Intestinal dysbiosis: novel mechanisms by which gut microbes trigger and prevent disease

Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data

BACKGROUND

The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This is due mainly to the current technical and analytical strategy limitations to characterise tumour-associated bacteria.

METHODS

Here, we propose an approach to detect bacterial signals in human RNA sequencing data and associate them with the clinical and molecular properties of the tumours. The method was tested on public datasets from The Cancer Genome Atlas, and its accuracy was assessed on a new cohort of colorectal cancer patients.

RESULTS

Our analysis shows that intratumoural microbiome composition is correlated with survival, anatomic location, microsatellite instability, consensus molecular subtype and immune cell infiltration in colon tumours. In particular, we find Faecalibacterium prausnitzii, Coprococcus comes, Bacteroides spp., Fusobacterium spp. and Clostridium spp. to be strongly associated with tumour properties.

CONCLUSIONS

We implemented an approach to concurrently analyse clinical and molecular properties of the tumour as well as the composition of the associated microbiome. Our results may improve patient stratification and pave the path for mechanistic studies on microbiota-tumour crosstalk.

Lactobacillus paracasei 24 Attenuates Lipid Accumulation in High-Fat Diet-Induced Obese Mice by Regulating the Gut Microbiota

Obesity has become a worldwide public health problem. Lactic acid bacteria have attracted extensive attention for alleviating obesity and fat accumulation. This study aimed to evaluate the alleviating effects of Lactobacillus paracasei 24 (LP24) on lipid accumulation in an obese mouse model induced by a high-fat diet (HFD). The results showed that LP24 treatment significantly reduced body weight and fat deposition in HFD mice, improved blood lipid levels and liver steatosis, reduced liver oxidative stress injury and the inflammatory response, and regulated fat metabolism-related factors. Moreover, LP24 regulated the abundance and diversity of the gut microbiota, reduced the abundance of Firmicutes and the ratio of Firmicutes/Bacteroidetes (F/B), and increased the abundance of Akkermansia. In summary, LP24 regulates lipid metabolism by activating the expression level of related genes and regulating the gut microbiota through the gut-liver axis to attenuate the development of obesity. This study provides a theoretical basis for probiotics to regulate gut microbiota to reduce lipid accumulation.

Lipopolysaccharide and the gut microbiota: Considering structural variation

Systemic inflammation is associated with chronic disease and is purported to be a main pathogenic mechanism underlying metabolic conditions. Microbes harbored in the host gastrointestinal tract release signaling byproducts from their cell wall, such as lipopolysaccharides (LPS), which can act locally and, after crossing the gut barrier and entering circulation, also systemically. Defined as metabolic endotoxemia, elevated concentrations of LPS in circulation are associated with metabolic conditions and chronic disease. As such, measurement of LPS is highly prevalent in animal and human research investigating these states. Indeed, LPS can be a potent stimulant of host immunity but this response depends on the microbial species' origin, a parameter often overlooked in both preclinical and clinical investigations. Indeed, the lipid A portion of LPS is mutable and comprises the main virulence and endotoxic component, thus contributing to the structural and functional diversity among LPSs from microbial species. In this review, we discuss how such structural differences in LPS can induce differential immunological responses in the host.

Аtherosclerosis and cardiovascular risk in patients with inflammatory bowel disease

Inflammatory bowel disease (IBD) can cause early atherosclerosis. There is a correlation between inflammatory activity in IBD and cardiovascular events. Chronic inflammation can lead to endothelial dysfunction. This review discusses the possibilities of the mechanisms underlying the relationship between IBD and atherosclerosis, the role of innate and humoral immunity, intestinal microbiota, biomarkers (C-reactive protein, homocysteine, etc.), as well as the possibility of early instrumental diagnosis of subclinical manifestations of atherosclerosis in patients with IBD by measuring carotid intimamedia thickness and aortic pulse wave velocity. The need for active prevention of cardiovascular diseases in this group of patients is emphasized, including through the control of inflammation activity, as well as the inclusion of IBD in one of the risk factors for cardiovascular diseases.

Fusobacterium nucleatum - Friend or foe?

Fusobacterium nucleatum (F. nucleatum) is one of the most abundant Gram-negative anaerobic bacteria, part of the gut, and oral commensal flora, generally found in human dental plaque. Its presence could be associated with various human diseases, including, e.g., periodontal, angina, lung and gynecological abscesses. This bacteria can enter the blood circulation as a result of periodontal infection. It was proven that F. nucleatum migrates from its primary site of colonization in the oral cavity to other parts of the body. It could cause numerous diseases, including cancers. On the other hand, it was shown that Fusobacterium produces significant amounts of butyric acid, which is a great source of energy for colonocytes (anti-inflammatory cells). Therefore, it is very interesting to get to know the two faces of F. nucleatum.

Fecal microbiota signatures of insulin resistance, inflammation, and metabolic syndrome in youth with obesity: a pilot study

AIMS

To identify fecal microbiota profiles associated with metabolic abnormalities belonging to the metabolic syndrome (MS), high count of white blood cells (WBCs) and insulin resistance (IR).

METHODS

Sixty-eight young patients with obesity were stratified for percentile distribution of MS abnormalities. A MS risk score was defined as low, medium, and high MS risk. High WBCs were defined as a count ≥ 7.0 10³/µL; severe obesity as body mass index Z-score ≥ 2 standard deviations; IR as homeostatic assessment model algorithm of IR (HOMA) ≥ 3.7. Stool samples were analyzed by 16S rRNA-based metagenomics.

RESULTS

We found reduced bacterial richness of fecal microbiota in patients with IR and high diastolic blood pressure (BP). Distinct microbial markers were associated to high BP (Clostridium and Clostridiaceae), low high-density lipoprotein cholesterol (Lachnospiraceae, Gemellaceae, Turicibacter), and high MS risk (Coriobacteriaceae), WBCs (Bacteroides caccae, Gemellaceae), severe obesity (Lachnospiraceae), and impaired glucose tolerance (Bacteroides ovatus and Enterobacteriaceae). Conversely, taxa such as Faecalibacterium prausnitzii, Parabacterodes, Bacteroides caccae, Oscillospira, Parabacterodes distasonis, Coprococcus, and Haemophilus parainfluenzae were associated to low MS risk score, triglycerides, fasting glucose and HOMA-IR, respectively. Supervised multilevel analysis grouped clearly "variable" patients based on the MS risk.

CONCLUSIONS

This was a proof-of-concept study opening the way at the identification of fecal microbiota signatures, precisely associated with cardiometabolic risk factors in young patients with obesity. These evidences led us to infer, while some gut bacteria have a detrimental role in exacerbating metabolic risk factors some others are beneficial ameliorating cardiovascular host health.

Protocol of proceedings with Fusobacterium nucleatum and optimization of ABTS method for detection of reactive oxygen species

Aim: Characterization of the ability of Fusobacterium nucleatum DSM 15643 and DSM 20482 strains in the presence of Cu²⁺ and H₂O₂ to reactive oxygen species generation. Method: Spectrophotometric ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) method was used. Results: Determination of: MIC for Cu²⁺, H₂O₂ and ABTS; survivability of F. nucleatum under atmospheric oxygen exposure; the level and rate constants of free radicals production by the bacteria. Conclusion: F. nucleatum in the presence of Cu²⁺ and H₂O₂ is able to generate free radicals. Reactive oxygen species are produced mainly outside the bacterial cell, which suggests that outer membrane proteins may be involved in oxidative process.

Effects of Pretreatment with Bifidobacterium bifidum Using 16S Ribosomal RNA Gene Sequencing in a Mouse Model of Acute Colitis Induced by Dextran Sulfate Sodium

Background

Bifidobacterium is a potentially effective and safe treatment for patients with inflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease. However, information on the influence of B. bifidum on gut microbial diversity of treated and pretreated IBD patients is limited.

Material/Methods

Our study investigated therapeutic and preventive effects of B. bifidum ATCC 29521 on C57BL/6 mice with dextran sulfate sodium (DSS)-induced acute colitis via 16S ribosomal ribonucleic acid (rRNA) gene sequencing.

Results

Treatment and pretreatment of mice with B. bifidum ATCC 29521 significantly alleviated the severity of acute colitis on the basis of clinical and pathologic indicators. 16S rRNA gene sequencing showed that administration of B. bifidum shifted composition of the gut microbiome in mice with DSS-induced colitis in both treated and pretreated groups. Mice pretreated with B. bifidum ATCC 29521 for 21 days exhibited a significant increase in diversity of the gut microbiome. Principal coordinate analysis showed that gut microbiota structure was shaped by different treatments and time points. On the basis of linear discriminant analysis of effect size, the abundance of the genus Escherichia-Shigella, belonging to the family Enterobacteriaceae, was reduced in the B. bifidum-treated group, indicating that pathogens were inhibited by the B. bifidum treatment. Furthermore, the genera Intestinimonas and Bacteroides were significantly associated with the B. bifidum-pretreated group.

Conclusions

16S rRNA gene sequencing showed that pretreatment with B. bifidum ATCC 29521 reduced intestinal inflammation and altered the gut microbiota to favor the genera Intestinimonas and Bacteroides.

Gut Microbiota and Oral Contraceptive Use in Overweight and Obese Patients with Polycystic Ovary Syndrome

CONTEXT

Polycystic ovary syndrome (PCOS) is a common and complex endocrine disorder. Emerging animal and human data point to various changes in microbiota that could be linked with the syndrome. However, the effects of therapeutic approaches on gut microbial composition in women with PCOS remain unknown.

OBJECTIVE

We aimed to assess whether gut microbial composition is altered in PCOS and to determine the potential impact of oral contraceptive (OC) use on gut microbiota.

DESIGN

Prospective observational study.

SETTING

Tertiary referral hospital.

PATIENTS AND OTHER PARTICIPANTS

The study included 17 overweight/obese patients with PCOS and 15 age- and body mass index-matched healthy control women.

MAIN OUTCOME MEASURES

At baseline, clinical, hormonal, and metabolic evaluations and gut microbial composition assessment by 16S rRNA gene amplicon sequencing were performed for both groups. All measurements were repeated in patients after receiving an OC along with general lifestyle advice for 3 months.

RESULTS

Alpha and beta diversity did not show a difference between patients with PCOS and healthy controls at baseline and remained unaltered after 3 months of OC use in the PCOS group. Relative abundance of Ruminococcaceae was higher in PCOS (P = 0.006) and did not show a significant change after treatment.

CONCLUSION

Women with PCOS have an increased abundance of Ruminococcaceae, whereas short-term OC use does not alter compositional features of gut microbiota in the syndrome.

Contributors to Dysbiosis in Very-Low-Birth-Weight Infants

The objective of this commentary was to analyze the causes and outcomes of gut microbiome dysbiosis in preterm infants who are born at very low birth weight (VLBW). The intrauterine development of VLBW infants is interrupted abruptly with preterm birth and followed by extrauterine, health-threatening conditions and sequelae. These infants develop intestinal microbial dysbiosis characterized by low diversity, an overall reduction in beneficial and/or commensal bacteria, and enrichment of opportunistic pathogens of the Gammaproteobacteria class. The origin of VLBW infant dysbiosis is not well understood and is likely the result of a combination of immaturity and medical care. We propose that these factors interact to produce inflammation in the gut, which further perpetuates dysbiosis. Understanding the sources of dysbiosis could result in interventions to reduce gut inflammation, decrease enteric pathology, and improve health outcomes for these vulnerable infants.

Polyethylene microplastics affect the distribution of gut microbiota and inflammation development in mice

Environmental pollution caused by plastics has become a public health problem. However, the effect of microplastics on gut microbiota, inflammation development and their underlying mechanisms are not well characterized. In the present study, we assessed the effect of exposure to different amounts of polyethylene microplastics (6, 60, and 600 μg/day for 5 consecutive weeks) in a C57BL/6 mice model. Treatment with a high concentration of microplastics increased the numbers of gut microbial species, bacterial abundance, and flora diversity. Feeding groups showed a significant increase in Staphylococcus abundance alongside a significant decrease in Parabacteroides abundance, as compared to the blank (untreated) group. In addition, serum levels of interleukin-1α in all feeding groups were significantly greater than that in the blank group. Of note, treatment with microplastics decreased the percentage of Th17 and Treg cells among CD4⁺ cells, while no significant difference was observed between the blank and treatment groups with respect to the Th17/Treg cell ratio. The intestine (colon and duodenum) of mice fed high-concentration microplastics showed obvious inflammation and higher TLR4, AP-1, and IRF5 expression. Thus, polyethylene microplastics can induce intestinal dysbacteriosis and inflammation, which provides a theoretical basis for the prevention and treatment of microplastics-related diseases.

Dietary Fiber, Gut Microbiota, and Metabolic Regulation-Current Status in Human Randomized Trials

New knowledge about the gut microbiota and its interaction with the host's metabolic regulation has emerged during the last few decades. Several factors may affect the composition of the gut microbiota, including dietary fiber. Dietary fiber is not hydrolyzed by human digestive enzymes, but it is acted upon by gut microbes, and metabolites like short-chain fatty acids are produced. The short-chain fatty acids may be absorbed into the circulation and affect metabolic regulation in the host or be a substrate for other microbes. Some studies have shown improved insulin sensitivity, weight regulation, and reduced inflammation with increases in gut-derived short-chain fatty acids, all of which may reduce the risk of developing metabolic diseases. To what extent a dietary intervention with fiber may affect the human gut microbiota and hence metabolic regulation, is however, currently not well described. The aim of the present review is to summarize recent research on human randomized, controlled intervention studies investigating the effect of dietary fiber on gut microbiota and metabolic regulation. Metabolic regulation is discussed with respect to markers relating to glycemic regulation and lipid metabolism. Taken together, the papers on which the current review is based, suggest that dietary fiber has the potential to change the gut microbiota and alter metabolic regulation. However, due to the heterogeneity of the studies, a firm conclusion describing the causal relationship between gut microbiota and metabolic regulation remains elusive.

Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform

Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.

Gut dysbiosis, leaky gut, and intestinal epithelial proliferation in neurological disorders: towards the development of a new therapeutic using amino acids, prebiotics, probiotics, and postbiotics

Here we offer a review of the evidence for a hypothesis that a combination of ingestible probiotics, prebiotics, postbiotics, and amino acids will help ameliorate dysbiosis and degeneration of the gut, and therefore promote restoration of nervous system function in a number of neurological indications.

Impact of a Healthy Dietary Pattern on Gut Microbiota and Systemic Inflammation in Humans

Gut microbiota have recently been suggested to play a part in low-grade systemic inflammation, which is considered a key risk factor for cardiometabolic disorders. Diet is known to affect gut microbiota; however, the effects of diet and dietary components on gut microbiota and inflammation are not fully understood. In the present review, we summarize recent research on human dietary intervention studies, investigating the effects of healthy diets or dietary components on gut microbiota and systemic inflammation. We included 18 studies that reported how different dietary components altered gut microbiota composition, short-chain fatty acid levels, and/or inflammatory markers. However, the heterogeneity among the intervention studies makes it difficult to conclude whether diets or dietary components affect gut microbiota homeostasis and inflammation. More appropriately designed studies are needed to better understand the effects of diet on the gut microbiota, systemic inflammation, and risk of cardiometabolic disorders.

The effects of a wool hydrolysate on short-chain fatty acid production and fecal microbial composition in the domestic cat (Felis catus)

Novel animal-derived fibers are of interest for the pet food industry.

The Gastrointestinal Microbiome: A Review

The gastrointestinal microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit the gut of all mammals. Studies in humans and other mammals have implicated the microbiome in a range of physiologic processes that are vital to host health including energy homeostasis, metabolism, gut epithelial health, immunologic activity, and neurobehavioral development. The microbial genome confers metabolic capabilities exceeding those of the host organism alone, making the gut microbiome an active participant in host physiology. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of microbiomics, permitting mechanistic evaluation of the relationships between an animal and its microbial symbionts. Changes in the gastrointestinal microbiome are associated with diseases in humans and animals including inflammatory bowel disease, asthma, obesity, metabolic syndrome, cardiovascular disease, immune-mediated conditions, and neurodevelopmental conditions such as autism spectrum disorder. While there remains a paucity of data regarding the intestinal microbiome in small animals, recent studies have helped to characterize its role in host animal health and associated disease states. This review is intended to familiarize small animal veterinarians with recent advances in the field of microbiomics and to prime them for a future in which diagnostic tests and therapies will incorporate these developments into clinical practice.

The risk of inflammatory bowel disease flares after fecal microbiota transplantation: Systematic review and meta-analysis

Several studies have suggested worsening in inflammatory bowel disease (IBD) activity following fecal microbiota transplantation (FMT). We aimed to assess the risk of worsening in IBD activity following FMT. An electronic search was conducted using MEDLINE (1946-June 2016), EMBASE (1954-June 2016) and Cochrane Central Register of Controlled Trials (2016). Studies in which FMT was provided to IBD patients for IBD management or (Clostridium difficile infection) CDI treatment were included. The primary outcome was the rate of worsening in IBD activity.

RESULTS

Twenty-nine studies with 514 FMT-treated IBD patients were included. Range of follow up was 4 weeks to 3 y. The pooled rate of IBD worsening was 14.9% (95% CI 10-21%). Heterogeneity was detected: I2 D 52.1%, Cochran Q test D 58.1, p D 0.01. A priori subgroup analyses were performed. Although not significant, the pooled rate of worsening in IBD activity following FMT for CDI (22.7% (95% CI: 13-36%)) was higher compared with FMT for IBD (11.1% (95% CI 7-17%)). Rates of worsening in IBD after lower GI FMT delivery revealed a higher rate of worsening in IBD activity (16.5% (95% CI: 11-24%)) compared with upper GI delivery (5.6% (95% CI: 2-16%)). Rates of worsening in high quality studies and randomized controls trials (RCTS) suggested a marginal risk of worsening in IBD activity (4.6%, (95% CI: 1.8-11%). Rates of IBD worsening are overall marginal across high quality RCTS. It is unknown if the FMT itself led to the worsening of IBD in this small fraction or if this represents alternative etiologies.

Obesity-associated cancer risk: the role of intestinal microbiota in the etiology of the host proinflammatory state

Obesity increases the risks of many cancers. One important mechanism behind this association is the obesity-associated proinflammatory state. Although the composition of the intestinal microbiome undoubtedly can contribute to the proinflammatory state, perhaps the most important aspect of host-microbiome interactions is host exposure to components of intestinal bacteria that stimulate inflammatory reactions. Systemic exposures to intestinal bacteria can be modulated by dietary factors through altering both the composition of the intestinal microbiota and the absorption of bacterial products from the intestinal lumen. In particular, high-fat and high-energy diets have been shown to facilitate absorption of bacterial lipopolysaccharide (LPS) from intestinal bacteria. Biomarkers of bacterial exposures that have been measured in blood include LPS-binding protein, sCD14, fatty acids characteristic of intestinal bacteria, and immunoglobulins specific for bacterial LPS and flagellin. The optimal strategies to reduce these proinflammatory exposures, whether by altering diet composition, avoiding a positive energy balance, or reducing adipose stores, likely differ in each individual. Biomarkers that assess systemic bacterial exposures therefore should be useful to (1) optimize and personalize preventive approaches for individuals and groups with specific characteristics and to (2) gain insight into the possible mechanisms involved with different preventive approaches.

Role of intestinal microecology in precision treatment of colorectal cancer

Recently, the role of intestinal microecology in diseases has attracted increasing attention. Some progress has been achieved in the study of the colorectum, which is the carrier of intestinal microecology, and the role of intestinal microecology in colorectal cancer (CRC) formation and progression has been clarified gradually. More and more studies show that intestinal microecology plays a key role in CRC related precision treatments, such as tumor immunotherapy, chemotherapy and probiotic intervention, which have achieved certain curative effects in clinical treatment, although the mechanism still needs further study. This review briefly discusses the intestinal microecology related precision treatments for CRC and their potential mechanisms.

Fusobacterium nucleatum-Induced Impairment of Autophagic Flux Enhances the Expression of Proinflammatory Cytokines via ROS in Caco-2 Cells

Fusobacterium nucleatum (F. nucleatum) plays a critical role in gastrointestinal inflammation. However, the exact mechanism by which F. nucleatum contributes to inflammation is unclear. In the present study, it was revealed that F. nucleatum could induce the production of proinflammatory cytokines (IL-8, IL-1β and TNF-α) and reactive oxygen species (ROS) in Caco-2 colorectal) adenocarcinoma cells. Furthermore, ROS scavengers (NAC or Tiron) could decrease the production of proinflammatory cytokines during F. nucleatum infection. In addition, we observed that autophagy is impaired in Caco-2 cells after F. nucleatum infection. The production of proinflammatory cytokines and ROS induced by F. nucleatum was enhanced with either autophagy pharmacologic inhibitors (3-methyladenine, bafilomycin A1) or RNA interference in essential autophagy genes (ATG5 or ATG12) in Caco-2 cells. Taken together, these results indicate that F. nucleatum-induced impairment of autophagic flux enhances the expression of proinflammatory cytokines via ROS in Caco-2 Cells.

Tea polyphenols inhibit the activation of NF-κB and the secretion of cytokines and matrix metalloproteinases by macrophages stimulated with Fusobacterium nucleatum

Fusobacterium nucleatum has been associated with both periodontal disease and inflammatory bowel disease. This Gram-negative bacterium possesses a high inflammatory potential that may contribute to the disease process. We hypothesized that green and black tea polyphenols attenuate the inflammatory response of monocytes/macrophages mediated by F. nucleatum. We first showed that the tea extracts, EGCG and theaflavins reduce the NF-κB activation induced by F. nucleatum in monocytes. Since NF-κB is a key regulator of genes coding for inflammatory mediators, we tested the effects of tea polyphenols on secretion of IL-1β, IL-6, TNF-α, and CXCL8 by macrophages. A pre-treatment of macrophages with the tea extracts, EGCG, or theaflavins prior to a stimulation with F. nucleatum significantly inhibited the secretion of all four cytokines and reduced the secretion of MMP-3 and MMP-9, two tissue destructive enzymes. TREM-1 expressed by macrophages is a cell-surface receptor involved in the propagation of the inflammatory response to bacterial challenges. Interestingly, tea polyphenols inhibited the secretion/shedding of soluble TREM-1 induced by a stimulation of macrophages with F. nucleatum. The anti-inflammatory properties of tea polyphenols identified in the present study suggested that they may be promising agents for the prevention and/or treatment of periodontal disease and inflammatory bowel disease.

Akkermansia muciniphila: a novel functional microbe with probiotic properties

Akkermansia muciniphila is an intestinal anaerobe which has been proposed as a new functional microbe with probiotic properties. However, the species is not included in the European Union qualified presumption of safety (QPS) list and has not yet been assessed. Moreover, products containing A. muciniphila are not on the market and are thus controlled by the Novel Foods Regulation, which requires extensive safety assessment. This review addresses the safety aspects of the use of A. muciniphila based on published information on its functions in humans and predictions based on its activity in model animals. Further, comprehensive studies related to A. muciniphila and its safety properties have gradually appeared and are summarised here. Many of the criteria required for novel food safety assessment in Europe can thus be fulfilled. However, studies focusing on the toxicological properties of A. muciniphila, including long-term and reproduction studies, have not so far been reported and are discussed in the light of the observation that most, if not all, healthy subjects are known to carry this intestinal anaerobe. As this also applies to other beneficial bacteria found in the human intestinal tract, the A. muciniphila case can be seen as a model for the comprehensive safety evaluations required by the European authorities.

Nonparametric Regularized Regression for Phenotype-Associated Taxa Selection and Network Construction with Metagenomic Count Data

We use a metagenomic approach and network analysis to investigate the relationships between phenotypes across taxa under different environmental conditions. The network structure of taxa can be affected by the disease-associated environmental conditions. In addition, taxa abundance is differentiated under conditions. Therefore, knowing how the correlation or relative abundance changes with these factors would be of great interest to researchers. We develop a nonparametric regularized regression method to construct taxa association networks under different clinical conditions. We let the coefficients be unknown functions of the environmental variable. The varying coefficients are estimated by using regression splines. The proposed method is regularized with concave penalties, and an efficient group descent algorithm is developed for computation. We also apply the varying coefficient model to estimate taxa abundance to see how it changes across different environmental conditions. Moreover, for conducting inference, we propose a bootstrap method to construct the simultaneous confidence bands for the corresponding coefficients. We use different simulated designs and a real data set to demonstrate that our method can identify the network structures successfully under different environmental conditions. As such, the proposed method has potential applications for researchers to construct differential networks and identify taxa.

Probiotic Administration in Infants With Gastroschisis: A Pilot Randomized Placebo-Controlled Trial

OBJECTIVES

Infants with gastroschisis often require long periods of gastric suctioning and hospitalization. The impact of these interventions on the intestinal microbiota and attempts to alter the microbial community have not been studied. We sought to determine how the intestinal microbiota is influenced by the current treatment of gastroschisis and whether alteration of the intestinal microbiota with a probiotic microbe will influence length of hospitalization.

METHODS

We performed a randomized, placebo-controlled pilot study of administration of probiotic Bifidobacterium longum subsp. infantis in 24 infants with gastroschisis. The primary outcome was changes in the fecal microbiota, and the secondary outcome was length of hospital stay.

RESULTS

Administration of the probiotic or placebo was well tolerated, even during the period of gastric suctioning. The overall microbial communities were not significantly different between groups, although analysis of the final specimens by family demonstrated higher Bifidobacteriaceae, lower Clostridiaceae, and trends toward lower Enterobacteriaceae, Enterococcaceae, Staphylococcaceae, and Streptococcaceae in the probiotic group. Clinical outcomes, including length of hospital stay, did not differ between groups.

CONCLUSIONS

In this pilot study, there was significant in infants with gastroschisis that was partially attenuated by the administration of B longum subsp. infantis.

Prevention of Necrotizing Enterocolitis Through Manipulation of the Intestinal Microbiota of the Premature Infant

PURPOSE

In spite of four decades of research, necrotizing enterocolitis (NEC) remains the most common gastrointestinal complication in premature infants with high mortality and long-term morbidity. The composition of the intestinal microbiota of the premature infant differs dramatically from that of the healthy term infant and appears to be an important risk factor for NEC.

METHODS

We review the evidence of an association between intestinal dysbiosis and NEC and summarize published English language clinical trials and cohort studies involving attempts to manipulate the intestinal microbiota in premature infants.

FINDINGS

Promising NEC prevention strategies that alter the intestinal microbiota include probiotics, prebiotics, synbiotics, lacteroferrin, and human milk feeding.

IMPLICATIONS

Shaping the intestinal microbiota of the premature infant through human milk feeding and dietary supplements decreases the risk of NEC. Further studies to identify the ideal microbial composition and the most effective combination of supplements are indicated.

Microbiota modulation of myeloid cells in cancer therapy

Myeloid cells represent a major component of the tumor microenvironment, where they play divergent dual roles. They can induce antitumor immune responses, but mostly they promote immune evasion, tumor progression, and metastasis formation. Thus, strategies aiming at reprogramming the tumor microenvironment represent a promising immunotherapy approach. Myeloid cells respond to environmental factors including signals derived from commensal microbes. In this Cancer Immunology at the Crossroads overview, we discuss recent advances on the effects of the commensal microbiota on myeloid-cell functions and how they affect the response to cancer therapy.

Cancer Immunity: Lessons From Infectious Diseases

Innate and adaptive immunity are activated by both infections and tumors. The immune cells infiltrating infected tissues are similar to those infiltrating neoplastic tissues, but their function in the first setting is quite different from that in the latter. Infected tissues are usually characterized by an acute inflammatory environment that favors the generation of protective immunity, whereas tumors are characterized by chronic inflammation that suppresses antitumor immune responses and promotes tumor growth and escape from the immune system. During resolution of the immune response to infection or in chronic infections, immunosuppressive mechanisms that are typical of the tumor microenvironment are observed in infected tissues. Conversely, immunotherapy and chemotherapy may redirect the tumor microenvironment and allow the activation of effective anticancer immune responses. The transformation of neoplastic cells is determined by intrinsic genetic alteration but tumor progression is controlled by the tumor microenvironment and by the inflammatory and immune response to the tumors. Commensal microorganisms live in great numbers in all our barrier epithelia and control inflammation and immunity both locally and systemically. The commensal microbiota is essential for optimal immune response to pathogens and for the establishment of autoimmunity. It also modulates inflammation and immune responses that affect tumor growth and it is required for the effectiveness of anticancer immunotherapy and chemotherapy.

Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission

Background

The equine faecal microbiota is very complex and remains largely unknown, while interspecies interactions have an important contribution to animal health. Clostridium difficile has been identified as an important cause of diarrhoea in horses. This study provides further information on the nature of the bacterial communities present in horses developing an episode of diarrhoea. The prevalence of C. difficile in hospitalised horses at the time of admission is also reported.

Results

Bacterial diversity of the gut microbiota in diarrhoea is lower than that in non-diarrhoeic horses in terms of species richness (p-value <0.002) and in population evenness (p-value: 0.02). Statistical differences for Actinobacillus, Porphyromonas, RC9 group, Roseburia and Ruminococcaceae were revealed. Fusobacteria was found in horses with diarrhoea but not in any of the horses with non-diarrheic faeces. In contrast, Akkermansia was among the three predominant taxa in all of the horses studied. The overall prevalence of C. difficile in the total samples of hospitalised horses at admission was 3.7 % (5/134), with five different PCR-ribotypes identified, including PCR-ribotype 014. Two colonised horses displayed a decreased bacterial species richness compared to the remaining subjects studied, which shared the same Bacteroides genus. However, none of the positive animals had diarrhoea at the moment of sampling.

Conclusions

The abundance of some taxa in the faecal microbiota of diarrhoeic horses can be a result of microbiome dysbiosis, and therefore a cause of intestinal disease, or some of these taxa may act as equine enteric pathogens. Clostridium difficile colonisation seems to be transient in all of the horses studied, without overgrowth to trigger infection. A large proportion of the sequences were unclassified, showing the complexity of horses’ faecal microbiota.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0514-5) contains supplementary material, which is available to authorized users.

Microbiome and potential targets for chemoprevention of esophageal adenocarcinoma

Esophageal cancer is one of the deadliest cancers, with a dismal prognosis. It is increasingly recognized that esophageal cancer is a heterogeneous disease. It can be subdivided into two distinct groups: squamous cell carcinoma and adenocarcinoma, based on histological appearance. In the Western world, the incidence of squamous cell carcinoma was considerably higher than esophageal adenocarcinoma (EA) until the 1990s when, due to a dramatic increase, the incidence of EA surpassed that of squamous cell carcinoma. EA typically follows a well-established stepwise evolution from chronic inflammation due to reflux esophagitis (RE) that progresses to metaplasia (Barrett's esophagus [BE]) to dysplasia, which often culminates in EA. The pathophysiology of EA is complex and involves diverse factors, including gastroesophageal reflux, gastric acid secretion, dysfunction of the antireflux barrier, gastric emptying disturbances, and abnormalities in esophageal defense mechanisms. The current understanding of the etiology of EA is mainly derived from epidemiological studies of risk factors such as cigarette smoking, obesity, gastroesophageal reflux disorders (GERD), and low fruit and vegetable consumption. Numerous studies have been done, but the factors that drive the dynamic increase in the incidence of EA remain elusive. The advent of widespread antibiotic use occurred in the 1950s, preceding the surge of EA. Based on this temporal sequence, it has been hypothesized that antibiotics alter the microbiome to which the esophagus is exposed in patients who have GERD and that chronic exposure to this abnormal microbiome (ie, changes in species diversity or abundance) accounts for the increase in EA. If changes in the proposed factors alter the stepwise progression (RE-BE-dysplasia-EA), they may represent potential targets for chemoprevention. New discoveries will help improve our understanding of the biology and pathogenesis of these cancers, and aid in finding novel therapeutic targets.

Bifidobacteria Enhance Antigen Sampling and Processing by Dendritic Cells in Pediatric Inflammatory Bowel Disease

Bifidobacteria have been reported to reduce inflammation and contribute to intestinal homeostasis. However, the interaction between these bacteria and the gut immune system remains largely unknown. Because of the central role played by dendritic cells (DCs) in immune responses, we examined in vitro the effects of a Bifidobacteria mixture (probiotic) on DC functionality from children with inflammatory bowel disease. DCs obtained from peripheral blood monocytes of patients with Crohn's disease (CD), ulcerative colitis, and noninflammatory bowel disease controls (HC) were incubated with fluorochrome-conjugated particles of Escherichia coli or DQ-Ovalbumin (DQ-OVA) after a pretreatment with the probiotic, to evaluate DC phenotype, antigen sampling and processing. Moreover, cell supernatants were collected to measure tumor necrosis factor alpha, interferon gamma, interleukin 17, and interleukin 10 production by enzyme-linked immunosorbent assay. DCs from CD children showed a higher bacteria particles uptake and DQ-OVA processing after incubation with the probiotic; in contrast, DC from both ulcerative colitis and HC showed no significant changes. Moreover, a marked tumor necrosis factor alpha release was observed in DC from CD after exposure to E. coli particles, whereas the probiotic did not affect the production of this proinflammatory cytokine. In conclusion, the Bifidobacteria significantly improved the antigen uptake and processing by DCs from patients with CD, which are known to present an impaired autophagic functionality, whereas, in DCs from ulcerative colitis and HC, no prominent effect of probiotic mixture was observed. This improvement of antigen sampling and processing could partially solve the impairment of intestinal innate immunity and reduce uncontrolled microorganism growth in the intestine of children with inflammatory bowel disease.

The role of the microbiota in inflammation, carcinogenesis, and cancer therapy

Commensal microorganisms colonize barrier surfaces of all multicellular organisms, including those of humans. For more than 500 million years, commensal microorganisms and their hosts have coevolved and adapted to each other. As a result, the commensal microbiota affects many immune and nonimmune functions of their hosts, and de facto the two together comprise one metaorganism. The commensal microbiota communicates with the host via biologically active molecules. Recently, it has been reported that microbial imbalance may play a critical role in the development of multiple diseases, such as cancer, autoimmune conditions, and increased susceptibility to infection. In this review, we focus on the role of the commensal microbiota in the development, progression, and immune evasion of cancer, as well as some modulatory effects on the treatment of cancer. In particular, we discuss the mechanisms of microbiota-mediated regulation of innate and adaptive immune responses to tumors, and the consequences on cancer progression and whether tumors subsequently become resistant or susceptible to different anticancer therapeutic regiments.