The intestinal microbiota dysbiosis and Clostridium difficile infection: is there a relationship with inflammatory bowel disease?

The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome

Clostridioides difficile disproportionally affects the elderly living in nursing homes (NHs). Our objective was to explore the prevalence of C. difficile in NH elders, over time and to determine whether the microbiome or other clinical factors are associated with C. difficile colonization.We collected serial stool samples from NH residents. C. difficile prevalence was determined by quantitative polymerase-chain reaction detection of Toxin genes tcdA and tcdB; microbiome composition was determined by shotgun metagenomic sequencing. We used mixed-effect random forest modeling machine to determine bacterial taxa whose abundance is associated with C. difficile prevalence while controlling for clinical covariates including demographics, medications, and past medical history.We enrolled 167 NH elders who contributed 506 stool samples. Of the 123 elders providing multiple samples, 30 (24.4%) elders yielded multiple samples in which C. difficile was detected and 78 (46.7%) had at least one C. difficile positive sample. Elders with C. difficile positive samples were characterized by increased abundances of pathogenic or inflammatory-associated bacterial taxa and by lower abundances of taxa with anti-inflammatory or symbiotic properties. Proton pump inhibitor (PPI) use is associated with lower prevalence of C. difficile (Odds Ratio 0.46; 95%CI, 0.22-0.99) and the abundance of bacterial species with known beneficial effects was higher in PPI users and markedly lower in elders with high C. difficile prevalence.C. difficile is prevalent among NH elders and a dysbiotic gut microbiome associates with C. difficile colonization status. Manipulating the gut microbiome may prove to be a key strategy in the reduction of C. difficile in the NH.

Gut associated metabolites and their roles in Clostridioides difficile pathogenesis

The nosocomial pathogen Clostridioides difficile is a burden to the healthcare system. Gut microbiome disruption, most commonly by broad-spectrum antibiotic treatment, is well established to generate a state that is susceptible to CDI. A variety of metabolites produced by the host and/or gut microbiota have been shown to interact with C. difficile. Certain bile acids promote/inhibit germination while other cholesterol-derived compounds and amino acids used in the Stickland metabolic pathway affect growth and CDI colonization. Short chain fatty acids maintain intestinal barrier integrity and a myriad of other metabolic compounds are used as nutritional sources or used by C. difficile to inhibit or outcompete other bacteria in the gut. As the move toward non-antibiotic CDI treatment takes place, a deeper understanding of interactions between C. difficile and the host's gut microbiome and metabolites becomes more relevant.

Characterization of the consensus mucosal microbiome of colorectal cancer

Dysbioisis is an imbalance of an organ's microbiome and plays a role in colorectal cancer pathogenesis. Characterizing the bacteria in the microenvironment of a cancer through genome sequencing has advantages compared to culture-based profiling. However, there are notable technical and analytical challenges in characterizing universal features of tumor microbiomes. Colorectal tumors demonstrate microbiome variation among different studies and across individual patients. To address these issues, we conducted a computational study to determine a consensus microbiome for colorectal cancer, analyzing 924 tumors from eight independent RNA-Seq data sets. A standardized meta-transcriptomic analysis pipeline was established with quality control metrics. Microbiome profiles across different cohorts were compared and recurrently altered microbial shifts specific to colorectal cancer were determined. We identified cancer-specific set of 114 microbial species associated with tumors that were found among all investigated studies. Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were among the four most abundant phyla for the colorectal cancer microbiome. Member species of Clostridia were depleted and Fusobacterium nucleatum was one of the most enriched bacterial species in tumors. Associations between the consensus species and specific immune cell types were noted. Our results are available as a web data resource for other researchers to explore (https://crc-microbiome.stanford.edu).

Dietary Supplementation With Lactobacillus plantarum Ameliorates Compromise of Growth Performance by Modulating Short-Chain Fatty Acids and Intestinal Dysbiosis in Broilers Under Clostridium perfringens Challenge

Clostridium perfringens is an important zoonotic pathogen associated with food contamination and poisoning, gas gangrene, necrotizing enterocolitis or necrotic enteritis in humans and animals. Dysbacteriosis is supposedly associated with the development of C. perfringens infection induced necrotic enteritis, but the detailed relationship between intestinal health, microbiome, and C. perfringens infection-induced necrotic enteritis remains poorly understood. This research investigated the effect of probiotics on the growth performance and intestinal health of broilers, and the involved roles of intestinal microbiota and microbial metabolic functions under C. perfringens infection. Results showed that subclinical necrotic enteritis was successfully induced as evidenced by the significant lower body weight (BW), suppressed feed conversion ratio (FCR), decreased ileal villus height and mucosal barrier function, and increased ileal histopathological score and bursal weight index. Lactobacillus plantarum or Paenibacillus polymyxa significantly attenuated C. perfringens-induced compromise of growth performance (BW, FCR) and ileal mucosa damage as illustrated by the increased ileal villus height and villus/crypt ratio, the decreased ileal histopathological score and the enhanced ileal mucosal barrier function. L. plantarum also significantly alleviated C. perfringens-induced enlarged bursa of fabricius and the decreased levels of ileal total SCFAs, acetate, lactate, and butyrate. Furthermore, dietary L. plantarum improved C. perfringens infection-induced intestinal dysbiosis as evidenced by significantly enriched short-chain fatty acids-producing bacteria (Lachnospiraceae, Ruminococcaceae, Oscillospira, Faecalibacterium, Blautia), reduced drug-resistant bacteria (Bacteroides, Alistipes) and enteric pathogens (Escherichia coli, Bacteroides fragilis) and bacterial metabolic dysfunctions as illustrated by significantly increased bacterial fatty acid biosynthesis, decreased bacterial lipopolysaccharide biosynthesis, and antibiotic biosynthesis (streptomycin and vancomycin). Additionally, the BW and intestinal SCFAs were the principal factors affecting the bacterial communities and microbial metabolic functions. The above findings indicate that dietary with L. plantarum attenuates C. perfringens-induced compromise of growth performance and intestinal dysbiosis by increasing SCFAs and improving intestinal health in broilers.

High association of COVID-19 severity with poor gut health score in Lebanese patients

Background

Coronavirus disease 2019 (COVID-19) has affected millions of lives globally. However, the disease has presented more extreme challenges for developing countries that are experiencing economic crises. Studies on COVID-19 symptoms and gut health are scarce and have not fully analyzed possible associations between gut health and disease pathophysiology. Therefore, this study aimed to demonstrate a potential association between gut health and COVID-19 severity in the Lebanese community, which has been experiencing a severe economic crisis.

Methods

This cross-sectional study investigated SARS-CoV-2 PCR-positive Lebanese patients. Participants were interviewed and gut health, COVID-19 symptoms, and different metrics were analyzed using simple and multiple logistic regression models.

Results

Analysis of the data showed that 25% of participants were asymptomatic, while an equal proportion experienced severe symptoms, including dyspnea (22.7%), oxygen need (7.5%), and hospitalization (3.1%). The mean age of the participants was 38.3 ±0.8 years, and the majority were males (63.9%), married (68.2%), and currently employed (66.7%). A negative correlation was found between gut health score and COVID-19 symptoms (Kendall’s tau-b = -0.153, P = 0.004); indicating that low gut health was associated with more severe COVID-19 cases. Additionally, participants who reported unhealthy food intake were more likely to experience severe symptoms (Kendall’s tau-b = 0.118, P = 0.049). When all items were taken into consideration, multiple ordinal logistic regression models showed a significant association between COVID-19 symptoms and each of the following variables: working status, flu-like illness episodes, and gut health score. COVID-19 severe symptoms were more common among patients having poor gut health scores (OR:1.31, 95%CI:1.07–1.61; P = 0.008), experiencing more than one episode of flu-like illness per year (OR:2.85, 95%CI:1.58–5.15; P = 0.001), and owning a job (OR:2.00, 95%CI:1.1–3.65; P = 0.023).

Conclusions

To our knowledge, this is the first study that showed the impact of gut health and exposure to respiratory viruses on COVID-19 severity in Lebanon. These findings can facilitate combating the pandemic in Lebanon.

The effect of benzo[a]pyrene on the gut microbiota of Nile tilapia (Oreochromis niloticus)

Benzo[a]pyrene (BaP) is a highly toxic and carcinogenic polycyclic aromatic hydrocarbon (PAH) whose toxicological effects in the gut microbiota of aquatic organisms have not yet been fully revealed. Therefore, in this study, we used high-throughput 16S rRNA gene sequencing to evaluate the effects of BaP in the gut microbiome of Oreochromis niloticus, including its possible participation in the process of detoxification and its ability to recover. The fish were injected with a single intraperitoneal dose of 20 mg kg^-1 of BaP, and the effects in the microbiome were evaluated at 24, 72, and 120 h post-injection. The results indicate a clear dysbiosis (in composition, relative abundance, diversity, and interaction networks) of the gut microbiota during 24 h post-injection, dominated by Fusobacteria and Bacteroidetes and a decrease in Proteobacteria and Spirochaetae. Interestingly, a slight recovery of the microbiome begins at 72 h and stabilises at 120 h post-injection. Pathway analysis revealed the participation of the gut microbiome in PAH degradation mainly at 24 h post-injection. This study provides new insights in the toxicology of BaP in O. niloticus and the first evidence of the ability of the gut microbiome to recovery after a chemical disturbance. KEY POINTS: • Benzo[a]pyrene caused a dysbiosis in the gut microbiota of Oreochromis niloticus. • We observed an enrichment of bacteria involved in the metabolism of xenobiotics. • The gut microbiota was recovered after exposure to benzo[a]pyrene.

Incidence and risk factors for 30-day readmission in ulcerative colitis: nationwide analysis in biologic era

BACKGROUND AND STUDY AIM

Ulcerative colitis (UC) is a chronic relapsing and remitting disease requiring frequent hospitalization. Biologics have become the recommended initial therapy for Biologics in patients with moderate to severe UC. Our aim was to estimate the changes in Nationwide Healthcare utilization and assess predictive factors of 30-day readmission, morbidity and mortality of UC.

METHODS

This is a retrospective observational study analyzing the Nationwide Readmission database from 2016 to 2017 using ICD-10 codes. The primary outcomes of the study were to assess the predictors of 30-day readmission in patients with UC.

RESULTS

Of the 54 138 adult patients with a primary diagnosis of UC, 13.2% were readmitted within 30 days of index hospitalization. The mortality rate (1.4 vs. 0.3%, P < 0.01), length of stay (7 vs. 4.9 days, P < 0.01) and hospital cost ($62 552 vs. $46 971, P < 0.01) were higher on readmission as compared to index hospitalization. We identified multiple patient-related factors (age <65years, men, VTE, protein calorie malnutrition, electrolyte imbalance, anemia, anxiety and alcohol abuse), hospital-related factors (teaching hospitals, high quintile hospitals), as independent predictors of 30-day UC readmission. Colonoscopy, Cannabis use, and colectomy were associated with decreased odds of 30-day readmission. The most common cause of UC was septicemia.

CONCLUSIONS

This is the largest nationwide study demonstrating predictors of 30-day readmission, mortality and morbidity associated with UC. Identification and amelioration of these risk factors will decrease readmission rate and mortality amongst UC patients.

Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies

A number of studies have shown that the microbial communities of the human body are integral for the maintenance of human health. Advances in next-generation sequencing have enabled rapid and large-scale quantification of the composition of microbial communities in health and disease. Microorganisms mediate diverse host responses including metabolic pathways and immune responses. Using a system biology approach to further understand the underlying alterations of the microbiota in physiological and pathological states can help reveal potential novel therapeutic and diagnostic interventions within the field of synthetic biology. Tools such as biosensors, memory arrays, and engineered bacteria can rewire the microbiome environment. In this article, we review the computational tools used to study microbiome communities and the current limitations of these methods. We evaluate how genome-scale metabolic models (GEMs) can advance our understanding of the microbe-microbe and microbe-host interactions. Moreover, we present how synergies between these system biology approaches and synthetic biology can be harnessed in human microbiome studies to improve future therapeutics and diagnostics and highlight important knowledge gaps for future research in these rapidly evolving fields.

Long-term impacts of appendectomy associated with increased incidence of inflammatory bowel disease, infection, and colorectal cancer

PURPOSE

Although the appendix has been suggested to play a role in maintaining the gut microbiome and immune system, the ramifications of appendectomy on the development inflammatory bowel disease, sepsis, and colorectal cancer are yet to be determined. The purpose of this study was to evaluate the potential long-term impacts of appendectomy, with a focus on inflammatory bowel disease, infection, and colorectal cancer, using the National Healthcare Insurance Service (NHIS) database of Korea.

METHODS

The National Healthcare Insurance Service database in Korea was used for analysis. Adult patients who received appendectomy between 2005 and 2013 were identified. The control group consisted of patients who did not receive appendectomy were matched by baseline characteristics including comorbidities and frequency of healthcare resource utilization. The primary outcome was the incidence-rate ratio (IRR) of Crohn's disease, ulcerative colitis, Clostridium difficile infection, sepsis, and colorectal cancer after appendectomy or the index date.

RESULTS

We identified 914,208 patients who underwent appendectomy, and after matching with control patients, a total of 486,844 patients were included for analysis. Patients who underwent appendectomy showed a significantly higher incidence of Crohn's disease (IRR 4.40, 95% confidence interval (CI) 3.78-5.13) and ulcerative colitis (IRR 1.78, 95% CI 1.63-1.93) compared to the control group during the 5-year follow-up period. The associations between appendectomy and Clostridium difficile infection, sepsis, and colorectal cancer were all found to be significant.

CONCLUSION

Patients who underwent appendectomy may be at increased risk for developing Crohn's disease, ulcerative colitis, Clostridium difficile infection, sepsis, and colorectal cancer.

Clostridium butyricum enhances colonization resistance against Clostridioides difficile by metabolic and immune modulation

Clostridioides difficile infection (CDI) represents the leading cause of nosocomial diarrhea worldwide and is associated with gut dysbiosis and intestinal damage. Clostridium butyricum MIYAIRI 588 (CBM 588) contributes significantly to reduce epithelial damage. However, the impacts of CBM 588 on antibacterial therapy for CDI are not clear. Here we show that CBM 588 enhanced the antibacterial activity of fidaxomicin against C. difficile and negatively modulated gut succinate levels to prevent C. difficile proliferation and downregulate tumor necrosis factor-α (TNF-α) producing macrophages in the colon lumina propria (cLP), resulting in a significant decrease in colon epithelial damage. Additionally, CBM 588 upregulated T cell-dependent pathogen specific immunoglobulin A (IgA) via interleukin (IL)-17A producing CD4⁺ cells and plasma B cells in the cLP, and Th17 cells in the cLP enhanced the gut epithelial barrier function. IL-17A and succinic acid modulations with CBM 588 enhance gut colonization resistance to C. difficile and protect the colon tissue from CDI.

Dysbiosis of Fecal Microbiota From Complement 3 Knockout Mice With Constipation Phenotypes Contributes to Development of Defecation Delay

Significant phenotypes for constipation were detected in complement 3 (C3) knockout (KO) mice, although no research has been conducted on an association with alteration of gut microbiota. To investigate the effects of dysbiosis on fecal microbiota from C3 KO mice with constipation, the composition of fecal microbiota was characterized in mid-colons of 16-week-old C3 KO mice, and their function for defecation delay development was examined after fecal microbiota transplantation (FMT) of C3 KO mice. Some significant alterations in constipation phenotypes, including stool parameters and histopathological structure, were detected in 16-week-old C3 KO mice compared to those of wild-type (WT) mice. Fecal microbiota of C3 KO mice exhibited decreases in Anaerocolumna, Caecibacterium, Christensenella, Kineothrix, and Oscillibacter populations and increases in Prevotellamassilia, Reuthenibacterium, Prevotella, Eubacterium, Culturomica, Bacteroides, and Muribaculum populations. In FMT study, key stool parameters, including weight and water content, were remarkably declined in a transplanted KO (KFMT) group of antibiotics-induced depletion of microbiota (AiDM)-WT and AiDM-KO mice, and a similar change was observed in fecal morphology. However, intestine length decreased in only the KFMT group of AiDM-WT mice compared with that of AiDM-KO mice. The mucosal layer and muscle thickness were commonly decreased in the KFMT group of AiDM-WT and AiDM-KO mice, and significant alterations in the crypt structure of Lieberkuhn and molecular regulators, including AQP8, C-kit, and 5-HT, were observed in the same group. Taken together, results of the present study indicate that dysbiosis of fecal microbiota from C3 KO mice with constipation phenotypes has a key role in the induction and regulation of defecation delay.

Gut Microbiota And Inflammatory Disorders

The gut has been colonized with bacteria, fungi, viruses, archaea, eukarya. The human and bacterial cells are found in a 1:1 ratio, while the variance in the diversity of gut microbiota may result in Dysbiosis. Gut dysbiosis may result in various pathological manifestations. Beneficial gut microbiota may synthesize short-chain fatty acids like acetate, butyrate, propionate, while -gram-negative organisms are the primary source of LPS, a potent pro-inflammatory mediator. Both gut microbiota and microbial products may be involved in immunomodulation as well as inflammation. Prebiotics and probiotics are being explored as therapeutic agents against various inflammatory and autoimmune disorders. Here we discuss the molecular mechanisms involved in gut bacteria-mediated modulation of various inflammatory and autoimmune disorders.

Inhibition of the Clostridioides difficile Class D β-Lactamase CDD-1 by Avibactam

Avibactam is a potent diazobicyclooctane inhibitor of class A and C β-lactamases. The inhibitor also exhibits variable activity against some class D enzymes from Gram-negative bacteria; however, its interaction with recently discovered class D β-lactamases from Gram-positive bacteria has not been studied. Here, we describe microbiological, kinetic, and mass spectrometry studies of the interaction of avibactam with CDD-1, a class D β-lactamase from the clinically important pathogen Clostridioides difficile, and show that avibactam is a potent irreversible mechanism-based inhibitor of the enzyme. X-ray crystallographic studies at three time-points demonstrate the rapid formation of a stable CDD-1-avibactam acyl-enzyme complex and highlight differences in the anchoring of the inhibitor by class D enzymes from Gram-positive and Gram-negative bacteria.

Candida Administration in Bilateral Nephrectomy Mice Elevates Serum (1→3)-β-D-glucan That Enhances Systemic Inflammation Through Energy Augmentation in Macrophages

Systemic inflammation, from gut translocation of organismal molecules, might worsen uremic complications in acute kidney injury (AKI). The monitoring of gut permeability integrity and/or organismal molecules in AKI might be clinically beneficial. Due to the less prominence of Candida albicans in human intestine compared with mouse gut, C. albicans were orally administered in bilateral nephrectomy (BiN) mice. Gut dysbiosis, using microbiome analysis, and gut permeability defect (gut leakage), which was determined by fluorescein isothiocyanate-dextran and intestinal tight-junction immunofluorescent staining, in mice with BiN-Candida was more severe than BiN without Candida. Additionally, profound gut leakage in BiN-Candida also resulted in gut translocation of lipopolysaccharide (LPS) and (1→3)-β-D-glucan (BG), the organismal components from gut contents, that induced more severe systemic inflammation than BiN without Candida. The co-presentation of LPS and BG in mouse serum enhanced inflammatory responses. As such, LPS with Whole Glucan Particle (WGP, a representative BG) induced more severe macrophage responses than LPS alone as determined by supernatant cytokines and gene expression of downstream signals (NFκB, Malt-1 and Syk). Meanwhile, WGP alone did not induced the responses. In parallel, WGP (with or without LPS), but not LPS alone, accelerated macrophage ATP production (extracellular flux analysis) through the upregulation of genes in mitochondria and glycolysis pathway (using RNA sequencing analysis), without the induction of cell activities. These data indicated a WGP pre-conditioning effect on cell energy augmentation. In conclusion, Candida in BiN mice accelerated gut translocation of BG that augmented cell energy status and enhanced pro-inflammatory macrophage responses. Hence, gut fungi and BG were associated with the enhanced systemic inflammation in acute uremia.

Early life stress in mice alters gut microbiota independent of maternal microbiota inheritance

Exposure to early life stress (ELS) is associated with a greater risk of chronic disease development including depression and cardiovascular disease. Altered gut microbiota has been linked to both depression and cardiovascular disease in mice and humans. Rodent models of early life neglect are used to characterize the mechanistic links between early life stress (ELS) and the risk of disease later in life. However, little is understood about ELS exposure and the gut microbiota in the young mice and the influence of the maternal inheritance of the gut microbiota. We used a mouse model of ELS, maternal separation with early weaning (MSEW), and normally reared mice to determine whether the neonate microbiota is altered, and if so, are the differences attributable to changes in dam microbiota that are then transmitted to their offspring. Individual amplicon sequence variants (ASVs) displayed differential abundance in the microbiota of MSEW compared with normally reared pups at postnatal day (PD) 28. Additionally, ELS exposure reduced the alpha diversity and altered microbial community composition at PD28. The composition, levels of alpha diversity, and abundance of individual ASVs in the microbiota of dams were similar from MSEW or normally reared cohorts. Thus, the observed shifts in the abundance of individual bacterial ASVs in the neonates and young pups are likely driven by endogenous effects of MSEW in the offspring host and are not due to inherited differences from the dam. This knowledge suggests that exposure to ELS has a direct effect on microbial factors on the risk of chronic disease development.

Alcohol Use in Patients With Inflammatory Bowel Disease

Alcohol consumption is common in patients with inflammatory bowel disease (IBD), but alcohol has been reported to be the most-avoided diet item by this patient population. This article explores the available evidence for the impact that alcohol use has on IBD development, relapse, symptom control, and medication interactions. Although evidence linking the consumption of alcoholic beverages and the development of new-onset IBD is controversial, prospective research has reported that alcohol use is associated with a higher risk of relapse. Moreover, patients with IBD report worse gastrointestinal symptoms following alcohol consumption. On the other hand, alcoholic beverages such as red wine may have anti-inflammatory properties capable of assisting in disease control, although they may also have a negative effect on disease monitoring, namely fecal calprotectin levels. Importantly, the use of alcohol can interfere with the metabolism of several medications, leading to increased adverse events or even loss of efficacy. In the available literature, alcohol use in patients with IBD trends toward harmful effects; however, more research is needed to provide confident recommendations.

Glycine regulates mucosal immunity and the intestinal microbial composition in weaned piglets

Glycine is an amino acid with a diverse array of health benefits regarding metabolism, immunity, and development. The aim of this study was to test the hypothesis that glycine supplementation alters the intestinal microbial composition and improves the intestinal mucosal immunity of weaned piglets. One hundred and twenty-eight weaned piglets divided into 4 groups were fed with a corn- and soybean meal-based diet supplemented with 0 (control), 0.5, 1, or 2% glycine for 7 days. The intestinal microbiota and tissue samples from the control and the 2% glycine-supplemented piglets were collected for determination of the composition of microbial community and the intestinal mucosal barrier function. Piglets fed with diet containing 2% glycine, instead of 0.5% or 1% glycine, presented elevated average daily gain and feed conversion ratio, as compared with the control. 2% glycine enhanced the abundance of mucins in the jejunum and ileum and mRNA level of porcine β-defensin (pBD) 2 and pBD-3, as well as the protein level of secretory immunoglobulin A (sIgA) in the jejunum. The mRNA expression of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6, and the protein level of phosphorylated p38 mitogen-activated protein kinase (MAPK), signal transducer and activator of transcription 3 (STAT3), nuclear factor (NF)-κB p65, and claudin-2 in the jejunum were lower in the 2% glycine group than that in the control. In addition, an elevated ratio of CD4+/CD8+ T lymphocytes was observed in the jejunum of piglets receiving diet supplemented with 2% glycine. The colon content of piglets fed with 2% glycine exhibited a reduction in abundance of pathogenic bacteria (Escherichia-Shigella, Clostridium, and Burkholderiales) and an increase in short-chain fatty acid-producing bacteria (Blautia, Lachnospiraceae, Anaerostipes, and Prevotella) in comparison with the control. We conclude that dietary supplementation with 2% glycine improves the intestinal immunological barrier function and the microbial composition, therefore, contributing to the growth performance of weaned piglets.

Administration of β-lactam antibiotics and delivery method correlate with intestinal abundances of Bifidobacteria and Bacteroides in early infancy, in Japan

The intestinal microbiome changes dynamically in early infancy. Colonisation by Bifidobacterium and Bacteroides and development of intestinal immunity is interconnected. We performed a prospective observational cohort study to determine the influence of antibiotics taken by the mother immediately before delivery on the intestinal microbiome of 130 healthy Japanese infants. Faecal samples (383) were collected at 1, 3, and 6 months and analysed using next-generation sequencing. Cefazolin was administered before caesarean sections, whereas ampicillin was administered in cases with premature rupture of the membranes and in Group B Streptococcus-positive cases. Bifidobacterium and Bacteroides were dominant (60–70% mean combined occupancy) at all ages. A low abundance of Bifidobacterium was observed in infants exposed to antibiotics at delivery and at 1 and 3 months, with no difference between delivery methods. A lower abundance of Bacteroides was observed after caesarean section than vaginal delivery, irrespective of antibiotic exposure. Additionally, occupancy by Bifidobacterium at 1 and 3 months and by Bacteroides at 3 months differed between infants with and without siblings. All these differences disappeared at 6 months. Infants exposed to intrapartum antibiotics displayed altered Bifidobacterium abundance, whereas abundance of Bacteroides was largely associated with the delivery method. Existence of siblings also significantly influenced the microbiota composition of infants.

Eubacterium rectale contributes to colorectal cancer initiation via promoting colitis

BACKGROUND

Inflammatory bowel disease caused by microbial dysbiosis is an important factor contributing to colorectal cancer (CRC) initiation. The 'driver-passenger' model in human gut microbial dysbiosis suggests that 'driver' bacteria may colonize with low relative abundance on tumor site but persistently induce chronic change in normal intestinal epithelium and initiate CRC. They are gradually replaced by 'passenger' bacteria later on, due to their low adaptability to the on-tumor site niche.

RESULTS

To reveal site-specific bacterial taxon markers in CRC patients, we analyzed the gut mucosal microbiome of 75 paired samples of on-tumor and tumor-adjacent sites, 75 off-tumor sites, and 26 healthy controls. Linear discriminant analysis of relative abundance profiles revealed unique bacterial taxon distribution correlated with specific tumor sites, with Eubacterium having the distribution characteristic of potential driver bacteria. We further show that Eubacterium rectale endotoxin activates the transcription factor NF-κΒ, which regulates multiple aspects of innate and adaptive immune responses in normal colon epithelial cells. Unlike the 'passenger' bacterium Fusobacterium nucleatum, E. rectale promotes dextran sodium sulfate-induced colitis in Balb/c mice.

CONCLUSIONS

Our findings reveal that E. rectale functions as a 'driver' bacterium and contributes to cancer initiation via promoting inflammation.

Navigating changes in Clostridioides difficile prevention and treatment

Clostridioides difficile (C. difficile, previously known as Clostridium difficile) infections are a major health care concern. The Centers for Disease Control and Prevention (CDC) estimates that C. difficile causes almost half a million illnesses in the United States yearly, and approximately 1 in 5 patients with a C. difficile infection (CDI) will experience 1 or more recurrent infections. The incidence of infection has risen dramatically in recent years, and infection severity has increased due to the emergence of hypervirulent strains. There have been noteworthy advances in the development of CDI prevention and treatment, including a growth in the understanding of the role a patient's gut microbiome plays. The 2017 Infectious Diseases Society of America (IDSA) guidelines made a significant change in treatment recommendations for first time CDI episodes by recommending the use of oral vancomycin or fidaxomicin in place of metronidazole as a first-line treatment. The guidelines also included detailed recommendations on the use of fecal microbiota transplant (FMT) in those patients who experience 3 or more recurrent CDI episodes. A number of novel therapies for the treatment of CDI are in various stages of development. Treatments currently in phase 3 trials include the antibiotic ridinilazole, the microbiome products SER-109 and RBX2660, and a vaccine. All of these agents have shown promise in phase 1 and 2 trials. Additionally, several other antibiotic and microbiome candidates are currently in phase 1 or phase 2 trials. A qualitative review and evaluation of the literature on the cost-effectiveness of treatments for CDI in the U.S. setting was conducted, and the summary provided herein. Due to the higher cost of newer agents, cost-effectiveness evaluations will continue to be critical in clinical decision making for CDI. This paper reviews the updated CDI guidelines for prevention and treatment, the role of the microbiome in new and recurrent infections, pipeline medications, and comparative effectiveness research (CER) data on these treatments. DISCLOSURES: Durham and Le have nothing to disclose. Cassano reports consulting fees from Baxter Healthcare. Peer reviewers Drs. Ami Gopalan and Mark Rubin and Ms. Kathleen Jarvis have nothing to disclose. Planners Dr. Christine L. Cooper and Ms. Susan Yarbrough have nothing to disclose.

Effect of Synbiotics on Amelioration of Intestinal Inflammation Under Hypobaric Hypoxia

Khanna, Kunjan, Kamla Prasad Mishra, Sudipta Chanda, Lilly Ganju, Shashi Bala Singh, and Bhuvnesh Kumar. Effect of synbiotics on amelioration of intestinal inflammation under hypobaric hypoxia. High Alt Med Biol. 22:32-44, 2021. Aim: High-altitude exposure alters the gastrointestinal (GI) system, which may be a cause of hypobaric hypoxia (HH)-induced microbial dysbiosis. Therefore, we investigated the effect of a combination of beneficial bacteria and nondigestible fiber popularly known as "synbiotics" (Syn) to mitigate intestinal inflammation and microbial dysbiosis post-HH exposure. Methods: Syn, that is, a combination of probiotics and prebiotics, was given to male Sprague-Dawley rats 3 days prior and along with the HH exposure to assess its effect on mucosal barrier injury and inflammation. Changes in the gut microbiota and functional analysis were assessed using 16S rRNA and whole-genome sequencing (WGS) analysis. Results: Syn treatment significantly improved mucosal barrier injury in terms of decreased serum fluorescein isothiocyanate dextran from 96.1 ± 7.95 μg/ml in HH-alone group to 38.35 ± 4.55 μg/ml in HH + Syn group (p < 0.01) and decreased serum zonulin levels, that is, from 134.7 ± 19.05 ng/ml (HH alone) to 64.02 ± 7.33 ng/ml (HH + Syn) (p < 0.05), along with improvement in the intestinal villi under HH exposure. Levels of proinflammatory cytokines and chemokines significantly reduced upon Syn treatment, indicating attenuation of inflammation and immune cell migration. Syn treatment significantly reduced Th17 biased immune response preventing interleukin (IL)-17-induced inflammatory response with 8.1 ± 0.5 ng/mg protein in HH exposure group, while treatment with Syn in HH-exposed group reduced IL-17 levels to 2.01 ± 0.3 ng/mg protein (p < 0.001). Analysis of 16S rRNA showed significant (p < 0.05) alterations in Deferribacteres, Firmicutes, and Verrucomicrobia at the phylum levels, whereas Prevotella, Paenibacillus, Clostridium, Turicibacter, Bacillus, Anoxybacillus, Enterococcus, SMB53, Mucispirillum, Allobaculum, and Lactococcus were significantly altered (p < 0.05) in abundance at the genus level. WGS analysis revealed improvement in GI health by regulating functional pathways post-Syn treatment. Conclusion: Our findings indicate that Syn treatment improves intestinal barrier function and curtailed inflammation in the HH-exposed rat models, proving it to be a promising potential countermeasure for HH-induced gut problems.

Lactobacillus plantarum BSGP201683 Improves the Intestinal Barrier of Giant Panda Microbiota-Associated Mouse Infected by Enterotoxigenic Escherichia coli K88

Giant pandas often suffered from gastrointestinal disease, especially the captive sub-adult one. Our study aims to investigate whether L. plantarum G83, a good panda-derived probiotic, can improve the intestinal barrier against the enterotoxigenic Escherichia coli K88 (E. coli K88) infection in giant panda microbiota-associated mice (GPAM). We treated SPF mice with antibiotics cocktail and transplanted the giant panda intestinal microbiota to set up a GPAM. Our results demonstrated that the microbiota of GPAM changed over time and was relatively stable in the short-term experiment (2-4 weeks). Whereafter, the GPAM pretreated with L. plantarum G83 for 15 days and infected with enterotoxigenic E. coli K88. The result indicated that the number of Bifidobacteria spp. increased in GPAM-G and GPAM-GE groups; the Lactobacillus spp. only increased in the GPAM-G group. Although the abundance of Enterobacteriaceae spp. only decreased in the GPAM-G group, the copy number of Escherichia coli in the GPAM-E group was significantly lower than that in the other groups. Meanwhile, the L. plantarum G83-induced alteration of microbiota could increase the mRNA expression of Claudin-1, Zo-1, and Occludin-1 in the GPAM-G group in the ileum; only Occludin-1 was increased in the GPAM-GE group. The sIgA in the ileum showed a positive response, also the result of body weight and histology in both the GPAM-G and GPAM-GE group. These results indicated that the L. plantarum G83 could improve the intestinal barrier to defense the enterotoxigenic E. coli K88 invasion.

Anti-virulence strategies for Clostridioides difficile infection: advances and roadblocks

Clostridioides difficile infection (CDI) is a common healthcare- and antibiotic-associated diarrheal disease. If mis-diagnosed, or incompletely treated, CDI can have serious, indeed fatal, consequences. The clinical and economic burden imposed by CDI is great, and the US Centers for Disease Control and Prevention has named the causative agent, C. difficile (CD), as an Urgent Threat To US healthcare. CDI is also a significant problem in the agriculture industry. Currently, there are no FDA-approved preventives for this disease, and the only approved treatments for both human and veterinary CDI involve antibiotic use, which, ironically, is associated with disease relapse and the threat of burgeoning antibiotic resistance. Research efforts in multiple laboratories have demonstrated that non-toxin factors also play key roles in CDI, and that these are critical for disease. Specifically, key CD adhesins, as well as other surface-displayed factors have been shown to be major contributors to host cell attachment, and as such, represent attractive targets for anti-CD interventions. However, research on anti-virulence approaches has been more limited, primarily due to the lack of genetic tools, and an as-yet nascent (but increasingly growing) appreciation of immunological impacts on CDI. The focus of this review is the conceptualization and development of specific anti-virulence strategies to combat CDI. Multiple laboratories are focused on this effort, and the field is now at an exciting stage with numerous products in development. Herein, however, we focus only on select technologies (Figure 1) that have advanced near, or beyond, pre-clinical testing (not those that are currently in clinical trial), and discuss roadblocks associated with their development and implementation.

The Gut Microbiota and Inflammation: An Overview

The gut microbiota encompasses a diverse community of bacteria that carry out various functions influencing the overall health of the host. These comprise nutrient metabolism, immune system regulation and natural defence against infection. The presence of certain bacteria is associated with inflammatory molecules that may bring about inflammation in various body tissues. Inflammation underlies many chronic multisystem conditions including obesity, atherosclerosis, type 2 diabetes mellitus and inflammatory bowel disease. Inflammation may be triggered by structural components of the bacteria which can result in a cascade of inflammatory pathways involving interleukins and other cytokines. Similarly, by-products of metabolic processes in bacteria, including some short-chain fatty acids, can play a role in inhibiting inflammatory processes. In this review, we aimed to provide an overview of the relationship between the gut microbiota and inflammatory molecules and to highlight relevant knowledge gaps in this field. Based on the current literature, it appears that as the gut microbiota composition differs between individuals and is contingent on a variety of factors like diet and genetics, some individuals may possess bacteria associated with pro-inflammatory effects whilst others may harbour those with anti-inflammatory effects. Recent technological advancements have allowed for better methods of characterising the gut microbiota. Further research to continually improve our understanding of the inflammatory pathways that interact with bacteria may elucidate reasons behind varying presentations of the same disease and varied responses to the same treatment in different individuals. Furthermore, it can inform clinical practice as anti-inflammatory microbes can be employed in probiotic therapies or used to identify suitable prebiotic therapies.

Candida Administration Worsens Cecal Ligation and Puncture-Induced Sepsis in Obese Mice Through Gut Dysbiosis Enhanced Systemic Inflammation, Impact of Pathogen-Associated Molecules From Gut Translocation and Saturated Fatty Acid

Obesity induces gut leakage and elevates serum lipopolysaccharide (LPS), a major cell wall component of Gram-negative bacteria, through gut translocation. Because Candida albicans is prominent in human gut but not in mouse, C. albicans, a source of (1→3)-β-D-glucan (BG) in gut contents, was administered in high-fat diet (HFD)–induced obese mice at 1 week before sepsis induction by cecal ligation and puncture (CLP). As such, sepsis in Candida-administered obese mice was more severe than obese mice without Candida as determined by mortality, organ injury (liver and kidney), serum cytokines, gut leakage, endotoxemia, serum BG, and fecal Gram-negative bacteria (microbiome analysis). Mice subjected to CLP and fed a HFD, but not treated with Candida demonstrated a similar mortality to non-obese mice with more severe gut leakage and higher serum cytokines. In vitro experiments demonstrated that LPS plus BG (LPS + BG) induced higher supernatant cytokines from hepatocytes (HepG2) and macrophages (RAW264.7), compared with the activation by each molecule alone, and were amplified by palmitic acid, a representative saturated fatty acid. The energy production capacity of HepG2 cells was also decreased by LPS + BG compared with LPS alone as evaluated by extracellular flux analysis. However, Lactobacillus rhamnosus L34 (L34) improved sepsis, regardless of Candida administration, through the attenuation of gut leakage and gut dysbiosis. In conclusion, an impact of gut Candida was demonstrated by Candida pretreatment in obese mice that worsened sepsis through (1) gut dysbiosis–induced gut leakage and (2) amplified systemic inflammation due to LPS, BG, and saturated fatty acid.

Divergent Effect of Cigarette Smoke on Innate Immunity in Inflammatory Bowel Disease: A Nicotine-Infection Interaction

Cigarette smoke (CS) has adverse effects in patients with Crohn’s disease (CD), an inflammatory bowel disease (IBD) that has been associated with microbial infection, immuno-dysregulation, and mucosal dysfunction. However, CS seems to provide relief and protection to patients with another IBD known as ulcerative colitis (UC). These two subsets are featured as M1- and M2-mediated responses, respectively. Nicotine is the most active, addictive, and studied ingredient in CS. The mechanism of how nicotine and/or other CS ingredients induce pro-inflammatory or anti-inflammatory phenotypes in IBD patients remains under investigation. Our most recent in vitro nicotine study provided significant insights toward understanding the contradictory effects of nicotine on IBD patients, and it elucidated the mechanistic role of α7nAChR in modulation of macrophages in tobacco smokers. Shifting the beneficial effect of nicotine to a harmful outcome in CD patients was linked to a nicotine-microbe interaction that supports a microbial etiology in CD pathogenesis. Among the most debated pathogens in CD etiology is Mycobacterium avium subspecies paratuberculosis (MAP). Other studies associated nicotine with upregulation of miR-124 expression in macrophages, which led to anti-inflammatory response. This review discusses published work on the role of nicotine in modulation of the innate immune response and subsequent signaling in macrophages in IBD subsets.

The pint- sized powerhouse: Illuminating the mighty role of the gut microbiome in improving the outcome of anti- cancer therapy

Cancer persists as a major health catastrophe and a leading cause of widespread mortality across every nation. Research of several decades has increased our understanding of the pivotal pathways and key players of the host during tumor development and progression, which has enabled generation of precision therapeutics with improved efficacy. Despite such tremendous advancements in our combat against this fatal disease, a majority of the cancer patients suffer from poor tumor- free survival owing to the increased incidence of recurrent tumor. This is primarily due to the development of resistance against contemporary anti- cancer strategies. Recent studies have pointed towards the involvement of the human symbiotic gut microbiota in regulating the outcome of chemotherapy and immunotherapy. It does so primarily by modulating the metabolism of the drugs and host immune response, thereby enhancing the efficacy and ameliorating the toxicity. The interactions between the therapeutic agents, microbial community and host immunity may provide a new avenue for the clinical management of cancer. In addition, consumption of dietary pro-, pre- and synbiotics has been recognized to confer protection against tumor genesis and also promote improved response to traditional tumor suppressive strategies. Naturally, the use of various combinatorial regimes containing dietary supplements that improve the gut microbiome in amalgamation with conventional cancer treatment methods may significantly augment the therapeutic outcome of cancer patients and circumnavigate the resistance mechanisms that confound traditional therapies. In this review, we have summarized the role of the gut microbiome, which is the largest assembly of commensals within the human body, in regulating the efficacy and toxicity of various existing anti- cancer therapies including chemotherapy, immunotherapy and surgery. Furthermore, we have discussed how novel strategies integrating the application of probiotics, prebiotics, synbiotics and antibiotics in combination with the aforementioned anti- cancer modules manipulate the gut microbiota and, therefore, augment their therapeutic outcome. Together, such innovative anti- tumorigenic approaches may prove highly effective in improving the prognosis of cancer patients.

Evodiamine has therapeutic efficacy in ulcerative colitis by increasing Lactobacillus acidophilus levels and acetate production

Emerging evidence implicates gut microbiota have an important role in ulcerative colitis (UC). Previous study indicated that Evodiamine (EVO) can alleviate colitis through downregulating inflammatory pathways. However, specific relationship between EVO-treated colitis relief and regulation of gut microbiota is still unclear. Here, our goal was to determine the potential role of gut microbiota in the relief of UC by EVO. By using pathology-related indicators, 16S rRNA sequencing and metabolomics profiling, we assessed the pharmacological effect of EVO on dextran sulfate sodium (DSS)-induced colitis rats as well as on the change of gut microbiota and metabolism. Fecal derived from EVO-treated rats was transplanted into colitis rats to verify the effect of EVO on gut microbiota, and 'driver bacteria' was found and validated by 16S rRNA sequencing, metagenome and qRT-PCR. The effect of Lactobacillus acidophilus (L. acidophilus) was investigated by vivo experiment, microbiota analysis, Short-chain fatty acids (SCFAs) quantification and colon transcriptomics. EVO reduced the susceptibility to DSS-induced destruction of epithelial integrity and severe inflammatory response, and regulated the gut microbiota and metabolites. Fecal Microbiota Transplantation (FMT) alleviated DSS-induced colitis, increased the abundance of L. acidophilus and the level of acetate. Furthermore, gavaged with L. acidophilus reduced pro-inflammatory cytokines, promoted the increase of goblet cells and the secretion of antimicrobial peptides, regulated the ratio of Firmicutes/Bacteroidetes and increased the level of acetate. Our results indicated that EVO mitigation of DSS-induced colitis is associated with increased in L. acidophilus and protective acetate production, which may be a promising strategy for treating UC.

Occurrence of Blastocystis in Patients with Clostridioides difficile Infection

Clostridiodes difficile comprises a public-health threat that has been understudied in Colombia. Hypervirulent strains of C. difficile harbor multiple toxins, can be easily spread, and can have their onset of disease within healthcare facilities (HCFO) and the community (CO). Studies have shown that a disrupted microbiota (e.g., dysbiosis) may allow C. difficile infection (CDI). It has been suggested that dysbiosis prevents colonization by the anaerobic eukaryote Blastocystis, possibly due to an increase in luminal oxygen tension. No study has found co-occurrence of CDI and Blastocystis. Therefore, we aimed to determine the frequencies of C. difficile and Blastocystis infection/colonization in 220 diarrheal fecal samples. Molecular detection by PCR for both microorganisms was performed, with descriptive analyses of four variables (CDI detection, determination of C. difficile toxigenic profiles, Blastocystis detection, and patient site of onset). We demonstrate a significant association between the presence of Blastocystis and CDI, with coinfection found in 61 patients, and show a high frequency of CDI among both HCFO and CO groups. Our results of coinfection frequencies could support hypotheses that suggest Blastocystis can adapt to dysbiosis and oxidative stress. Further, the presence of toxigenic C. difficile occurring outside healthcare facilities shown here raises the alarm for community wide spread.

The impact of Lactococcus lactis (probiotic nasal rinse) co-culture on growth of patient-derived strains of Pseudomonas aeruginosa

BACKGROUND

The Lactococcus strain of bacteria has been introduced as a probiotic nasal rinse for alleged salubrious effects on the sinonasal bacterial microbiome. However, data regarding interactions with pathogenic bacteria within the sinuses are lacking. The purpose of this study is to assess the interaction between L. lactis and patient-derived Pseudomonas aeruginosa, an opportunistic pathogen in recalcitrant chronic rhinosinusitis (CRS).

METHODS

Commercially available probiotic suspension containing L. lactis W136 was grown in an anaerobic chamber and colonies were isolated. Colonies were co-cultured with patient-derived P. aeruginosa strains in the presence of porcine gastric mucin (mimicking human mucus) for 72 hours. P. aeruginosa cultures without L. lactis served as controls. Colony forming units (CFUs) were compared.

RESULTS

Six P. aeruginosa isolates collected from 5 CRS patients (3 isolates from cystic fibrosis [CF], 1 mucoid strain) and laboratory strain PAO1 were co-cultured with L. lactis. There was no statistical difference in CFUs of 5 P. aeruginosa isolates grown with L. lactis compared to CFUs without presence of L. lactis. CFU counts were much higher when the mucoid strain was co-cultured with L. lactis (CFU+L.lactis = 1.9 × 108 ± 1.44 × 107, CFU-L.lactis = 1.3 × 108 ± 8.9 × 106, p = 0.01, n = 7). L. lactis suppressed the growth of 1 P. aeruginosa strain (CFU+L.lactis = 2.15 × 108 ± 2.9 × 107, CFU-L.lactis = 3.95 × 108 ± 4.8 × 106, p = 0.03, n = 7).

CONCLUSION

L. lactis suppressed the growth of 1 patient P. aeruginosa isolate and induced growth of another (a mucoid strain) in in vitro co-culture setting in the presence of mucin. Further experiments are required to assess the underlying interactions between L. lactis and P. aeruginosa.

Effects of enrofloxacin treatment on the bacterial microbiota of milk from goats with persistent mastitis

Antibiotic resistance has become a major concern for human and animal health. As fluoroquinolones have been extensively used in human and veterinary medicine, there has also been the rapid emergence and spread of antimicrobial resistance around the world. Here, we analysed the microbiome of goat milk using samples from healthy goats and those diagnosed with persistent mastitis and treated using the antibiotic enrofloxacin with 16S rRNA amplicon sequencing. We selected a group of 11 goats and 22 samples of milk that did not respond clinically to enrofloxacin treatment. Milk samples were evaluated before and after treatment to verify changes of the microbiota; the three first lactating goats were selected from the healthy control group. The milk samples from the healthy control animals presented a larger abundance of different species of bacteria of the Staphylococcus genus, but a smaller number of different genera, which indicated a more specific niche of resident bacteria. The Firmicutes phylum was predominantly different between the studied groups. Samples from before-treatment animals had a higher number of new species than those from the control group, and after being treated again. These microbiota received new bacteria, increasing the differences in bacteria even more in relation to the control group. Genotypes such as Trueperella and Mannheimia, between other genera, had a high abundance in the samples from animals with persistent mastitis. The dysbiosis in this study, with marked evidence of a complex microbiota in activity in cases of the failure of antimicrobial treatment for persistent chronic mastitis, demonstrates a need to improve the accuracy of pathogen identification and increases concern regarding antibiotic treatments in milk production herds.

Selenium affects the activity of black tea in preventing metabolic syndrome in high-fat diet-fed Sprague-Dawley rats

BACKGROUND

Metabolic syndrome, a group of factors that increase the risk of health problems, is becoming increasingly common. Strategies to prevent metabolic syndrome have received substantial attention. Black tea consumption and selenium (Se) intake have been reported to be associated negatively with the prevalence of metabolic syndrome. We therefore sought to investigate whether Se-rich black tea might have a stronger effect than Se-deficient black tea in the prevention of metabolic syndrome.

RESULTS

Sprague-Dawley rats were divided into four groups and fed a normal rodent diet, high-fat diet, high-fat diet containing 3% Se-rich black tea, or a high-fat diet containing 3% Se-deficient black tea for 4 weeks. Blood and tissue samples were tested at the end of the experiment. The results suggested that both types of black tea ameliorated high-fat diet-induced body-weight gain, lowered serum triglycerides and attenuated intestinal barrier dysfunction. Selenium-rich black tea showed stronger activity in decreasing fasting serum glucose and increasing insulin sensitivity, as well as stronger hepatoprotection, owing to higher total antioxidant capacity and activated hepatic antioxidant enzymes. However, it did not exhibit better effects in preventing fat accumulation. The different effects of Se-rich and Se-deficient black tea on the gut microbiota might have been partially responsible for the results.

CONCLUSION

Compared with Se-deficient black tea, Se-rich black tea displayed stronger activity in preventing high-fat diet-induced hyperglycemia and liver damage but was not better at preventing fat accumulation and attenuating dysbiosis. More experiments are needed to understand the underlying mechanisms further. © 2019 Society of Chemical Industry.

The role of gut microbiota in atopic asthma and allergy, implications in the understanding of disease pathogenesis

Asthma is a clinical syndrome characterized by chronic airway inflammation. There is mounting evidence on the role of microbiota in the development of asthma. This review focuses on the role of microbiota in maintaining the integrity of the epithelia and their role in regulating the immune response. The review compiles data from multiple studies on the role of microbiota in the innate immune response and the development and differentiation of CD4⁺ T cells, a major component of the adaptive arm of the immune response. As a result of dysbiosis, invariant natural killer T cells may induce T helper 2 cell differentiation and immunoglobulin E isotype switching through the release of interleukin-4 and interleukin-13. Furthermore, degradation of immunoglobulin A antibodies, increased circulating mast cells and basophils, and inflammation are among other mechanisms by which dysbiosis can induce or exacerbate asthma. After explaining the underlying mechanisms, the review derives conclusions from studies that investigate dysbiosis in infancy and the development of asthma later in life. The review also includes studies that investigate asthmatic mothers and the development of asthma in children and the role of dysbiosis in that regard. Finally, the review explains the statistical relationship between eczema and asthma through multiple studies that investigate the role of dysbiosis in both atopic states. This review provides insight into the role of dysbiosis in asthma, and an understanding that is required to establish clinical trials which aim to modulate the gut microbiota as a means of preventing and treating asthma.

Prebiotics and Probiotics in Inflammatory Bowel Disease: Where are we now and where are we going?

The incidence, prevalence, and cost of care associated with diagnosis and management of inflammatory bowel disease are on the rise. The role of gut microbiota in the causation of Crohn's disease and ulcerative colitis has not been established yet. Nevertheless, several animal models and human studies point towards the association. Targeting intestinal dysbiosis for remission induction, maintenance, and relapse prevention is an attractive treatment approach with minimal adverse effects. However, the data is still conflicting. The purpose of this article is to provide the most comprehensive and updated review on the utility of prebiotics and probiotics in the management of active Crohn's disease and ulcerative colitis/pouchitis and their role in the remission induction, maintenance, and relapse prevention. A thorough literature review was performed on PubMed, Ovid Medline, and EMBASE using the terms "prebiotics AND ulcerative colitis", "probiotics AND ulcerative colitis", "prebiotics AND Crohn's disease", "probiotics AND Crohn's disease", "probiotics AND acute pouchitis", "probiotics AND chronic pouchitis" and "prebiotics AND pouchitis". Observational studies and clinical trials conducted on humans and published in the English language were included. A total of 71 clinical trials evaluating the utility of prebiotics and probiotics in the management of inflammatory bowel disease were reviewed and the findings were summarized. Most of these studies on probiotics evaluated lactobacillus, De Simone Formulation or Escherichia coli Nissle 1917 and there is some evidence supporting these agents for induction and maintenance of remission in ulcerative colitis and prevention of pouchitis relapse with minimal adverse effects. The efficacy of prebiotics such as fructooligosaccharides and Plantago ovata seeds in ulcerative colitis are inconclusive and the data regarding the utility of prebiotics in pouchitis is limited. The results of the clinical trials for remission induction and maintenance in active Crohn's disease or post-operative relapse with probiotics and prebiotics are inadequate and not very convincing. Prebiotics and probiotics are safe, effective and have great therapeutic potential. However, better designed clinical trials in the multicenter setting with a large sample and long duration of intervention are needed to identify the specific strain or combination of probiotics and prebiotics which will be more beneficial and effective in patients with inflammatory bowel disease.

Clostridium Difficile Infection in Patients Impact Suspected Cytomegalovirus Infection in Patients with Inflammatory Bowel Disease

Introduction

Clostridium difficile infection (CDI) has been reported to be a cause of flare-ups in patients with inflammatory bowel disease (IBD). Cytomegalovirus (CMV) infection can cause severe disease and complications in immunocompromised patients in consequence of disease or therapy.

Aim

Our aim was to describe the prevalence and clinical outcomes of CDI with concomitant CMV infection in IBD patients hospitalized for flare-ups in association with the disease itself and medication used.

Methods

We prospectively identified consecutive patients referred for CDI management during 2015-2017. Stool samples were tested for Clostridium difficile toxin A and/or B and Glutamate Dehydrogenase in patients with clinical symptoms. CDI patients with IBD history were tested for anti-CMV IgG and IgM antibodies by chemiluminescent microparticle immunoassay and underwent histological analysis for CMV on colon biopsies. Data were collected for demographic characteristics, treatment and outcome.

Results

125 patients with CDI were enrolled. Among these patients, 14 (11.2%) were diagnosed with IBD. The mean patient age of IBD patients was 52.5±15.4 years at diagnosis of CDI, 85.7% had UC, 14.3% CD, while the age of patients was shared. Eleven of the total of 14 patients (78.6%) tested positive for anti-CMV IgG. Of these, 3 patients (21.4%) exhibited high CMV IgG avidity, without detectable anti-CMV IgM and biopsy-proven CMV colitis. Of the 14 IBD patients with CDI, 8 patients (57.1%) were receiving anti-tumor necrosis factor (anti-TNF) therapy (21.4 % infliximab or golimumab, 7.1% vedolizumab or adalimumab) and 43.5% of patients were being treated with systemic corticosteroids. Four UC patients (28.6%) on steroids of the 14 CDI patients underwent a colectomy whereas none of the not on steroids patients underwent colectomy (p=0.25). Among them, 1 patient (7.1%) had recurrent CDI after 5 months from the first episode of CDI.These patients were treated with vancomycin, metronidazole and fidaxomicin. The mean age of patients that had a colectomy 65.5±9.32 (n=4) was higher than the mean age of those 47.30±14.49 (n=10) who improved (U_Mann-Whitney=6. p=0.04).

Conclusions

Immunosuppressive medications and older age are associated with increased risk of CDI and poor outcome. Although, CMV is a rare colonic pathogen in the immunocompetent patient, it should be included and screened when exacerbation of IBD occurs in patients receiving any type of immunosuppressive therapy.

Vitamin D and microbiota: Two sides of the same coin in the immunomodulatory aspects

The gut microbiota is crucial for host immune response, vitamin synthesis, short chain fatty acids (SCFAs) production, intestinal permeability, nutrient digestion energy metabolism and protection from pathogens. Therefore, gut microbiota guarantees the host's predisposition to gastrointestinal diseases. Intestinal microbiota may be damaged by environmental components with negative health conditions. Dysbiosis consisting in alteration in the gut microbiota has been involved in several disorders including inflammation, allergic reactions, autoimmune diseases, heart diseases, obesity, and metabolic syndrome and even in the state of malignant carcinogenesis existing in humans. Several epidemiological studies have shown that inadequate solar exposure results in vitamin D insufficiency/deficiency which has a strong impact on different immune responses and the occurrence of a wide range of pathological conditions. Additionally, new evidence indicates that the vitamin D pathway plays a key role in gut homeostasis. Due to the strong connection between vitamin D and microbiota, herein we focus on the new findings about intestinal bacteria-immune crosstalk and the impact of vitamin D in gut microbiota regulation, in order to offer new clarifications on their interaction. Understanding the mechanism by which vitamin D can affect the gut microbiota composition and its dynamic activities, as well as the innate and adaptive state of the immune system, is not only a fundamental research but also an opportunity to improve health status.

Nonsteroidal Anti-Inflammatory Drugs Impact on the Outcomes of Hospitalized Patients with Clostridium difficile Infection

PURPOSE

Mouse model experiments have demonstrated an increased Clostridium difficile infection (CDI) severity with Nonsteroidal Anti-Inflammatory Drugs (NSAIDs) use. We aim to evaluate the impact of NSAIDs in humans after a diagnosis of CDI on primary outcomes defined as I) all-cause mortality and II) toxic mega-colon attributable to CDI.

PATIENTS AND METHODS

All hospitalized patients with a diagnosis of CDI were divided into two groups; those with NSAIDs administered up to 10 days after onset of CDI versus no NSAIDs use. The primary outcomes were analyzed between the groups, while controlling for severity of CDI. A logistic regression analysis was performed to identify the predictors of worse outcomes.

RESULTS

NSAIDs were administered in 14% (n=80) of the 568 hospitalized visits for an average of 2.5 days after the CDI diagnosis. All-cause mortality was high in patients who did not receive NSAIDs as compared to those who did receive NSAIDs (16.6% vs 12.5%, p 0.354). Patients who were prescribed NSAIDs were more likely to have toxic mega-colon as compared to those who were not prescribed NSAIDs (2.5% vs 0.6%, p 0.094). Results were not statistically significant, even after controlling for CDI severity. Logistic regression analysis did not identify NSAIDs administration as a significant factor for all-cause mortality in CDI patients.

CONCLUSION

This retrospective study results, contrary to mouse model, did not show association between NSAID use and CDI related mortality and toxic mega-colon. Shorter duration of NSAIDs use, younger people in study group, and timely CDI treatment may have resulted in contrasting results.

Role of the microbiome in occurrence, development and treatment of pancreatic cancer

Pancreatic cancer is one of the most lethal malignancies. Recent studies indicated that development of pancreatic cancer may be intimately connected with the microbiome. In this review, we discuss the mechanisms through which microbiomes affect the development of pancreatic cancer, including inflammation and immunomodulation. Potential therapeutic and diagnostic applications of microbiomes are also discussed. For example, microbiomes may serve as diagnostic markers for pancreatic cancer, and may also play an important role in determining the efficacies of treatments such as chemo- and immunotherapies. Future studies will provide additional insights into the various roles of microbiomes in pancreatic cancer.

K5 Capsule and Lipopolysaccharide Are Important in Resistance to T4 Phage Attack in Probiotic E. coli Strain Nissle 1917

Rapidly growing antibiotic resistance among gastrointestinal pathogens, and the ability of antibiotics to induce the virulence of these pathogens makes it increasingly difficult to rely on antibiotics to treat gastrointestinal infections. The probiotic Escherichia coli strain Nissle 1917 (EcN) is the active component of the pharmaceutical preparation Mutaflor^® and has been successfully used in the treatment of gastrointestinal disorders. Gut bacteriophages are dominant players in maintaining the microbial homeostasis in the gut, however, their interaction with incoming probiotic bacteria remains to be at conception. The presence of bacteriophages in the gut makes it inevitable for any probiotic bacteria to be phage resistant, in order to survive and successfully colonize the gut. This study addresses the phage resistance of EcN, specifically against lytic T4 phage infection. From various experiments we could show that (i) EcN is resistant toward T4 phage infection, (ii) EcN's K5 polysaccharide capsule plays a crucial role in T4 phage resistance and (iii) EcN's lipopolysaccharide (LPS) inactivates T4 phages and notably, treatment with the antibiotic polymyxin B which neutralizes the LPS destroyed the phage inactivation ability of isolated LPS from EcN. Combination of these identified properties in EcN was not found in other tested commensal E. coli strains. Our results further indicated that N-acetylglucosamine at the distal end of O6 antigen in EcN's LPS could be the interacting partner with T4 phages. From our findings, we have reported for the first time, the role of EcN's K5 capsule and LPS in its defense against T4 phages. In addition, by inactivating the T4 phages, EcN also protects E. coli K-12 strains from phage infection in tri-culture experiments. Our research highlights phage resistance as an additional safety feature of EcN, a clinically successful probiotic E. coli strain.

Immunomodulating Activity and Therapeutic Effects of Short Chain Fatty Acids and Tryptophan Post-biotics in Inflammatory Bowel Disease

Crohn's disease (CD) and Ulcerative colitis (UC) are grouped as Inflammatory Bowel Diseases (IBD). The IBD is associated to a multifaceted interplay between immunologic, microbial, genetic, and environmental factors. Nowadays, the gut microbiota (GM) dysbiosis has been indicated as a cause in the IBD development, affecting the impaired cross-talk between GM and immune cells. Moreover, recent studies have uncovered a crucial role for bacterial post-biotics (metabolites) in the orchestration of the host immune response, as they could be messengers between the GM and the immune system. In addition, transgenic mouse models showed that SCFAs (Short Chain Fatty Acids) and Tryptophan (Trp) post-biotics play important immunomodulatory effects, regulating both innate and adaptive immune cell generation, their function and trafficking. Here, we present an overview on the main microbial post-biotics and their effects on the gut mucosa with specific emphasis on their relevance for IBD. Finally, we discuss the therapeutic potential of SCFA and Trp post-biotics on IBD through approaches based on the "immunonutrition," defined as a modulation of the immune system provided by specific interventions that modify dietary nutrients.

"Photobiomics": Can Light, Including Photobiomodulation, Alter the Microbiome?

Objective: The objective of this review is to consider the dual effects of microbiome and photobiomodulation (PBM) on human health and to suggest a relationship between these two as a novel mechanism. Background: PBM describes the use of low levels of visible or near-infrared (NIR) light to heal and stimulate tissue, and to relieve pain and inflammation. In recent years, PBM has been applied to the head as an investigative approach to treat diverse brain diseases such as stroke, traumatic brain injury (TBI), Alzheimer's and Parkinson's diseases, and psychiatric disorders. Also, in recent years, increasing attention has been paid to the total microbial population that colonizes the human body, chiefly in the gut and the mouth, called the microbiome. It is known that the composition and health of the gut microbiome affects many diseases related to metabolism, obesity, cardiovascular disorders, autoimmunity, and even brain disorders. Materials and methods: A literature search was conducted for published reports on the effect of light on the microbiome. Results: Recent work by our research group has demonstrated that PBM (red and NIR light) delivered to the abdomen in mice, can alter the gut microbiome in a potentially beneficial way. This has also now been demonstrated in human subjects. Conclusions: In consideration of the known effects of PBM on metabolomics, and the now demonstrated effects of PBM on the microbiome, as well as other effects of light on the microbiome, including modulating circadian rhythms, the present perspective introduces a new term "photobiomics" and looks forward to the application of PBM to influence the microbiome in humans. Some mechanisms by which this phenomenon might occur are considered.

Oral Bacteria and Intestinal Dysbiosis in Colorectal Cancer

The human organism coexists with its microbiota in a symbiotic relationship. These polymicrobial communities are involved in many crucial functions, such as immunity, protection against pathogens, and metabolism of dietary compounds, thus maintaining homeostasis. The oral cavity and the colon, although distant anatomic regions, are both highly colonized by distinct microbiotas. However, studies indicate that oral bacteria are able to disseminate into the colon. This is mostly evident in conditions such as periodontitis, where specific bacteria, namely Fusobacterium nucrelatum and Porphyromonas gingivalis project a pathogenic profile. In the colon these bacteria can alter the composition of the residual microbiota, in the context of complex biofilms, resulting in intestinal dysbiosis. This orally-driven disruption promotes aberrant immune and inflammatory responses, eventually leading to colorectal cancer (CRC) tumorigenesis. Understanding the exact mechanisms of these interactions will yield future opportunities regarding prevention and treatment of CRC.

Factors affecting the composition of the gut microbiota, and its modulation

Gut microbiota have important functions in the body, and imbalances in the composition and diversity of those microbiota can cause several diseases. The host fosters favorable microbiota by releasing specific factors, such as microRNAs, and nonspecific factors, such as antimicrobial peptides, mucus and immunoglobulin A that encourage the growth of specific types of bacteria and inhibit the growth of others. Diet, antibiotics, and age can change gut microbiota, and many studies have shown the relationship between disorders of the microbiota and several diseases and reported some ways to modulate that balance. In this review, we highlight how the host shapes its gut microbiota via specific and nonspecific factors, how environmental and nutritional factors affect it, and how to modulate it using prebiotics, probiotics, and fecal microbiota transplantation.

Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome

Inflammatory bowel disease (IBD) is a chronic complex inflammatory gut pathological condition, examples of which include Crohn’s disease (CD) and ulcerative colitis (UC), which is associated with significant morbidity. Although the etiology of IBD is unknown, gut microbiota alteration (dysbiosis) is considered a novel factor involved in the pathogenesis of IBD. The gut microbiota acts as a metabolic organ and contributes to human health by performing various physiological functions; deviation in the gut flora composition is involved in various disease pathologies, including IBD. This review aims to summarize the current knowledge of gut microbiota alteration in IBD and how this contributes to intestinal inflammation, as well as explore the potential role of gut microbiota-based treatment approaches for the prevention and treatment of IBD. The current literature has clearly demonstrated a perturbation of the gut microbiota in IBD patients and mice colitis models, but a clear causal link of cause and effect has not yet been presented. In addition, gut microbiota-based therapeutic approaches have also shown good evidence of their effects in the amelioration of colitis in animal models (mice) and IBD patients, which indicates that gut flora might be a new promising therapeutic target for the treatment of IBD. However, insufficient data and confusing results from previous studies have led to a failure to define a core microbiome associated with IBD and the hidden mechanism of pathogenesis, which suggests that well-designed randomized control trials and mouse models are required for further research. In addition, a better understanding of this ecosystem will also determine the role of prebiotics and probiotics as therapeutic agents in the management of IBD.

Microbiota-Immune Interaction in the Pathogenesis of Gut-Derived Infection

Gut-derived infection is among the most common complications in patients who underwent severe trauma, serious burn, major surgery, hemorrhagic shock or severe acute pancreatitis (SAP). It could cause sepsis and multiple organ dysfunction syndrome (MODS), which are regarded as a leading cause of mortality in these cases. Gut-derived infection is commonly caused by pathological translocation of intestinal bacteria or endotoxins, resulting from the dysfunction of the gut barrier. In the last decades, the studies regarding to the pathogenesis of gut-derived infection mainly focused on the breakdown of intestinal epithelial tight junction and increased permeability. Limited information is available on the roles of intestinal microbial barrier in the development of gut-derived infection. Recently, advances of next-generation DNA sequencing techniques and its utilization has revolutionized the gut microecology, leading to novel views into the composition of the intestinal microbiota and its connections with multiple diseases. Here, we reviewed the recent progress in the research field of intestinal barrier disruption and gut-derived infection, mainly through the perspectives of the dysbiosis of intestinal microbiota and its interaction with intestinal mucosal immune cells. This review presents novel insights into how the gut microbiota collaborates with mucosal immune cells to involve the development of pathological bacterial translocation. The data might have important implication to better understand the mechanism underlying pathological bacterial translocation, contributing us to develop new strategies for prevention and treatment of gut-derived sepsis.

Interplay Between the Host, the Human Microbiome, and Drug Metabolism

The human microbiome is composed of four major areas including intestinal, skin, vaginal, and oral microbiomes, with each area containing unique species and unique functionalities. The human microbiome may be modulated with prebiotics, probiotics, and postbiotics to potentially aid in the treatment of diseases like irritable bowel syndrome, bacterial vaginosis, atopic dermatitis, gingivitis, obesity, or cancer. There is also potential for many of the inhabitants of the human microbiome to directly modulate host gene expression and modulate host detoxifying enzyme activity like cytochrome P450s (CYPs), dehydrogenases, and carboxylesterases. Therefore, the microbiome may be important to consider during drug discovery, risk assessment, and dosing regimens for various diseases given that the human microbiome has been shown to impact host detoxification processes.

The Association Between Disease Severity and Microbiome in Chronic Rhinosinusitis

OBJECTIVE

The role of the microbiome in the etiology of chronic rhinosinusitis (CRS) is still in debate. Reductions in richness and diversity have been implicated in CRS; however, limited knowledge exists regarding the impact of the severity of disease on the microbiome. The associations between constituents of the microbiome and the degree of mucosal inflammation and tissue eosinophilia are described.

METHODS

A cross-sectional study of CRS and non-CRS patients who underwent endoscopic sinus surgery was performed. Sinus mucosal biopsies were assessed for the degree of inflammation and tissue eosinophilia. Middle-meatal swabs were subjected to 16S rRNA gene sequencing, which quantified the prevalence, mean relative abundance, richness, and diversity. Comparisons between the microbiome at the genus level and degree of inflammation (absent, mild, moderate, severe) and tissue eosinophilia (absent, < 10, 10-100, > 100 per high-powered field) were performed.

RESULTS

Eight-nine patients (52.8 ± 14.21 years, 64.0% male) were assessed. Of those, 52 had CRS and 37 were controls. Corynebacterium and Staphylococcus were the most abundant genera in both the CRS (29% and 16%) and non-CRS groups (40% and 20%). Richness decreased in more severely inflamed patients (23.2 ± 13.9 vs. 18.1 ± 16.1 vs. 16.8 ± 12.3 vs. 14.7 ± 10.9; P < 0.01), as did diversity (1.4 ± 0.7 vs. 1.2 ± 1.0 vs. 1.2 ± 0.8 vs. 0.9 ± 0.7; P = 0.05). Richness was associated with higher tissue eosinophilia (23.2 ± 13.9 vs. 19.3 ± 17.2 vs. 15.9 ± 11.6 vs. 13.4 ± 6.6; P < 0.01).

CONCLUSION

The loss of richness and diversity seen in the CRS microbiome appears to be a product of severity of inflammation and tissue eosinophilia. Whether this dysbiosis is causative or a result of the disease with impaired epithelial integrity requires ongoing research.

LEVEL OF EVIDENCE

4 Laryngoscope, 129:1265-1273, 2019.