Inflammatory bowel disease and Streptococcus bovis

Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease

Developing microbiome-based markers for pediatric inflammatory bowel disease (PIBD) is challenging. Here, we evaluated the diagnostic and prognostic potential of the gut microbiome in PIBD through a case-control study and cross-cohort analyses. In a Korean PIBD cohort (24 patients with PIBD, 43 controls), we observed that microbial diversity and composition shifted in patients with active PIBD versus controls and recovered at remission. We employed a differential abundance meta-analysis approach to identify microbial markers consistently associated with active inflammation and remission across seven PIBD cohorts from six countries (n = 1,670) including our dataset. Finally, we trained and tested various machine learning models for their ability to predict a patient's future remission based on baseline bacterial composition. An ensemble model trained with the amplicon sequence variants effectively predicted future remission of PIBD. This research highlights the gut microbiome's potential to guide precision therapy for PIBD.

Partially hydrolyzed guar gum suppresses binge alcohol-induced liver fat accumulation via gut environment modulation in mice

Alcohol-associated liver disease (ALD), including alcoholic fatty liver, is a serious problem in many countries, and its economic costs to society are enormous. There is evidence indicating the relations between gut environments and liver disease, and thus, improvement of gut environment is expected to be an effective approach for ALD prevention. In this study, we explored the preventive effect of partially hydrolyzed guar gum (PHGG) on ALD focusing on the gut-liver axis. Two weeks of PHGG pre-feeding suppressed the liver fat accumulation in the experimental binge alcohol model mouse. In cecal microbiome, PHGG pre-feeding increased beneficial Bifidobacterium with its metabolite acetate concentration and suppressed the alcohol-induced increase in the potential pathobiont Streptococcus. PHGG pre-feeding increased colonic gene expression of angiogenin genes, which act as antimicrobial peptides and decreased expression of genes for mast cell protease, which suggests a potential involvement in leaky gut. Correlation network analysis based on evaluated parameters revealed four relations worth noticing. (i) The abundance of Bifidobacterium positively correlated with cecal acetate. (ii) Cecal acetate negatively correlated with Streptococcus via colonic angiogenin expression. (iii) Streptococcus positively correlated with liver fat area. (iv) Cecal acetate had direct negative correlation with liver fat area. Considering these relations comprehensively, acetate produced by Bifidobacterium may be a key mediator in ALD prevention; it inhibited growth of potential pathobiont Streptococcus and also directly regulated liver lipid metabolism reaching through portal vein. This study demonstrated that regularly intake of PHGG may be effective in reducing the risk of alcoholic fatty liver via gut-liver axis.

Meta-analysis identifies common gut microbiota associated with multiple sclerosis

BACKGROUND

Previous studies have identified a diverse group of microbial taxa that differ between patients with multiple sclerosis (MS) and the healthy population. However, interpreting findings on MS-associated microbiota is challenging, as there is no true consensus. It is unclear whether there is gut microbiota commonly altered in MS across studies.

METHODS

To answer this, we performed a meta-analysis based on the 16S rRNA gene sequencing data from seven geographically and technically diverse studies comprising a total of 524 adult subjects (257 MS and 267 healthy controls). Analysis was conducted for each individual study after reprocessing the data and also by combining all data together. The blocked Wilcoxon rank-sum test and linear mixed-effects regression were used to identify differences in microbial composition and diversity between MS and healthy controls. Network analysis was conducted to identify bacterial correlations. A leave-one-out sensitivity analysis was performed to ensure the robustness of the findings.

RESULTS

The microbiome community structure was significantly different between studies. Re-analysis of data from individual studies revealed a lower relative abundance of Prevotella in MS across studies, compared to controls. Meta-analysis found that although alpha and beta diversity did not differ between MS and controls, a higher abundance of Actinomyces and a lower abundance of Faecalibacterium were reproducibly associated with MS. Additionally, network analysis revealed that the recognized negative Bacteroides-Prevotella correlation in controls was disrupted in patients with MS.

CONCLUSIONS

Our meta-analysis identified common gut microbiota associated with MS across geographically and technically diverse studies.

Novel microbiota Mesosutterella faecium sp. nov. has a protective effect against inflammatory bowel disease

A novel Gram-negative, obligate anaerobe, non-motile, flagella-lacking, catalase- and oxidase-negative, coccobacilli-shaped bacterial strain designated AGMB02718T was isolated from swine feces. The 16S rRNA gene analysis indicated that strain AGMB02718T belonged to the genus Mesosutterella with the highest similarity to M. multiformis 4NBBH2T (= DSM 106860T) (sequence similarity of 96.2%), forming a distinct phylogenetic lineage. Its growth occurred at 25-45°C (optimal 37°C) and in 0.5-1% NaCl (optimal 0.5%). Strain AGMB02718T was asaccharolytic and contained menaquinone 6 (MK-6) and methylmenaquinone 6 (MMK-6) as the predominant respiratory quinones. The major cellular fatty acids in the isolate were C18:1ω9c and C16:0. Based on the whole-genome sequencing analysis, strain AGMB02718T had a 2,606,253 bp circular chromosome with a G + C content of 62.2%. The average nucleotide identity value between strain AGMB02718T and M. multiformis 4NBBH2T was 72.1%, while the digital DNA-DNA hybridization value was 20.9%. Interestingly, genome analysis suggested that strain AGMB02718T possessed a low-toxicity lipopolysaccharide (LPS) because the genome of the isolate does not include lpxJ and lpxM genes for Kdo2-Lipid A (KLA) assembly, which confers high toxicity to LPS. Moreover, in vitro macrophage stimulation assay confirmed that AGMB02718T produced LPS with low toxicity. Because the low-toxicity LPS produced by the Sutterellaceae family is involved in regulating host immunity and low-toxicity LPS-producing strains can help maintain host immune homeostasis, we evaluated the anti-inflammatory activity of strain AGMB02718T against inflammatory bowel disease (IBD). As a result, strain AGMB02718T was able to prevent the inflammatory response in a dextran sulfate sodium (DSS)-induced colitis model. Therefore, this strain represents a novel species of Mesosutterella that has a protective effect against DSS-induced colitis, and the proposed name is Mesosutterella faecium sp. nov. The type strain is AGMB02718T (=GDMCC 1.2717T = KCTC 25541T).

Metabarcoding of colonic cleansing fluid reveals unique bacterial members of mucosal microbiota associated with Inflammatory Bowel Disease

BACKGROUND

Inflammatory Bowel Disease (IBD) is a group of chronic idiopathic inflammatory diseases of the gastrointestinal (GI) tract associated with the dysbiosis of gut microbiota. Metabarcoding-based profiling of the gut microbiota of IBD patients is generally based on the stool samples collected from individual patients which rarely represent the mucosa-associated microbiota. The ideal sampling strategy for routine monitoring of the mucosal component of IBD has yet to be determined.

METHODS

We hereby compare the microbiota composition of the colonic cleansing fluid (CCF) collected during colonoscopy with stool samples from IBD patients. The relationship between IBD and gut microbiota was revealed through the application of the 16S rRNA amplicon sequencing-based metabarcoding approach. CCF and stool samples were collected from IBD patients with Crohn's disease and ulcerative colitis.

RESULTS

The present study shows significant differences in the microbial composition of CCF samples, presumably indicating changes in the mucosal microbiota of IBD patients as compared to the control group. Short-chain fatty acid-producing bacteria under the family Lachnospiraceae, the actinobacterial genus Bifidobacterium, the proteobacterial Sutterella and Raoultella are found to contribute to the microbial dysbiosis of the mucosal flora in IBD patients.

CONCLUSIONS

CCF microbiota has the capacity to distinguish IBD patients from healthy controls and, thus, may constitute an alternative analysis strategy for the early diagnosis and disease progression in IBD biomarker research.

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.

Detection of Streptococcus gallolyticus in colorectal cancer and inflammatory bowel disease patients compared to control group in southwest of Iran

There are several pieces of evidence regarding the role of bacteria, such as Streptococcus bovis/gallolyticus in the etiology of gastrointestinal diseases such as colorectal cancer (CRC) and inflammatory bowel disease (IBD). Therefore, the aim of this study was to detect S. gallolyticus subsp. gallolyticus (Sgg) in fecal samples of CRC and IBD patients by culture and molecular methods, in Ahvaz, southwest of Iran. A total of 106 fecal samples were collected from 22 CRC patients, 44 IBD patients, and 40 healthy individuals. The prevalence of Sgg was investigated by culture and polymerase chain reaction (PCR) with specific primers for sodA gene. The results of the stool culture showed that the overall prevalence of Sgg was 9 (13.6%) out of 66 patients. Meanwhile, the number of Sgg isolated from IBD and CRC patients was 7 (15.9%) and 2 (9%), respectively. The bacteria were not isolated from any of the control groups. On the basis of PCR, S. gallolyticus was detected in 24 (36.4%) out of 66 patients. Meanwhile, the number of IBD patients with positive sodA gene was 15 (34.1%) out of 44 cases. In CRC patients, the sodA gene was detected in 9 (40.9%) of 22 cases. Two (5%) of the specimens in the control group had the sodA gene. According to our results, S. gallolyticus subsp. gallolyticus might be involved in CRC and IBD pathogenesis. More investigation with different samples in the various areas might be shaded light on these results.

Gut microbiota, inflammation and colorectal cancer

Although genes contribute to colorectal cancer, the gut microbiota are an important player. Accumulating evidence suggests that chronic infection and the ensuing inflammation contributes to tumor initiation and tumor progression. A variety of bacterial species and tumor-promoting virulence mechanisms have been investigated. Significant advances have been made in understanding the composition and functional capabilities of the gut microbiota and its roles in cancer. In the current review, we discuss the novel roles of microbiota in the progression of colon cancer. Although microbiota technically include organisms other than bacteria e.g., viruses and fungi, this review will primarily focus on bacteria. We summarize epidemiological studies of human microbiome and colon cancer. We discuss the progress in the scientific understanding of the interplay between the gut microbiota, barrier function, and host responses in experimental models. Further, we discuss the potential application in prevention, diagnosis, and therapy of colon cancer by targeting microbiota. We discuss the challenges lie ahead and the future direction in studying gut microbiome in colon cancer to close the gap between the basic sciences and clinical application.

Inflammatory bowel disease: role of diet, microbiota, life style

Inflammatory bowel disease (IBD) encompassed several chronic inflammatory disorders leading to damage of the gastrointestinal tract (GI). The 2 principal forms of these disorders are ulcerative colitis (UC) and Crohn disease (CD). Bacteria are involved in the etiology of IBD, and the genetic susceptibility, environmental factors, and lifestyle factors can affect the individual's predisposition to IBD. The review discusses the potential role of environmental factors such as diet and microbiota as well as genetics in the etiology of IBD. It is suggested that microbial ecosystem in the human bowel colonizing the gut in many different microhabitats can be influence by diet, leading to formation of metabolic processes that are essential form the bowel metabolism.

Screening of species-specific lactic acid bacteria for veal calves multi-strain probiotic adjuncts

The selection of promising specific species of lactic acid bacteria with potential probiotic characteristics is of particular interest in producing multi species-specific probiotic adjuncts in veal calves rearing. The aim of the present work was to select and evaluate in vitro the functional activity of lactic acid bacteria, Bifidobacterium longum and Bacillus coagulans strains isolated from veal calves in order to assess their potential use as multi species-specific probiotics for veal calves. For this purpose, bacterial strains isolated from faeces collected from 40 healthy 50-day-calves, were identified by RiboPrinter and 16s rRNA gene sequence. The most frequent strains belonged to the species B. longum, Streptococcus bovis, Lactobacillus animalis and Streptococcus macedonicus. Among these, 7 strains were chosen for testing their probiotic characteristics in vitro. Three strains, namely L. animalis SB310, Lactobacillus paracasei subsp. paracasei SB137 and B. coagulans SB117 showed varying individual but promising capabilities to survive in the gastrointestinal tract, to adhere, to produce antimicrobial compounds. These three selected species-specific bacteria demonstrated in vitro, both singularly and mixed, the functional properties needed for their use as potential probiotics in veal calves.

The association of Streptococcus bovis/gallolyticus with colorectal tumors: the nature and the underlying mechanisms of its etiological role

Streptococcus bovis (S. bovis) bacteria are associated with colorectal cancer and adenoma. S. bovis is currently named S. gallolyticus. 25 to 80% of patients with S. bovis/gallolyticus bacteremia have concomitant colorectal tumors. Colonic neoplasia may arise years after the presentation of bacteremia or infectious endocarditis of S. bovis/gallolyticus. The presence of S. bovis/gallolyticus bacteremia and/or endocarditis is also related to the presence of villous or tubular-villous adenomas in the large intestine. In addition, serological relationship of S. gallolyticus with colorectal tumors and direct colonization of S. gallolyticus in tissues of colorectal tumors were found. However, this association is still under controversy and has long been underestimated. Moreover, the etiological versus non-etiological nature of this associationis not settled yet. Therefore, by covering the most of up to date studies, this review attempts to clarify the nature and the core of S. bovis/gallolyicus association with colorectal tumors and analyze the possible underlying mechanisms.