Gut microbiota and related diseases: clinical features

Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach

Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition. SIGNIFICANCE: This paper would represent a reference work for investigations on gut microbiota in early life, from both a microbiological and a functional proteomic point of view. We focused on the shaping of the mouse gut microbiota in dependence on the feeding modality, defining a reliable taxonomic description, highlighting some functional characteristics of the microbial community, and performing a first quantitative evaluation by data independent analysis in metaproteomics.

Gut microbiota in multiple sclerosis: possible influence of immunomodulators

OBJECTIVES

Differences in gut bacteria have been described in several autoimmune disorders. In this exploratory pilot study, we compared gut bacteria in patients with multiple sclerosis and healthy controls and evaluated the influence of glatiramer acetate and vitamin D treatment on the microbiota.

METHODS

Subjects were otherwise healthy white women with or without relapsing-remitting multiple sclerosis who were vitamin D insufficient. Patients with multiple sclerosis were untreated or were receiving glatiramer acetate. Subjects collected stool at baseline and after 90 days of vitamin D3 (5000 IU/d) supplementation. The abundance of operational taxonomic units was evaluated by hybridization of 16S rRNA to a DNA microarray.

RESULTS

While there was overlap of gut bacterial communities, the abundance of some operational taxonomic units, including Faecalibacterium, was lower in patients with multiple sclerosis. Glatiramer acetate-treated patients with multiple sclerosis showed differences in community composition compared with untreated subjects, including Bacteroidaceae, Faecalibacterium, Ruminococcus, Lactobacillaceae, Clostridium, and other Clostridiales. Compared with the other groups, untreated patients with multiple sclerosis had an increase in the Akkermansia, Faecalibacterium, and Coprococcus genera after vitamin D supplementation.

CONCLUSIONS

While overall bacterial communities were similar, specific operational taxonomic units differed between healthy controls and patients with multiple sclerosis. Glatiramer acetate and vitamin D supplementation were associated with differences or changes in the microbiota. This study was exploratory, and larger studies are needed to confirm these preliminary results.

Gut microbiota imbalance and colorectal cancer

The gut microbiota acts as a real organ. The symbiotic interactions between resident micro-organisms and the digestive tract highly contribute to maintain the gut homeostasis. However, alterations to the microbiome caused by environmental changes (e.g., infection, diet and/or lifestyle) can disturb this symbiotic relationship and promote disease, such as inflammatory bowel diseases and cancer. Colorectal cancer is a complex association of tumoral cells, non-neoplastic cells and a large amount of micro-organisms, and the involvement of the microbiota in colorectal carcinogenesis is becoming increasingly clear. Indeed, many changes in the bacterial composition of the gut microbiota have been reported in colorectal cancer, suggesting a major role of dysbiosis in colorectal carcinogenesis. Some bacterial species have been identified and suspected to play a role in colorectal carcinogenesis, such as Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis, Enterococcus faecalis, Clostridium septicum, Fusobacterium spp. and Escherichia coli. The potential pro-carcinogenic effects of these bacteria are now better understood. In this review, we discuss the possible links between the bacterial microbiota and colorectal carcinogenesis, focusing on dysbiosis and the potential pro-carcinogenic properties of bacteria, such as genotoxicity and other virulence factors, inflammation, host defenses modulation, bacterial-derived metabolism, oxidative stress and anti-oxidative defenses modulation. We lastly describe how bacterial microbiota modifications could represent novel prognosis markers and/or targets for innovative therapeutic strategies.

The interrelationships of the gut microbiome and inflammation in colorectal carcinogenesis

The cause of colorectal cancer (CRC) is multifactorial, with genetic, molecular, inflammatory, and environmental risk factors. Recently, the gut microbiota has been recognized as a new environmental contributor to CRC in both animal models and human studies. An additional interplay of the gut microbiome with inflammation is also evident in studies that have shown that inflammation alone or the presence of bacteria/bacterial metabolites alone is not enough to promote tumorigenesis. Rather, complex interrelationships with the gut microbiome, inflammation, genetics, and other environmental factors are evident in progression of colorectal tumors.

The human gut microbiota: a dynamic interplay with the host from birth to senescence settled during childhood

The microbiota "organ" is the central bioreactor of the gastrointestinal tract, populated by a total of 10(14) bacteria and characterized by a genomic content (microbiome), which represents more than 100 times the human genome. The microbiota plays an important role in child health by acting as a barrier against pathogens and their invasion with a highly dynamic modality, exerting metabolic multistep functions and stimulating the development of the host immune system, through well-organized programming, which influences all of the growth and aging processes. The advent of "omics" technologies (genomics, proteomics, metabolomics), characterized by complex technological platforms and advanced analytical and computational procedures, has opened new avenues to the knowledge of the gut microbiota ecosystem, clarifying some aspects on the establishment of microbial communities that constitute it, their modulation and active interaction with external stimuli as well as food, within the host genetic variability. With a huge interdisciplinary effort and an interface work between basic, translational, and clinical research, microbiologists, specialists in "-omics" disciplines, and clinicians are now clarifying the role of the microbiota in the programming process of several gut-related diseases, from the physiological symbiosis to the microbial dysbiosis stage, through an integrated systems biology approach.

Potential probiotic Escherichia coli 16 harboring the Vitreoscilla hemoglobin gene improves gastrointestinal tract colonization and ameliorates carbon tetrachloride induced hepatotoxicity in rats

The present study describes the beneficial effects of potential probiotic E. coli 16 (pUC8:16gfp) expressing Vitreoscilla hemoglobin (vgb) gene, associated with bacterial respiration under microaerobic condition, on gastrointestinal (GI) colonization and its antioxidant activity on carbon tetrachloride (CCl₄) induced toxicity in Charles Foster rats. In vitro, catalase activity in E. coli 16 (pUC8:16gfp) was 1.8 times higher compared to E. coli 16 (pUC-gfp) control. In vivo, E. coli 16 (pUC8:16gfp) not only was recovered in the fecal matter after 70 days of oral administration but also retained antibacterial activities, whereas E. coli 16 (pUC-gfp) was not detected. Oral administration of 200 and 500 μL/kg body weight of CCl₄ to rats at weekly interval resulted in elevated serum glutamyl pyruvate transaminase (SGPT) and serum glutamyl oxalacetate transaminase (SGOT) levels compared to controls. Rats prefed with E. coli 16 (pUC8:16gfp) demonstrated near to normal levels for SGPT and SGOT, whereas the liver homogenate catalase activity was significantly increased compared to CCl₄ treated rats. Thus, pUC8:16gfp plasmid encoding vgb improved the growth and GI tract colonization of E. coli 16. In addition, it also enhanced catalase activity in rats harboring E. coli 16 (pUC8:16gfp), thereby preventing the absorption of CCl₄ to GI tract.

The role of gut microbiota in the pathogenesis of colorectal cancer

The human gastrointestinal tract harbors a complex and abundant microbial community that can reach levels as high as 10(13)-10(14) microorganisms in the colon. These microorganisms are essential to a host's well-being in terms of nutrition and mucosa immunity. However, numerous studies have also implicated members of the colonic microbiota in the development of colorectal cancer (CRC). While CRC involves a genetic component where damaged DNA and genetic instability initiates a malignant transformation, environmental factors can also contribute to the onset of CRC. Furthermore, considering the constant exposure of the colonic mucosa to the microbiome and/or its metabolites, the mucosa has long been proposed to contribute to colon tumorigenesis. However, the mechanistic details of these associations remain unknown. Fortunately, due to technical and conceptual advances, progress in characterizing the taxonomic composition, metabolic capacity, and immunomodulatory activity of human gut microbiota have been made, thereby elucidating its role in human health and disease. Furthermore, the use of experimental animal models and clinical/epidemiological studies of environmental etiological factors has identified a correlation between gut microbiota composition and gastrointestinal cancers. Bacteria continuously stimulate activated immunity in the gut mucosa and also contribute to the metabolism of bile and food components. However, the highest levels of carcinogen production are also associated with gut anaerobic bacteria and can be lowered with live lactobacilli supplements. In this review, evidence regarding the relationship between microbiota and the development of CRC will be discussed, as well as the role for microbial manipulation in affecting disease development.

Drug development for the irritable bowel syndrome: current challenges and future perspectives

Medications are frequently used for the treatment of patients with the irritable bowel syndrome (IBS), although their actual benefit is often debated. In fact, the recent progress in our understanding of the pathophysiology of IBS, accompanied by a large number of preclinical and clinical studies of new drugs, has not been matched by a significant improvement of the armamentarium of medications available to treat IBS. The aim of this review is to outline the current challenges in drug development for IBS, taking advantage of what we have learnt through the Rome process (Rome I, Rome II, and Rome III). The key questions that will be addressed are: (a) do we still believe in the "magic bullet," i.e., a very selective drug displaying a single receptor mechanism capable of controlling IBS symptoms? (b) IBS is a "functional disorder" where complex neuroimmune and brain-gut interactions occur and minimal inflammation is often documented: do we need to target gut motility, visceral sensitivity, or minimal inflammation? (c) are there validated biomarkers (accepted by regulatory agencies) for studies of sensation and motility with experimental medications in humans? (d) do animal models have predictive and translational value? (e) in the era of personalized medicine, does pharmacogenomics applied to these medications already play a role? Finally, this review will briefly outline medications currently used or in development for IBS. It is anticipated that a more focused interaction between basic science investigators, pharmacologists, and clinicians will lead to better treatment of IBS.

Programmed death-1 gene polymorphism (PD-1.5 C/T) is associated with colon cancer

Programmed death-1 (PD-1), expressed by activated T cells, is a negative regulator of T lymphocytes. The associations of the immune response-related genes with cancer have been demonstrated. In this study, the PD-1.5 C/T (+7785) polymorphism was investigated in 200 colorectal cancer patients and 200 healthy individuals as controls by nested polymerase chain reaction-restriction fragment length polymorphism method. The genotype and allele frequencies at PD-1.5 position were not significantly different between control individuals and the overall colorectal cancer patients. However, subdivision of the patients by the location (175 colon cancer and 25 rectal cancer) revealed a significant difference between colon cancer patients and healthy individuals (p=0.026), and between colon and rectal cancer patients (p=0.017). The frequency of the CT genotype was significantly higher in colon cancer patients than in control individuals (58.3% vs. 44.8%, Bonferroni corrected p-value=0.024; OR=1.74; 95% CI=1.15-2.62), and in rectal cancer patients (58.3% vs. 28.0%, Bonferroni corrected p-value=0.012; OR=3.59; 95% CI=1.42-9.04). Characteristics of the patients including age, sex, tumor grade and stage were not associated with the PD-1.5 polymorphism. Our results show a significant association between PD-1.5 polymorphism and colon cancer. Larger numbers of patients are required to investigate comprehensively the association of rectal cancer with PD-1.5 polymorphism.

Blastocystis: past pitfalls and future perspectives

Blastocystis is a genetically heterogeneous protist found in the intestinal tract (IT) of many vertebrates, and although it is implicated in a variety of human intestinal disorders, data regarding the clinical relevance of Blastocystis is at best speculative. Several research issues, including a lack of standardization across studies, the potential for intrasubtype variation in pathogenicity, and difficulties associated with diagnostics for many idiopathic disorders of the human IT have led to conflicting reports in support of a role for Blastocystis pathogenicity. Here, several research areas and methodologies are reviewed that if integrated appropriately into a prospective study may prove useful and facilitate a better understanding of the role of Blastocystis in human health and disease.