota between two groups of elderly individuals: community-dwelling older adults and physically active senior orienteering athletes, where the latter group has less gastrointestinal symptoms and a reported better well-being. With this approach, we explored if certain gut microbiota were related to healthy ageing. The participant data and faecal samples were collected from these two groups and the microbiota was whole-genome sequenced and taxonomically classified with MetaPhlAn. Results: The physically active senior orienteers had a more homogeneous microbiota within the group and a higher abundance of Faecalibacterium prausnitzii compared to the community-dwelling older adults. Faecalibacterium prausnitzii has previously shown to have beneficial properties. Senior orienteers also had a lower abundance of Parasutterella excrementihominis and Bilophila unclassified, which have been associated with impaired GI health. We could not observe any difference between the groups in terms of Shannon diversity index. Interestingly, a subgroup of community-dwelling older adults showed an atypical microbiota profile as well as the parameters for gastrointestinal symptoms and well-being closer to senior orienteers. Conclusions: Our results suggest specific composition characteristics of healthy microbiota in the elderly, and show that certain components of nutrition as well as psychological distress are not as tightly connected with composition or diversity variation in faecal microbiota samples.

Barrier integrity and chronic inflammation mediated by HIF-1 impact on intestinal tumorigenesis

Colorectal cancer ranks among the top three most frequent malignancies in the world. While overall incidence and mortality of colorectal cancer has substantially decreased in recent years, tumor subtypes with poor response rates to standard antiproliferative therapies remain particularly challenging. Hypoxia in the microenvironment of solid tumors is associated with malignant progression, e.g. local invasion, systemic spread and therapy resistance. A detailed molecular understanding of hypoxia's role for the pathobiology of colorectal cancer is a prerequisite to design and evaluate the consequences of interference with hypoxic signaling for the progression of this cancer type. Here, we summarize the current knowledge about the role of hypoxia-inducible factor 1, an essential molecular mediator of the hypoxic response, for colorectal cancer pathogenesis. Special attention is given to intestinal microbiota, gut barrier integrity and chronic inflammation as these are of pivotal importance for intestinal tumorigenesis and noticeably associated with hypoxic signaling.

Microbiota and Lifestyle: A Special Focus on Diet

It is widely known that a good balance and healthy function for bacteria groups in the colon are necessary to maintain homeostasis and preserve health. However, the lack of consensus on what defines a healthy gut microbiota and the multitude of factors that influence human gut microbiota composition complicate the development of appropriate dietary recommendations for our gut microbiota. Furthermore, the varied response to the intake of probiotics and prebiotics observed in healthy adults suggests the existence of potential inter- and intra-individual factors, which might account for gut microbiota changes to a greater extent than diet. The changing dietary habits worldwide involving consumption of processed foods containing artificial ingredients, such as sweeteners; the coincident rise in emotional disorders; and the worsening of other lifestyle habits, such as smoking habits, drug consumption, and sleep, can together contribute to gut dysbiosis and health impairment, as well as the development of chronic diseases. This review summarizes the current literature on the effects of specific dietary ingredients (probiotics, prebiotics, alcohol, refined sugars and sweeteners, fats) in the gut microbiota of healthy adults and the potential inter- and intra-individual factors involved, as well as the influence of other potential lifestyle factors that are dramatically increasing nowadays.

Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men

BACKGROUND & AIMS

Sulfur-metabolizing microbes, which convert dietary sources of sulfur into genotoxic hydrogen sulfide (H2S), have been associated with development of colorectal cancer (CRC). We identified a dietary pattern associated with sulfur-metabolizing bacteria in stool and then investigated its association with risk of incident CRC using data from a large prospective study of men.

METHODS

We collected data from 51,529 men enrolled in the Health Professionals Follow-up Study since 1986 to determine the association between sulfur-metabolizing bacteria in stool and risk of CRC over 26 years of follow-up. First, in a subcohort of 307 healthy men, we profiled serial stool metagenomes and metatranscriptomes and assessed diet using semiquantitative food frequency questionnaires to identify food groups associated with 43 bacterial species involved in sulfur metabolism. We used these data to develop a sulfur microbial dietary score. We then used Cox proportional hazards modeling to evaluate adherence to this pattern among eligible individuals (n = 48,246) from 1986 through 2012 with risk for incident CRC.

RESULTS

Foods associated with higher sulfur microbial diet scores included increased consumption of processed meats and low-calorie drinks and lower consumption of vegetables and legumes. Increased sulfur microbial diet scores were associated with risk of distal colon and rectal cancers, after adjusting for other risk factors (multivariable relative risk, highest vs lowest quartile, 1.43; 95% confidence interval 1.14-1.81; P-trend = .002). In contrast, sulfur microbial diet scores were not associated with risk of proximal colon cancer (multivariable relative risk 0.86; 95% CI 0.65-1.14; P-trend = .31).

CONCLUSIONS

In an analysis of participants in the Health Professionals Follow-up Study, we found that long-term adherence to a dietary pattern associated with sulfur-metabolizing bacteria in stool was associated with an increased risk of distal CRC. Further studies are needed to determine how sulfur-metabolizing bacteria might contribute to CRC pathogenesis.

Inhibitory Effects of Bound Polyphenol from Foxtail Millet Bran on Colitis-Associated Carcinogenesis by the Restoration of Gut Microbiota in a Mice Model

Colorectal cancer (CRC) is a common malignant tumor occurring in the colon. It has been known that the gut microbiota is a complex ecosystem and plays an important role in the pathogenesis of colorectal cancer. Our previous study showed that bound polyphenol of the inner shell (BPIS) from foxtail millet bran exhibited significant antitumor activities in cancer cells and nude mice models. In the present study, the anticancer potential of BPIS is evaluated in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced mouse CRC model. Results showed that BPIS could decrease the number and volume of tumors and protect the epithelial architecture from damage. Certain biomarkers associated with CRC formation, such as COX-2, EMR1, PCNA, and caspase-3, were strongly changed by BPIS. Moreover, by 16S rRNA gene sequence analysis, it was found that BPIS could remodel the overall structure of the gut microbiota from tumor-bearing mice toward that of the normal counterparts, including two phyla and eight genera, together with regulations on several genes that are responsible for 17 signaling pathways.

Changes to the gut microbiota in mice induced by infection with Toxoplasma gondii

Toxoplasma gondii (T. gondii) is a common parasite worldwide, which can cause encephalitis, enteritis and miscarriage in abortion women. This study examined the cecal microbiome of mice infected with T. gondii through analysis of 16S rRNA genes determined by Illumina sequencing. BALB/c mice were orally infected with sporulated T. gondii oocysts. Mice were killed after 13-days- and 21-days- post infection, respectively, then their cecal contents were extracted and examined to determine the composition of gut microflora by illumina sequencing of the V3 +V4 region of the 16S rRNA genes. Our results showed the alterations in the gut microbes of BALB/c mice infected with T. gondii infection, where we observed a significant shift in the relative abundance of cecal bacteria. In mice at 13 days post-infection, the relative abundance of Proteobacteria increased, along with that of harmful bacteria, such as Bilopha and Desulfovibrio. However, the abundance of Lactobacillus decreased. At 21 days post-infection, the abundance of Lactobacillus was more than that observed for the uninfected control, with harmful bacteria, such as Bilopha and Desulfovibrio being reduced. The mice at 21-days post-infection had more beneficial intestinal bacteria than the control group. Our results suggested that the gut microbiota play an important role in disease progression from acute infection to chronic infection.

Strategies to Dissect Host-Microbial Immune Interactions That Determine Mucosal Homeostasis vs. Intestinal Inflammation in Gnotobiotic Mice

When identifying the key immunologic-microbial interactions leading to either mucosal homeostasis in normal hosts or intestinal inflammatory responses in genetically susceptible individuals, it is important to not only identify microbial community correlations but to also define the functional pathways involved. Gnotobiotic rodents are a very effective tool for this purpose as they provide a highly controlled environment in which to identify the function of complex intestinal microbiota, their individual components, and metabolic products. Herein we review specific strategies using gnotobiotic mice to functionally evaluate the role of various intestinal microbiota in host responses. These studies include basic comparisons between host responses in germ-free (GF), specific-pathogen-free or conventionally raised wild-type mice or those with underlying genetic susceptibilities to intestinal inflammation. We also discuss what can be learned from studies in which GF mice are colonized with single wild-type or genetically-modified microbial isolates to examine the functions of individual bacteria and their targeted bacterial genes, or colonized by multiple defined isolates to determine interactions between members of defined consortia. Additionally, we discuss studies to identify functions of complex microbial communities from healthy or diseased human or murine hosts via fecal transplant into GF mice. Finally, we conclude by suggesting ways to improve studies of immune-microbial interactions using gnotobiotic mice.

Foes or Friends? Bacteria Enriched in the Tumor Microenvironment of Colorectal Cancer

Colorectal cancer (CRC) is the second most commonly diagnosed cancer and the third cause of cancer death in the world, while intestinal microbiota is a community of microbes living in human intestine that can potentially impact human health in many ways. Accumulating evidence suggests that intestinal microbiota, especially that from the intestinal bacteria, play a key role in the CRC development; therefore, identification of bacteria involved in CRC development can provide new targets for the CRC diagnosis, prevention, and treatment. Over the past decade, there have been considerable advances in applying 16S rDNA sequencing data to verify associated intestinal bacteria in CRC patients; however, due to variations of individual and environment factors, these results seem to be inconsistent. In this review, we scrutinized the previous 16S rDNA sequencing data of intestinal bacteria from CRC patients, and identified twelve genera that are specifically enriched in the tumor microenvironment. We have focused on their relationship with the CRC development, and shown that some bacteria could promote CRC development, acting as foes, while others could inhibit CRC development, serving as friends, for human health. Finally, we highlighted their potential applications for the CRC diagnosis, prevention, and treatment.

Arsenic disturbs the gut microbiome of individuals in a disadvantaged community in Nepal

Arsenic is ubiquitous in nature, highly toxic, and is particularly abundant in Southern Asia. While many studies have focused on areas like Bangladesh and West Bengal, India, disadvantaged regions within Nepal have also suffered from arsenic contamination levels, with wells and other water sources possessing arsenic contamination over the recommended WHO and EPA limit of 10 μg/L, some wells reporting levels as high as 500 μg/L. Despite the region's pronounced arsenic concentrations within community water sources, few investigations have been conducted to understand the impact of arsenic contamination on host gut microbiota health. This study aims to examine differential arsenic exposure on the gut microbiome structure within two disadvantaged communities in southern Nepal. Fecal samples (n = 42) were collected from members of the Mahuawa (n = 20) and Ghanashyampur (n = 22) communities in southern Nepal. The 16S rRNA gene was amplified from fecal samples using Illumina-tag PCR and subject to high-throughput sequencing to generate the bacterial community structure of each sample. Bioinformatics analysis and multivariate statistics were conducted to identify if specific fecal bacterial assemblages and predicted functions were correlated with urine arsenic concentration. Our results revealed unique assemblages of arsenic volatilizing and pathogenic bacteria positively correlated with increased arsenic concentration in individuals within the two respective communities. Additionally, we observed that commensal gut bacteria negatively correlated with increased arsenic concentration in the two respective communities. Our study has revealed that arsenic poses a broader human health risk than was previously known. It is influential in shaping the gut microbiome through its enrichment of arsenic volatilizing and pathogenic bacteria and subsequent depletion of gut commensals. This aspect of arsenic has the potential to debilitate healthy humans by contributing to disorders like heart and liver cancers and diabetes, and it has already been shown to contribute to serious diseases and disorders, including skin lesions, gangrene and several types of skin, renal, lung, and liver cancers in disadvantaged areas of the world like Nepal.

Gut Bacteria and their Metabolites: Which One Is the Defendant for Colorectal Cancer?

Colorectal cancer (CRC) is a worldwide health concern which requires efficient therapeutic strategies. The mechanisms underlying CRC remain an essential subject of investigations in the cancer biology field. The evaluation of human microbiota can be critical in this regard, since the disruption of the normal community of gut bacteria is an important issue in the development of CRC. However, several studies have already evaluated the different aspects of the association between microbiota and CRC. The current study aimed at reviewing and summarizing most of the studies on the modifications of gut bacteria detected in stool and tissue samples of CRC cases. In addition, the importance of metabolites derived from gut bacteria, their relationship with the microbiota, and epigenetic modifications have been evaluated.

The Role of the Gut Microbiota in Colorectal Cancer Causation

Here, we reviewed emerging evidence on the role of the microbial community in colorectal carcinogenesis. A healthy gut microbiota promotes intestinal homeostasis and can exert anti-cancer effects; however, this microbiota also produces a variety of metabolites that are genotoxic and which can negatively influence epithelial cell behaviour. Disturbances in the normal microbial balance, known as dysbiosis, are frequently observed in colorectal cancer (CRC) patients. Microbial species linked to CRC include certain strains of Bacteroides fragilis, Escherichia coli, Streptococcus gallolyticus, Enterococcus faecalis and Fusobacterium nucleatum, amongst others. Whether these microbes are merely passive dwellers exploiting the tumour environment, or rather, active protagonists in the carcinogenic process is the subject of much research. The incidence of chemically-induced tumours in mice models varies, depending upon the presence or absence of these microorganisms, thus strongly suggesting influences on disease causation. Putative mechanistic explanations differentially link these strains to DNA damage, inflammation, aberrant cell behaviour and immune suppression. In the future, modulating the composition and metabolic activity of this microbial community may have a role in prevention and therapy.

A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria

Sulphate-reducing bacteria (SRB) are studied across a range of scientific fields due to their characteristic ability to metabolise sulphate and produce hydrogen sulphide, which can lead to significant consequences for human activities. Importantly, they are members of the human gastrointestinal microbial population, contributing to the metabolism of dietary and host secreted molecules found in this environment. The role of the microbiota in host digestion is well studied, but the full role of SRB in this process has not been established. Moreover, from a human health perspective, SRB have been implicated in a number of functional gastrointestinal disorders such as Irritable Bowel Syndrome and the development of colorectal cancer. To assist with the study of SRB, we present a mathematical model for the growth and metabolism of the well-studied SRB, Desulfovibrio vulgaris in a closed system. Previous attempts to model SRB have resulted in complex or highly specific models that are not easily adapted to the study of SRB in different environments, such as the gastrointestinal tract. We propose a simpler, Monod-based model that allows for easy alteration of both key parameter values and the governing equations to enable model adaptation. To prevent any incorrect assumptions about the nature of SRB metabolic pathways, we structure the model to consider only the concentrations of initial and final metabolites in a pathway, which circumvents the current uncertainty around hydrogen cycling by SRB. We parameterise our model using experiments with varied initial substrate conditions, obtaining parameter values that compare well with experimental estimates in the literature. We then validate our model against four independent experiments involving D. vulgaris with further variations to substrate availability. Further use of the model will be possible in a number of settings, notably as part of larger models studying the metabolic interactions between SRB and other hydrogenotrophic microbes in the human gastrointestinal tract and how this relates to functional disorders.

Sulfur metabolism and its contribution to malignancy

Metabolic dysregulation is an appreciated hallmark of cancer and a target for therapeutic intervention. Cellular metabolism involves a series of oxidation/reduction (redox) reactions that yield the energy and biomass required for tumor growth. Cells require diverse molecular species with constituent sulfur atoms to facilitate these processes. For humans, this sulfur is derived from the dietary consumption of the proteinogenic amino acids cysteine and methionine, as only lower organisms (e.g., bacteria, fungi, and plants) can synthesize them de novo. In addition to providing the sulfur required to sustain redox chemistry, the metabolism of these sulfur-containing amino acids yield intermediate metabolites that constitute the cellular antioxidant system, mediate inter- and intracellular signaling, and facilitate the epigenetic regulation of gene expression, all of which contribute to tumorigenesis.

Diversity and community pattern of sulfate-reducing bacteria in piglet gut

Background

Among the gut microbiota, sulfate-reducing bacteria (SRB) is a kind of hydrogen-utilizing functional bacteria that plays an important role in intestinal hydrogen and sulfur metabolism. However, information is lacking regarding diversity and community structure of SRB in the gut of piglets. Middle cecum contents were collected from 6 Yorkshire and 6 Meishan piglets at postnatal days (PND) 14, 28 and 49. Piglets were weaned at PND28. Real-time quantitative PCR was performed to detect the number of SRB in the cecum based on dissimilatory sulfite reductase subunit A (dsrA) gene. Prior to real-time PCR, plasmid containing the dsrA gene was constructed and used as external standard to create a standard curve, from which the gene copies of dsrA were calculated. H₂S concentration in the cecal contents was measured. Illumina PE250 sequencing of dsrA gene was used to investigate SRB diversity in cecum contents.

Results

The qPCR results showed that the number of SRB at PND49 was significantly higher than that at PND28 in Meishan piglets. The concentration of H₂S has no significant difference between piglet breeds and between different ages. The Illumina sequencing analysis revealed that the Chao1 richness index was significantly higher at PND49 than that at PND14 and PND28 in Yorkshire piglets. Based on dsrA gene similarities, Proteobacteria, Actinobacteria, and Firmicutes were identified at the phylum level, and most sequences were classified as Proteobacteria. At the genus level, most of sequences were classified as Desulfovibrio. At the species level, Desulfovibrio intestinalis was the predominant SRB in the piglet cecum. The relative abundance and the inferred absolute abundance of Faecalibacterium prausnitzii at PND49 were significantly higher than that at PND14 in Yorkshire piglets. Pig breeds did not affect the dsrA gene copies of SRB, diversity index and community pattern of SRB.

Conclusions

Sulfate-reducing bacteria are widely colonized in the cecum of piglets and D. intestinalis is the dominant SRB. The age of piglets, but not the pig breeds affects the diversity and community pattern of SRB.

Electronic supplementary material

The online version of this article (10.1186/s40104-019-0346-5) contains supplementary material, which is available to authorized users.

Dietary Factors in Sulfur Metabolism and Pathogenesis of Ulcerative Colitis

The biogeography of inflammation in ulcerative colitis (UC) suggests a proximal to distal concentration gradient of a toxin. Hydrogen sulfide (H₂S) has long been considered one such toxin candidate, and dietary sulfur along with the abundance of sulfate reducing bacteria (SRB) were considered the primary determinants of H₂S production and clinical course of UC. The metabolic milieu in the lumen of the colon, however, is the result of a multitude of factors beyond dietary sulfur intake and SRB abundance. Here we present an updated formulation of the H₂S toxin hypothesis for UC pathogenesis, which strives to incorporate the interdependency of diet composition and the metabolic activity of the entire colon microbial community. Specifically, we suggest that the increasing severity of inflammation along the proximal-to-distal axis in UC is due to the dilution of beneficial factors, concentration of toxic factors, and changing detoxification capacity of the host, all of which are intimately linked to the nutrient flow from the diet.

PHAGE Study: Effects of Supplemental Bacteriophage Intake on Inflammation and Gut Microbiota in Healthy Adults

The gut microbiota is increasingly recognized as an important modulator of human health. As such, there is a growing need to identify effective means of selectively modifying gut microbial communities. Bacteriophages, which were briefly utilized as clinical antimicrobials in the early 20th century, present an opportunity to selectively reduce populations of undesirable microorganisms. However, whether intentional consumption of specific bacteriophages affects overall gut ecology is not yet known. Using a commercial cocktail of Escherichia coli-targeting bacteriophages, we examined their effects on gut microbiota and markers of intestinal and systemic inflammation in a healthy human population. In a double-blinded, placebo-controlled crossover trial, normal to overweight adults consumed bacteriophages for 28 days. Stool and blood samples were collected and used to examine inflammatory markers, lipid metabolism, and gut microbiota. Reductions in fecal E. coli loads were observed with phage consumption. However, there were no significant changes to alpha and beta diversity parameters, suggesting that consumed phages did not globally disrupt the microbiota. However, specific populations were altered in response to treatment, including increases in members of the butyrate-producing genera Eubacterium and a decreased proportion of taxa most closely related to Clostridium perfringens. Short-chain fatty acid production, inflammatory markers, and lipid metabolism were largely unaltered, but there was a small but significant decrease in circulating interleukin-4 (Il-4). Together, these data demonstrate the potential of bacteriophages to selectively reduce target organisms without global disruption of the gut community.

Stability and resilience of the intestinal microbiota in children in daycare - a 12 month cohort study

BACKGROUND

We performed a 12-month cohort study of the stability and resilience of the intestinal microbiota of healthy children in daycare in Denmark in relation to diarrheal events and exposure to known risk factors for gastrointestinal health such as travelling and antibiotic use. In addition, we analyzed how gut microbiota recover from such exposures.

RESULTS

We monitored 32 children in daycare aged 1-6 years. Fecal samples were submitted every second month during a one-year observational period. Information regarding exposures and diarrheal episodes was obtained through questionnaires. Bacterial communities were identified using 16S rRNA gene sequencing. The core microbiota (mean abundance > 95%) dominated the intestinal microbiota, and none of the tested exposures (diarrheal events, travel, antibiotic use) were associated with decreases in the relative abundance of the core microbiota. Samples exhibited lower intra-individual variation than inter-individual variation. Half of all the variation between samples was explained by which child a sample originated from. Age explained 7.6-9.6% of the variation, while traveling, diarrheal events, and antibiotic use explained minor parts of the beta diversity. We found an age-dependent increase of alpha diversity in children aged 1-3 years, and while diarrheal events caused a decrease in alpha diversity, a recovery time of 40-45 days was observed. Among children having had a diarrheal event, we observed a 10x higher relative abundance of Prevotella. After travelling, a higher abundance of two Bacteroides species and 40% less Lachnospiraceae were seen. Antibiotic use did not correlate with changes in the abundance of any bacteria.

CONCLUSION

We present data showing that Danish children in daycare have stable intestinal microbiota, resilient to the exposures investigated. An early age-dependent increase in the diversity was demonstrated. Diarrheal episodes decreased alpha diversity with an estimated recovery time of 40-45 days.

A Pilot Study: Changes of Gut Microbiota in Post-surgery Colorectal Cancer Patients

Colorectal cancer (CRC) is a growing health problem throughout the world. Strong evidences have supported that gut microbiota can influence tumorigenesis; however, little is known about what happens to gut microbiota following surgical resection. Here, we examined the changes of gut microbiota in CRC patients after the surgical resection. Using the PCoA analysis and dissimilarity tests, the microbial taxonomic compositions and diversities of gut microbiota in post-surgery CRC patients (A1) were significantly different from those in pre-surgery CRC patients (A0) and healthy individuals (H). Compared with A0 and H, the Shannon diversity and Simpson diversity were significantly decreased in A1 (P < 0.05). Based on the LEfSe analysis, the relative abundance of phylum Proteobacteria in A1 was significantly increased than that in A0 and H. The genus Klebsiella in A1 had higher proportions than that in A0 (P < 0.05). Individual variation was distinct; however, 90% of CRC patients in A1 had more abundances of Klebsiella than A0. The Klebsiella in A1 was significantly associated with infectious diseases (P < 0.05), revealed by the correlation analysis between differentiated genera and metabolic pathway. The Klebsiella (Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae) in A1 was significantly linked with lymphatic invasion (P < 0.05). Furthermore, the PCA of KEGG pathways indicated that gut microbiota with a more scattered distribution in A1 was noticeably different from that in A0 and H. The nodes, the links, and the kinds of phylum in each module in A1 were less than those in A0 and H, indicating that gut microbiota in A1 had a relatively looser ecologcial interaction network. To sum up, this pilot study identified the changes of gut microbiota in post-surgery CRC patients, and highlights future avenues in which the gut microbiota is likely to be of increasing importance in the care of surgical patients.