Microbial-gut interactions in health and disease. Antibiotic-associated diarrhoea

Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients

The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.

Gut-Lung Axis in Focus: Deciphering the Impact of Gut Microbiota on Pulmonary Arterial Hypertension

Recent advancements in the understanding of pulmonary arterial hypertension (PAH) have highlighted the significant role of the gut microbiota (GM) in its pathogenesis. This comprehensive review delves into the intricate relationship between the GM and PAH, emphasizing the influence of gut microbial composition and the critical metabolites produced. We particularly focus on the dynamic interaction between the gut and lung, examining how microbial dysbiosis contributes to PAH development through inflammation, altered immune responses, and changes in the gut-lung axis. Noteworthy findings include variations in the ratios of key bacterial groups such as Firmicutes and Bacteroidetes in PAH and the pivotal roles of metabolites like trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), and serotonin in the disease's progression. Additionally, the review elucidates potential diagnostic biomarkers and novel therapeutic approaches, including the use of probiotics and fecal microbiota transplantation, which leverage the gut microbiota for managing PAH. This review encapsulates the current state of research in this field, offering insights into the potential of gut microbiota modulation as a promising strategy in PAH diagnosing and treatment.

Relationship among Chinese herb polysaccharide (CHP), gut microbiota, and chronic diarrhea and impact of CHP on chronic diarrhea

Chronic diarrhea, including diarrhea-predominant irritable bowel syndrome (IBS-D), osmotic diarrhea, bile acid diarrhea, and antibiotic-associated diarrhea, is a common problem which is highly associated with disorders of the gut microbiota composition such as small intestinal bacterial overgrowth (SIBO) and so on. A growing number of studies have supported the view that Chinese herbal formula alleviates the symptoms of diarrhea by modulating the fecal microbiota. Chinese herbal polysaccharides (CHPs) are natural polymers composed of monosaccharides that are widely found in Chinese herbs and function as important active ingredients. Commensal gut microbiota has an extensive capacity to utilize CHPs and play a vital role in degrading polysaccharides into short-chain fatty acids (SCFAs). Many CHPs, as prebiotics, have an antidiarrheal role to promote the growth of beneficial bacteria and inhibit the colonization of pathogenic bacteria. This review systematically summarizes the relationship among gut microbiota, chronic diarrhea, and CHPs as well as recent progress on the impacts of CHPs on the gut microbiota and recent advances on the possible role of CHPs in chronic diarrhea.

Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis

Antibiotic-induced gut microbiome dysbiosis (AID) is known to be influenced by host dietary composition. However, how and when diet modulates gut dysbiosis remains poorly characterized. Thus, here, we utilize a multi-omics approach to characterize how a diet supplemented with oats, a rich source of microbiota-accessible carbohydrates, or dextrose impacts amoxicillin-induced changes to gut microbiome structure and transcriptional activity. We demonstrate that oat administration during amoxicillin challenge provides greater protection from AID than the always oats or recovery oats diet groups. In particular, the group in which oats were provided at the time of antibiotic exposure induced the greatest protection against AID while the other oat diets saw greater effects after amoxicillin challenge. The oat diets likewise reduced amoxicillin-driven elimination of Firmicutes compared to the dextrose diet. Functionally, gut communities fed dextrose were carbohydrate starved and favored respiratory metabolism and consequent metabolic stress management while oat-fed communities shifted their transcriptomic profile and emphasized antibiotic stress management. The metabolic trends were exemplified when assessing transcriptional activity of the following two common gut commensal bacteria: Akkermansia muciniphila and Bacteroides thetaiotaomicron. These findings demonstrate that while host diet is important in shaping how antibiotics effect the gut microbiome composition and function, diet timing may play an even greater role in dietary intervention-based therapeutics. IMPORTANCE We utilize a multi-omics approach to demonstrate that diets supplemented with oats, a rich source of microbiota-accessible carbohydrates, are able to confer protection against antibiotic-induced dysbiosis (AID). Our findings affirm that not only is host diet important in shaping antibiotics effects on gut microbiome composition and function but also that the timing of these diets may play an even greater role in managing AID. This work provides a nuanced perspective on dietary intervention against AID and may be informative on preventing AID during routine antibiotic treatment.

Probiotic yeast Saccharomyces cerevisiae Az-12 isolated from pomegranate juice presented inhibitory effects against pathogenic bacteria

The potential probiotic yeast was isolated from the Kyzyl Anor pomegranate variety growing in the Turkestan region (Kazakhstan). The yeast strain was identified as Saccharomyces cerevisiae Az-12. Molecular genetic identification was carried out using the Sanger sequencing method. The degree of homology of the S. cerevisiae Az-12 strain with the strain MH608341.1 Saccharomyces cerevisiae isolate extr03 was 99.65%. Antagonistic effect of the yeast against pathogenic bacteria was confirmed according inhibition zones for Staphylococcus aureus 13.5 ± 0.05 mm; the inhibition zones for Escherichia coli 12.8 ± 0.05 mm; and 10.7 ± 0.05 mm for Pseudomonas aeruginosa. Scanning microscopy of S. cerevisiae Az-12 and S. aureus confirmed the adhesive ability of the yeast cell surface to S. aureus. S. cerevisiae Az-12 were chosen as the most promising, as they are able to quickly ferment juices. Functional drinks containing pomegranate juice and yeast with a probiotic effect can be considered as a useful synbiotic product formulation.

Research progress regarding the effect and mechanism of dietary phenolic acids for improving nonalcoholic fatty liver disease via gut microbiota

Phenolic acids (PAs), a class of small bioactive molecules widely distributed in food and mainly found as secondary plant metabolites, present significant advantages such as antioxidant activity and other health benefits. The global epidemic of nonalcoholic fatty liver disease (NAFLD) is becoming a serious public health problem. Existing studies showed that gut microbiota (GM) dysbiosis is highly associated with the occurrence and development of NAFLD. In recent years, progress has been made in the study of the relationship among PA compounds, GM, and NAFLD. PAs can regulate the composition and functions of the GM to promote human health, while GM can increase the dietary sources of PAs and improve its bioavailability. This paper discussed PAs, GM, and their interrelationship while introducing several representative dietary PA sources and examining the absorption and metabolism of PAs mediated by GM. It also summarizes the effect and mechanisms of PAs in improving and regulating NAFLD via GM and their metabolites. This helps to better evaluate the potential preventive effect of PAs on NAFLD via the regulation of GM and expands the utilization of PAs and PA-rich food resources.

Efficacy of <i>Saccharomyces boulardii</i> CNCM I-745 probiotic drug in the prevention and treatment of diarrhea in hospitalized patients with new coronavirus infection COVID-19

Aim. To evaluate the efficacy of Saccharomyces boulardii (S. boulardii) CNCM I-745 probiotic drug in preventing and treating diarrhea in hospitalized patients with COVID-19. Materials and methods. A prospective comparative study was conducted in two parallel groups. The study included males and females aged 18 to 60 with the following diagnosis confirmed by polymerase chain reaction: U07.2 Coronavirus infection COVID-19, caused by SARS-CoV-2 virus (grade 13 pneumonia according to CT scan). All patients received antibiotic therapy. The patients were subdivided into two equal groups (n=60) depending on the administration of S. boulardii CNCM I-745 probiotic drug in addition to standard treatment. The probiotic was prescribed by the attending physician; the dose was 2 capsules per day (500 mg/day) 30 min before the meal for 10 days. All patients were monitored for main clinical, laboratory, and instrumental parameters during the study. In addition, the symptom of diarrhea (stool with a frequency of more than 3 times a day of type 6 and 7 according to the Bristol stool scale), including its frequency, duration, and the number of bowel movements of loose stool per day were precisely evaluated in both groups. Results. In the overall patient pool, diarrhea was reported in 21.7% of in-patients during the observation period (95% confidence interval [CI] 14.229.1) with a mean duration of 4.6154 days (95% CI 3.7910-5.4398). The incidence of diarrhea in group 1 was 13.3% (95% CI 4.522.2), and in group 2, it was 30.0% (95% CI 18.141.9). Relative risk showed that the use of the S. boulardii CNCM I-745 probiotic drug leads to a significant reduction in the risk of diarrhea in hospitalized patients with COVID-19 infection receiving antibiotic therapy (odds ratio [OR] 0.3590, 95% CI 0.14210.9069; p=0.0303). In group 1, the duration of diarrhea was 3.1250 days (95% CI 2.58923.6608) versus 5.2778 days (95% CI 4.22906.3265) in group 2, p=0.0112. The mean daily frequency of loose stools in patients with diarrhea in group 1 was 3.2500 (95% CI 2.65883.8412) versus 4.3889 (95% CI 3.72525.0525) in group 2, p=0.0272. The secondary endpoint, duration of hospital stay, was also significantly shorter in group 1 patients 11.6833 days (95% CI 11.204212.1625) versus 12.7333 days (95% CI 12.135713.3309) in group 2, p=0.0120. Conclusion. The present prospective comparative study demonstrated that adding S. boulardii CNCM I-745 probiotic drug into the standard treatment regimen of patients with new coronavirus infection COVID-19 receiving antibiotic therapy helps reduce the incidence of diarrhea and its severity during hospitalization, as well as the duration of hospital stay.

Orally fed EGCG coronate food released TiO2 and enhanced penetrability into body organs via gut

Owing to unique nano-scale properties, TiO₂-NPs (T-NPs) are employed as food-quality enhancers in >900 processed food products. Whereas, epigallocatechin-3-gallate (EGCG), a green tea polyphenol is consumed in traditional brewed tea, globally. Taken together, we aimed to investigate whether human gastric-acid digested T-NPs and complex tea catechins yield ionic species (Ti⁴⁺_, Ti³⁺ etc.) and active EGCG forms to meet favourable conditions for in vivo bio-genesis of EGCG-coronated TiO₂-NPs (ET-NPs) in human gut. Secondly, compared to bare-surface micro and nano-scale TiO₂, i.e., T-MPs and T-NPs, respectively, how EGCG coronation on ET-NPs in the gut facilitates the modulation of intrinsic propensity of internalization of TiO₂ species into bacteria, body-organs, and gut-microbiota (GM), and immune system. ET-NPs were synthesized in non-toxic aqueous solution at varied pH (3-10) and characterised by state-of-the-arts for crystallinity, surface-charge, EGCG-encapsulation, stability, size, composition and morphology. Besides, flow-cytometry (FCM), TEM, EDS, histopathology, RT-PCR, 16S-rRNA metagenomics and ELISA were also performed to assess the size and surface dependent activities of ET-NPs, T-NPs and T-MPs vis-a-vis planktonic bacteria, biofilm, GM bacterial communities and animal's organs. Electron-microscopic, NMR, FTIR, DLS, XRD and EDS confirmed the EGCG coronation, dispersity, size-stability of ET-NPs, crystallinity and elemental composition of ET-NPs-8 and T-NPs. Besides, FCM, RT-PCR, 16S-rRNA metagenomics, histopathology, SEM and EDS analyses exhibited that EGCG coronation in ET-NPs-8 enhanced the penetration into body organs (i.e., liver and kidney etc.) and metabolically active bacterial communities of GM.

Improved diagnosis of antibiotic-associated haemorrhagic colitis (AAHC) in faecal specimens by a new qualitative real-time PCR assay detecting relevant toxin genes of Klebsiella oxytoca sensu lato

OBJECTIVE

Toxin-producing Klebsiella oxytoca causes antibiotic-associated haemorrhagic colitis (AAHC). The disease-relevant cytotoxins tilivalline and tilimycine produced by certain K. oxytoca isolates are encoded by the non-ribosomal peptide synthetase genes A (npsA) and B (npsB). In this study, the new LightMix® Modular kit for the detection of relevant K. oxytoca sensu lato (s.l.) toxin genes was evaluated.

METHODS

DNA was extracted on the automated EMAG® platform. Amplification was done on the Light Cycler® 480 II instrument. In total, 130 residual faecal specimens collected from patients with antibiotic-associated diarrhoea were studied to determine the clinical sensitivity and specificity. Toxigenic culture served as reference method.

RESULTS

With the new kit, the limit of detection was 15 CFU/mL for all targets. For the pehX target specific to K. oxytoca s.l., 65 of 130 clinical specimens were positive, while toxin-specific targets (npsA/npsB) were positive in 47 of 130. The npsA/npsB PCR targets showed a clinical sensitivity of 100% (95%CI 80.5-100%) and a specificity of 73.5% (95%CI 64.3-81.3%) with a positive predictive value of 16.5% (95%CI 12.7-21.2%) and a negative predictive value of 100%.

CONCLUSION

Compared with culture, additional clinical specimens positive for K. oxytoca s.l. were detected with real-time PCR. The specificity of the toxin targets appears moderate due to the inferior sensitivity of the culture-based reference method. Since the developed assay is highly sensitive, it may be used as first-line method to improve the diagnosis of AAHC.

Predictive Microbial Community and Functional Gene Expression Profiles in Pineapple Peel Fermentation Using 16S rRNA Gene Sequences

Pineapple peel (PP) is a by-product with the potential to be used as a raw material for functional beverages. Traditional PP fermentation has so far paid little attention to the microbial community and its role in the fermentation process. As a result, the current research looked into the microbial communities and their roles during PP fermentation. A metagenomic approach based on the 16S rRNA sequencing data was used to assess the microbial communities. Subsequent analysis was performed using PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) to analyze the microbial functions in the fermentation system. The microecology of the fermentation process in three samples was predominated by Firmicutes. Furthermore, the well-known probiotic genera Weissella, Lactobacillus, and Lactococcus were found to be predominating in the gumer, promic, and control samples, respectively. It was obvious that microenvironmental differences have an effect on the microbial composition of PP fermentation. Moreover, functional prediction revealed that carbohydrate metabolism was the most prevalent metabolic pathway during the fermentation process. Additionally, it was discovered that all of the bacteria found in the samples played significant roles in carbohydrate, amino acid, vitamin, and co-factor metabolism, which can be inferred to result in the production of beneficial metabolites.

Gut Ruminococcaceae levels at baseline correlate with risk of antibiotic-associated diarrhea

Antibiotic-associated diarrhea (AAD) affects a significant proportion of patients receiving antibiotics. We sought to understand if differences in the gut microbiome would influence the development of AAD. We administered a 3-day course of amoxicillin-clavulanate to 30 healthy adult volunteers, and analyzed their stool microbiome, using 16S rRNA gene sequencing, at baseline and up to 4 weeks post antibiotic administration. Lower levels of gut Ruminococcaceae were significantly and consistently observed from baseline until day 7 in participants who developed AAD. Overall, participants who developed AAD experienced a greater decrease in microbial diversity. The probability of AAD could be predicted based on qPCR-derived levels of Faecalibacterium prausnitzii at baseline. Our findings suggest that a lack of gut Ruminococcaceae influences development of AAD. Quantification of F. prausnitzii in stool prior to antibiotic administration may help identify patients at risk of AAD, and aid clinicians in devising individualized treatment regimens to minimize such adverse effects.

Structural Changes in Trabecular Bone, Cortical Bone and Hyaline Cartilage as Well as Disturbances in Bone Metabolism and Mineralization in an Animal Model of Secondary Osteoporosis in Clostridium perfringens Infection

There is no information regarding whether changes in the microbiological balance of the gastrointestinal tract as a result of an infection with Clostridium perfringens influence the development of metabolic bone disorders. The experiment was carried out on male broiler chickens divided into two groups: control (n = 10) and experimental (n = 10). The experimental animals were infected with Clostridium perfringens between 17 and 20 days of age. The animals were euthanized at 42 days of age. The structural parameters of the trabecular bone, cortical bone, and hyaline cartilage as well as the mineralization of the bone were determined. The metabolism of the skeletal system was assessed by determining the levels of bone turnover markers, hormones, and minerals in the blood serum. The results confirm that the disturbed composition of the gastrointestinal microflora has an impact on the mineralization and metabolism of bone tissue, leading to the structural changes in cortical bone, trabecular bone, and hyaline cartilage. On the basis of the obtained results, it can be concluded that changes in the microenvironment of the gastrointestinal tract by infection with C. perfringens may have an impact on the earlier development of osteoporosis.

Why use nutraceutical strategies for the Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is a chronic functional bowel disorder, often stress-related, identified by many abdominal symptoms, the most important of which is the chronic visceral abdominal pain. Therefore, IBS commonly impairs the quality of life of patients, moreover it is frequently linked to depressive and anxiety symptoms. The treatment of IBS primarily focuses on symptoms relief. Unfortunately, up to now, no efficacious therapies have been found. Therefore, it would be important to develop new anti-IBS interventions. The aim of this brief review is to summarize the current evidence of nutraceutical supplementation in IBS treatment, with probiotics, prebiotics, synbiotics, butyrate, palmitoylethanolamide and colostrum. Since nutraceutics are over the counter products, the review has the purpose to better inform the medicinal chemist and the practitioner about the possible benefit mechanisms and the many advantages that these therapies offer. All of these compounds present multiple mechanisms of action, such as restoring the physiological microbiota, potentiating gastrointestinal barrier's function, immunomodulatory, anti-inflammatory and antinociceptive activities. From the literature data it results that these compounds are not only capable to improve IBS symptomatology, but mainly display an optimal safety and tolerability profile. Although extensive studies must be carried out to reinforce the evidences from the so far limited clinical trials, the supplementation with these compounds may be useful considering the warnings of prescription medicines for special populations of patients, such as elders, youngsters, or patients who need a combination therapy. Finally, the nutraceutical approach may improve adherence to treatment, given its better acceptance by the patients compared to pharmacological therapy.

Diarrhoea and preadmission antibiotic exposure in COVID-19: a retrospective cohort study of 1153 hospitalised patients

OBJECTIVE

The aims of this study were to describe community antibiotic prescribing patterns in individuals hospitalised with COVID-19, and to determine the association between experiencing diarrhoea, stratified by preadmission exposure to antibiotics, and mortality risk in this cohort.

DESIGN/METHODS

Retrospective study of the index presentations of 1153 adult patients with COVID-19, admitted between 1 March 2020 and 29 June 2020 in a South London NHS Trust. Data on patients' medical history (presence of diarrhoea, antibiotic use in the previous 14 days, comorbidities); demographics (age, ethnicity, and body mass index); and blood test results were extracted. Time to event modelling was used to determine the risk of mortality for patients with diarrhoea and/or exposure to antibiotics.

RESULTS

19.2% of the cohort reported diarrhoea on presentation; these patients tended to be younger, and were less likely to have recent exposure to antibiotics (unadjusted OR 0.64, 95% CI 0.42 to 0.97). 19.1% of the cohort had a course of antibiotics in the 2 weeks preceding admission; this was associated with dementia (unadjusted OR 2.92, 95% CI 1.14 to 7.49). After adjusting for confounders, neither diarrhoea nor recent antibiotic exposure was associated with increased mortality risk. However, the absence of diarrhoea in the presence of recent antibiotic exposure was associated with a 30% increased risk of mortality.

CONCLUSION

Community antibiotic use in patients with COVID-19, prior to hospitalisation, is relatively common, and absence of diarrhoea in antibiotic-exposed patients may be associated with increased risk of mortality. However, it is unclear whether this represents a causal physiological relationship or residual confounding.

Probiotics for the Prevention of Antibiotic-associated Diarrhea in Adults: A Meta-Analysis of Randomized Placebo-Controlled Trials

OBJECTIVE

This meta-analysis aims to combine the latest research evidence to assess the effect of probiotics on preventing antibiotic-associated diarrhea (AAD) in adults.

METHODS

PubMed, Cochrane Library, EMBASE, and Web of Science were searched for randomized placebo-controlled trials on probiotics preventing AAD. A random or fixed effect model was used to combine the incidence of AAD (primary outcome) and the adverse event rates. The authors performed subgroup analyses to explore the effects of different participants population, probiotics species, and dosage.

RESULTS

Thirty-six studies were included with 9312 participants. Probiotics reduced the incidence of AAD by 38% (pooled relative risk, 0.62; 95% confidence interval, 0.51-0.74). The protective effect of probiotics was still significant when grouped by reasons for antibiotics treatment, probiotic duration, probiotic dosage, and time from antibiotic to probiotic. However, there were no statistically significant increased adverse events in the probiotics group (relative risk, 1.00; 95% confidence interval, 0.87-1.14).

CONCLUSIONS

This updated meta-analysis suggested that using probiotics as early as possible during antibiotic therapy has a positive and safe effect on preventing AAD in adults. Further studies should focus on the optimal dosage and duration of probiotics to develop a specific recommendation.

Phytochemicals as modifiers of gut microbial communities

A healthy gut microbiota (GM) is paramount for a healthy lifestyle. Alterations of the GM have been involved in the aetiology of several chronic diseases, including obesity and type 2 diabetes, as well as cardiovascular and neurodegenerative diseases. In pathological conditions, the diversity of the GM is commonly reduced or altered, often toward an increased Firmicutes/Bacteroidetes ratio. The colonic fermentation of dietary fiber has shown to stimulate the fraction of bacteria purported to have beneficial health effects, acting as prebiotics, and to increase the production of short chain fatty acids, e.g. propionate and butyrate, while also improving gut epithelium integrity such as tight junction functionality. However, a variety of phytochemicals, often associated with dietary fiber, have also been proposed to modulate the GM. Many phytochemicals possess antioxidant and anti-inflammatory properties that may positively affect the GM, including polyphenols, carotenoids, phytosterols/phytostanols, lignans, alkaloids, glucosinolates and terpenes. Some polyphenols may act as prebiotics, while carotenoids have been shown to alter immunoglobulin A expression, an important factor for bacteria colonization. Other phytochemicals may interact with the mucosa, another important factor for colonization, and prevent its degradation. Certain polyphenols have shown to influence bacterial communication, interacting with quorum sensing. Finally, phytochemicals can be metabolized in the gut into bioactive constituents, e.g. equol from daidzein and enterolactone from secoisolariciresinol, while bacteria can use glycosides for energy. In this review, we strive to highlight the potential interactions between prominent phytochemicals and health benefits related to the GM, emphasizing their potential as adjuvant strategies for GM-related diseases.

Genome sequence and annotation of Bacteroides sp aff. Thetaiotaomicron strain isolated from blood

This study is focused on genome sequence and annotation of the Bacteroides strain isolated from the blood of a patient with descending colon cancer. According to a comparison of the 16S ribosomal RNA sequence with the National Center for Biotechnology Information database, this strain was identified as Bacteroides sp. aff. Thetaiotaomicron. The next-generation sequencing of the strain was performed in a GENEWIZ laboratory (Jiangsu, China) on Illumina HiSeq device. According to CAZy classification, metabolic pathways related to carbohydrate metabolism of this strain engage the following enzymes: 427 glycosylhydrolases, 277 glycosyltransferases, 137 carbohydrate-binding modules, 48 carbohydrate esterases, and 24 polysaccharide lyases. According to the KEGG pathway database, Bacteroides sp. aff thetaiotaomicron strain is reported to incorporate 199 pathway associated genes. Bacteroides sp. aff. Thetaiotaomicron exposes the capacity of metabolizing a variety of polysaccharides. Its genome is enriched with an expanded repertoire of enzymes for the hydrolysis of glycosidic bonds and, thus, likely to hydrolyze most of glycosidic bonds in biological polysaccharides. The advanced capabilities of the studied strain to recognize and respond to environmental signals are expressed in the rich representation of one- and two-component signal transduction systems.

The relevance of DHA with modulating of host-gut microbiome signatures alterations and repairing of lipids metabolism shifts

Huge of previous reports recommended that gut microbiome have a crucial role in the human health and its change was profound impact for the metabolic improvements associated with lipids metabolism. In order to explore the relevance of a direct dysbiosis effect of gut microbiome on lipids metabolism shifts and repaired position of DHA, we built the animal model for the study with gut microbiome dysbiosis administrated by i.g. with CRO and intervened by DHA in the present work. Gut microbiome was analyzed by high throughput sequencing and bioinformatics analyses of bacteria. The composition of fatty acids and short chain fatty acids (SCFAs) were determined by gas chromatography. Blood lipids and bile acids were assayed by kit and UPLC-MS/MS, respectively. The expressions of enzymes of long chain fatty acid metabolism were analyzed by qRT-PCR. The results showed that gut microbiome dysbiosis caused lipid metabolism abnormal, and DHA was able to repair the lipids metabolism shifts resulted from gut microbiome dysbiosis. DHA could modulate host-gut microbiome signatures, improve concentrations of SCFAs, regulate fatty acids metabolism but modify bile acid profiles. In conclusion, we considered that DHA repaired lipid metabolism by modulating gut microbiome and regulating fatty acids metabolism pathway.

Impact on the Gut Microbiota of Intensive and Prolonged Antimicrobial Therapy in Patients With Bone and Joint Infection

There is a growing interest in the potentially deleterious impact of antibiotics on gut microbiota. Patients with bone and joint infection (BJI) require prolonged treatment that may impact significantly the gut microbiota. We collected samples from patients with BJI at baseline, end of antibiotics (EOT), and 2 weeks after antibiotic withdrawal (follow-up, FU) in a multicenter prospective cohort in France. Microbiota composition was determined by shotgun metagenomic sequencing. Fecal markers of gut permeability and inflammation as well as multi-drug-resistant bacteria (MDRB) and Clostridioides difficile carriage were assessed at each time point. Sixty-two patients were enrolled: 27 native BJI, 14 osteosynthesis-related BJI, and 21 prosthetic joint infections (PJI). At EOT, there was a significant loss of alpha-diversity that recovered at FU in patients with native BJI and PJI, but not in patients with osteosynthesis-related BJI. At EOT, we observed an increase of Proteobacteria and Bacteroidetes that partially recovered at FU. The principal component analysis (PCoA) of the Bray–Curtis distance showed a significant change of the gut microbiota at the end of treatment compared to baseline that only partially recover at FU. Microbiota composition at FU does not differ significantly at the genus level when comparing patients treated for 6 weeks vs. those treated for 12 weeks. The use of fluoroquinolones was not associated with a lower Shannon index at the end of treatment; however, the PCoA of the Bray–Curtis distance showed a significant change at EOT, compared to baseline, that fully recovered at FU. Levels of fecal neopterin were negatively correlated with the Shannon index along with the follow-up (r² = 0.17; p < 0.0001). The PCoA analysis of the Bray–Curtis distance shows that patients with an elevated plasma level of C-reactive protein (≥5 mg/L) at EOT had a distinct gut microbial composition compared to others. MDRB and C. difficile acquisition at EOT and FU represented 20% (7/35) and 37.1% (13/35) of all MDRB/C. difficile-free patients at the beginning of the study, respectively. In patients with BJI, antibiotics altered the gut microbiota diversity and composition with only partial recovery, mucosal inflammation, and permeability and acquisition of MDRB carriage. Microbiome interventions should be explored in patients with BJI to address these issues.

Evaluation of recreational risks due to exposure of antibiotic-resistance bacteria from environmental water: A proposed framework

This research provides a framework for the human health risk assessment due to exposure of AR (antibiotic resistance) E. coli from recreational water (swimming activity). Literature-based epidemiological studies were used for f-value formulation (i.e., AR E. coli/total number of E. coli isolates) and the theoretical calculation of AR and non-AR E. coli concentrations. Risk was estimated using calculated values by considering four different dose-response (D-R) scenarios with known characteristics due to current lack of availability of D-R for AR bacteria. f-values ranged between 0.14 and 0.59 and the order of calculated theoretical values of maximum AR E. coli are as follows: ampicillin or amoxicillin (38 CFU/dip) > co-trimoxazole (19 CFU/dip) ~ tetracycline (18 CFU/dip) > ceftriaxone or cefotaxime or ceftazidime (10 CFU/dip) ~ ciprofloxacin or ofloxacin (9 CFU/dip). The risk of infection was considerably high for theoretical calculated concentration values regardless of the chosen D-R model (annual risk of infection (95th percentile) = 1, Spearman's rank correlation coefficient = -0.06 to 0.94), under the conditions studied. Further, AR levels of human gastrointestinal-tract were determined using literature-reported data in stool samples and indicated that the resistance level was very high in healthy human (range: 3.7 × 10⁷-8.4 × 10⁷ CFU/g of wet lumen content). The maximum allowable concentration values for AR E. coli and non-ARB (0.0075 CFU/dip and 2.56 CFU/dip) were found to be smaller than the USEPA recreational water quality guidelines (≤126 CFU/100 mL), which can help the USEPA and other regulatory bodies in revisiting the current guidelines. So based on the noted results, we can conclude that the maintenance of inventory of actual measured concentration of ARB in the recreational water sites is needed to prevent unwanted complication related to the treatment of infectious sustained by resistant microbes.

Implications of the Human Gut-Brain and Gut-Cancer Axes for Future Nanomedicine

Recent clinical and pathological evidence have implicated the gut microbiota as a nexus for modulating the homeostasis of the human body, impacting conditions from cancer and dementia to obesity and social behavior. The connections between microbiota and human diseases offer numerous opportunities in medicine, most of which have limited or no therapeutic solutions available. In light of this paradigm-setting trend in science, this review aims to provide a comprehensive and timely summary of the mechanistic pathways governing the gut microbiota and their implications for nanomedicines targeting cancer and neurodegenerative diseases. Specifically, we discuss in parallel the beneficial and pathogenic relationship of the gut microbiota along the gut-brain and gut-cancer axes, elaborate on the impact of dysbiosis and the gastrointestinal corona on the efficacy of nanomedicines, and highlight a molecular mimicry that manipulates the universal cross-β backbone of bacterial amyloid to accelerate neurological disorders. This review further offers a forward-looking section on the rational design of cancer and dementia nanomedicines exploiting the gut-brain and gut-cancer axes.

Antibiotics Disturb Dentin Formation and Differentiation of Dental Pulp Stem Cells: The Role of Microbiota in Cellular Turnover of Mouse Incisor

Dentin formation was dependent on osteo-/odontogenic differentiation of dental pulp stem cells (DPSCs). It was observed in previous studies that antibiotic treatment in a clinical and animal model resulted in impaired mineralization of dental tissues. We previously reported that microbiota maintained the function of bone marrow mesenchymal stem cells, while whether microbiota dysbiosis caused by antibiotic treatment contributed to DPSCs dysfunction and impaired dentin formation is still not known. In this study, we aimed to clarify the role of microbiota or its metabolic products on dental mineralization and the function of DPSCs. Mice were treated with antibiotics to disrupt microbiota; then, the growth rate and histological characteristics of incisors as well as the biological characteristics of DPSCs in vitro were compared with specific pathogen-free (SPF) mice. In antibiotic-treated mice (AbT), we found a diminished quantity of microbiota and reduced growth rate of mechanical injured incisor, as well as decreased colony-forming rate and impaired ability of osteo-/odontogenic differentiation of DPSCs, in comparison to SPF mice. Colonization of AbT mice with SPF mice replanted the microbiota by cohousing (conventionalized (ConvD)) and normalized the growth rate of injured incisors and colony-forming and osteo-/odontogenic differentiation ability of DPSCs. Giving short-chain fatty acids (SCFAs) by oral gavage after antibiotic treatment also rescued the growth rate of incisors and the differentiation ability of DPSCs and enhanced proliferation ability of DPSCs. Collectively, gut microbiota could make contribution to maintain continuous growth of injured rodent incisor and differentiation capacity of DPSCs; SCFAs might play a crucial role in this process.

Effect of Limosilactobacillus reuteri LRE02-Lacticaseibacillus rhamnosus LR04 Combination on Antibiotic-Associated Diarrhea in a Pediatric Population: A National Survey

Probiotics are living microorganisms, which, upon oral ingestion, may prevent antibiotic-associated diarrhea (AAD) through the normalization of an unbalanced gastrointestinal flora. The objective of this study was to evaluate the benefits of a probiotic combination (Limosilactibacillus reuteri LRE02-DSM 23878 and Lacticaseibacillus rhamnosus LR04-DSM 16605) on the prevention of AAD in an outpatient pediatric setting. Questionnaires were delivered to pediatricians by each patient/parent during the visits after antibiotics and probiotics treatment to monitor physiological parameters. The primary outcome of both groups (probiotics and no probiotics treated) was the evaluation of the prevalence of AAD between the two groups. Evaluation of stool consistency using the Bristol Stool Scale (BSS) score was performed, as well as the evaluation of AAD duration, frequencies of daily evacuation, and the beginning of diarrhea and weight loss during AAD in both groups and related to antibiotic categories. Results indicated that probiotics, at the recommended dosage of 1.2 × 10⁹ CFU (Colony Forming Unit) per day for 30 days, are associated with lower rates of AAD and a decreased number of days with diarrhea, independent of the type of antibiotic used. Moreover, the use of probiotics resulted in a normal stool consistency in a shorter time period, as evaluated by the BSS.

Prevention of enteric bacterial infections and modulation of gut microbiota with conjugated linoleic acids producing Lactobacillus in mice

Probiotics are recognized for outcompeting pathogenic bacteria by competitive receptor-mediated colonization and secretion of functional metabolites which are antimicrobial against certain microbes as well as improving host's gut health and immunity. Recently, we have constructed a bioactive Lactobacillus casei (LC) strain, LC^+mcra , by inserting mcra (myosin cross-reactive antigen) gene, which stimulates the conversion of conjugated linoleic acids. In this study, we evaluated the modulation of gut microbiome and protective roles of LC^+mcra against pathogenic Salmonella enterica serovar Typhimurium (ST) and enterohemorrhagic E. coli (EHEC) infections in BALB/cJ mice. We observed that LC^+mcra colonized efficiently in mice gut intestine and competitively reduced the infection with ST and EHEC in various locations of small and large intestine, specifically cecum, jejunum, and ileum (p < 0.05). Positive modulation of the cecal microbiota, for example, higher relative abundances of Firmicutes, lower relative abundances of Proteobacteria, and increased bacterial species diversity/richness, was detected in ST-challenged mice pretreated with LC^+mcra based on 16S metagenomic sequencing. Cytokine gene expression analysis indicated that mice pretreated with LC^+mcra associated with attenuated bacterial pathogen-induced gut inflammation. Furthermore, mice fed daily with LC^+mcra for one week could protect themselves from the impairments caused by enteric infections with ST or EHEC. These impairments include weight loss, negative hematological changes, intestinal histological alterations, and potential death. This in vivo study suggests that daily consumption of novel conjugated linoleic acids over-producing probiotic effectively improves intestinal microbiota composition and prevents/combats foodborne enteric bacterial infections with pathogenic Salmonella and diarrheagenic E. coli.

Changes in Gut Microbiota and Hormones After Bariatric Surgery: a Bench-to-Bedside Review

Overweight and obesity are among the most prevalent non-communicable diseases which are generally treated successfully by bariatric or sleeve surgery. There are evidences affirming that sleeve surgery can manipulate the pH of the stomach and interact with the metabolism of fatty acids, carbohydrates, and bile acid transfer, leading to the overgrowth of gut microbiota. Therefore, this study aims to review the changes in gut microbiota and hormones after bariatric surgery.

Exposure to chemicals formed from natural processes is ubiquitous

Exposure to chemicals produced by natural processes is ubiquitous. First, in addition to the products of normal metabolism produced in humans of normal body weight, adipose tissue produces a large number of chemicals, including estrogen, testosterone from the produced estrogen, thyroid-stimulating hormone, leptin and approximately 500 other molecules termed adipokines, and a large number of inflammatory mediators. Second, the gut biome contains approximately the same number of bacteria as cells found in the entire body and produces a large number of small molecules. Third, the overwhelming majority (99.9%) of pesticide exposure occurs during ingestion of natural plant pesticides from eating vegetables. Fourth, consumption of cooked muscles meats leads to significant exposure to mutagenic and carcinogenic heterocyclic amines, polycyclic aromatic amines, and nitropyrenes. Fifth, many common beverages, for example, beer, coffee, and tea contain organic chemicals that display mutagenic activity. As compared with man-made production levels, from 1945 to 2015, an estimated 5000-fold more organic compounds were produced by a variety of natural processes, including common wood-degrading and forest litter-degrading fungi, microorganisms in temperate and boreal forest soils, bacteria in marine sponges, marine macro-algae, volcanoes, and forest fires. Exposure to these naturally produced organic compounds occurs via inhalation of ambient air, ingestion of food and water, and contact with soil, freshwater, and seawater. Contact with several thousand different endogenous or exogenous chemicals per day is unavoidable. This understanding might assist in better allocating resources toward controlling exposures to agents of highest concern as determined by current concepts of chronic disease causation.

Effects of peanut meal extracts fermented by Bacillus natto on the growth performance, learning and memory skills and gut microbiota modulation in mice

Recent studies have demonstrated that the nutritional properties of peanut meal (PM) can be improved after being fermented. The assessment of fermented PM has been reported to be limited to various physical and chemical evaluations in vitro. In the present study, PM was fermented by Bacillus natto to explore the effects of fermented PM extract (FE) on growth performance, learning and memory ability and intestinal microflora in mice. Ninety newly weaned male Kunming (KM) mice were randomly divided into seven groups: normal group (n 20), low-dose FE group (n 10), middle-dose FE group (MFE) (n 10), high-dose FE group (HFE) (n 20), unfermented extraction group (n 10), model group (10) and natural recovery group (10). Learning and memory skills were performed by the Morris water maze (MWM) test, and the variation in gut microbiota (GM) composition was assessed by 16S rDNA amplicon sequencing. The results show that HFE remarkably improved the growth performance in mice. In the MWM test, escape latency was shortened in both MFE and HFE groups, while the percentage of time, distance in target quadrant and the number crossing over the platform were significantly increased in the HFE group. Moreover, the FE played a preventive role in the dysbacteriosis of mice induced by antibiotic and increased the richness and species evenness of GM in mice.

Evaluation of the effect of HIV virus on the digestive flora of infected versus non infected infants

Introduction

HIV infection is characterized by changes in the composition and functions of gut microbiota. We carried out a study aiming at comparing the compositional changes of the digestive flora of HIV infected infants versus that of non infected infants in Cameroon.

Methods

A case-control study was carried out during which stool sample was collected from each participant after obtaining the proxy consent. Stools were cultured using aerobic, strict anaerobic, 10% CO2 and micro-aerophilic conditions and specific culture media and bacteria were identified biochemically. Fisher's exact test was used for data analyses.

Results

From the 80 infants enrolled for the study, 33 (41.3%) were HIV positive. A statistically significant difference was observed between the number of infected versus non infected infants harboring the following bacteria: Clostridium spp. (P=0.009); Enterococcus spp. (p<0.001); Klebsiella (p<0.001); Shigella (<0.001); Staphylococcus aureus (p=0.006) and Streptococcus spp. (P=0.015). Among infected infants, WHO-stage 3 and 4 infants harbored more opportunistic bacteria than stage 1 and stage 2 and Bacteriodes spp. population was depleted as the disease progresses, although not significantly. There was an imbalance in bacteria flora in HIV infected infants harboring qualitatively more bacteria including more opportunistic and pathogenic bacteria than in HIV non-infected infants.

Conclusion

HIV infected infants presented a qualitatively different flora from HIV non infected infants. They habored more pathogenic bacteria Than non infected infants. Systematic stool culture could benefit for follow-up of HIV infected infants to reduce the risk of gastrointestinal disorders and thus the risk of high morbidity or high mortability.

Effect of chicken egg yolk immunoglobulins on serum biochemical profiles and intestinal bacterial populations in early-weaned piglets

This study was conducted to test the hypothesis that dietary supplementation with anti-E. coli, chicken egg yolk immunoglobulins (IgY), may affect early weaned piglet (EWP) intestinal functions and enteric micro-organisms. One hundred and forty-eight ([Landrace × Yorkshire] × Duroc) piglets, weaned at age day 21, were randomly assigned to receive one of three diets for 14 days. Treatment group one (control group) was fed the base diet. Treatment group two (antibiotics group) was fed the base diet which was supplemented with 100 ppm colistin sulphate and 15 ppm enramycin; treatment group three (IgY group) was fed the base diet which was supplemented with 500 mg/kg anti-E. coli IgY. The study evaluated the effects on EWPs of IgY on growth, serum biochemical, inflammatory profiles and also digestion content intestinal bacterial populations. Results showed no significant difference in diarrhoea rates between IgY-fed EWPs and antibiotic-treated EWPs. Serum biochemical analysis showed that EWPs fed an IgY-containing diet had both lower (p < 0.05) cholesterol and low-density lipoprotein compared to antibiotic-treated EWPs. Escherichia coli populations measured in IgY-fed EWP ileal contents, compared to the control group, were significantly reduced (p < 0.05). Enterococcus, Lactobacillus, Clostridium and Bifidobacterium populations were unaffected by the IgY treatment. Larger (p < 0.05) Enterococcus populations and lower (p < 0.05) expression levels of heat-stable enterotoxin b (STb) were observed in IgY-fed EWP caecal digesta compared to the control group. Enteric Lactobacillus significantly decreased (p < 0.05) in EWPs fed antibiotics while it was unaffected by IgY treatment. Dietary supplementation with anti-E. coli IgY has the potential to suppress enteric E. coli growth, but not Lactobacillus, Clostridium and Bifidobacterium. This promotes and maintains a healthy EWP intestinal environment. These findings suggest that IgY may be used as an alternative to antibiotics in EWP diets.

Bacterial Metabolism and Antibiotic Efficacy

Antibiotics target energy-consuming processes. As such, perturbations to bacterial metabolic homeostasis are significant consequences of treatment. Here, we describe three postulates that collectively define antibiotic efficacy in the context of bacterial metabolism: (1) antibiotics alter the metabolic state of bacteria, which contributes to the resulting death or stasis; (2) the metabolic state of bacteria influences their susceptibility to antibiotics; and (3) antibiotic efficacy can be enhanced by altering the metabolic state of bacteria. Altogether, we aim to emphasize the close relationship between bacterial metabolism and antibiotic efficacy as well as propose areas of exploration to develop novel antibiotics that optimally exploit bacterial metabolic networks.

Surveys of parents and clinicians concerning the minimally important difference of probiotic therapy for prevention of paediatric antibiotic-associated diarrhoea

OBJECTIVES

To establish the minimally important difference (MID) that would prompt parents and clinicians to use probiotics for prevention of paediatric antibiotic-associated diarrhoea (AAD) and to obtain parent and clinician opinion about the most important outcomes in clinical trials of AAD.

METHODS

In this survey, parents of children presenting to the emergency department of a Canadian tertiary care children's hospital and paediatricians working in that hospital were approached. A range of potential MIDs were presented and participants selected one that they would require to use probiotics for AAD prevention. In addition, participants were asked to rate a list of outcomes they would consider to be important in clinical trials of AAD.

RESULTS

In total, 127 parents and 45 paediatricians participated. About 51% (64/125) of parents and 51% (21/41) of clinicians responding to the MID question reported they would use probiotics if it reduced the risk of AAD by 39% (ie, reduce the risk of AAD from 19% to 12%). The most important outcomes to parents, in descending order, were need for hospitalisation, prevention of dehydration, disruption of normal daily activities, diarrhoea duration and physician revisit. Paediatricians considered need for hospitalisation along with physician revisit as the most important outcomes. They rated prevention of dehydration, diarrhoea duration and stool frequency as important outcomes as well.

CONCLUSION

There is good agreement between parents and clinicians regarding how effective probiotics would need to be in preventing AAD in order to warrant use. This information, along with outcomes perceived to be most important, will help in the design of future clinical trials.

Phytochemicals and inflammatory bowel disease: a review

Gastrointestinal tract is the second largest organ in the body that mainly functions in nutrients and minerals intake through the intestinal barrier. Intestinal permeability maintains the circulation of minerals and nutrients from digested foods. Life and all the metabolic processes depend either directly or indirectly on proper functioning of GI tract. Compromised intestinal permeability and related disorders are common among all the patients with inflammatory bowel disease (IBD), which is a collective term of inflammatory diseases including Crohn's disease and ulcerative colitis. Many synthetic drugs are currently in use to treat IBD such as 5-aminosalicylic acid corticosteroids. However, they all have some drawbacks as long-term use result in many complications. These problems encourage us to look out for alternative medicine. Numerous in vitro and in vivo experiments showed that the plant-derived secondary metabolites including phenolic compounds, glucosinolates, alkaloids, terpenoids, oligosaccharides, and quinones could reduce permeability, ameliorate-related dysfunctions with promising results. In addition, many of them could modulate enzymatic activity, suppress the inflammatory transcriptional factors, ease oxidative stress, and reduce pro-inflammatory cytokines secretion. In this review, we summarized the phytochemicals, which were proven potent in treating increased intestinal permeability and related complication along with their mechanism of action.

Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach

The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.

Bacteriophages Synergize with the Gut Microbial Community To Combat Salmonella

Antibiotic-resistant bacteria are a global threat. Therefore, alternative approaches for combatting bacteria, especially antibiotic-resistant bacteria, are urgently needed. Using a human gut microbiota model, we demonstrate that bacteriophages (phages) are able to substantially decrease pathogenic Salmonella without perturbing the microbiota. Conversely, antibiotic treatment leads to the eradication of close to all commensal bacteria, leaving only antibiotic-resistant bacteria. An unbalanced microbiota has been linked to many diseases both in the gastrointestinal tract or “nonintestinal” diseases. In our study, we show that the microbiota provides a protective effect against Salmonella. Since phage treatment preserves the healthy gut microbiota, it is a feasible superior alternative to antibiotic treatment. Furthermore, when combating infections caused by pathogenic bacteria, gut microbiota should be considered.

Salmonella infection is one of the main causes of food-borne diarrheal diseases worldwide. Although most Salmonella infections can be cleared without treatment, some cause serious illnesses that require antibiotic treatment. In view of the growing emergence of antibiotic-resistant Salmonella strains, novel treatments are increasingly required. Furthermore, there is a striking paucity of data on how a balanced human gut microbiota responds to Salmonella infection. This study aimed to evaluate whether a balanced gut microbiota protects against Salmonella growth and to compare two antimicrobial approaches for managing Salmonella infection: bacteriophage (phage) treatment and antibiotic treatment. Anaerobically cultivated human intestinal microflora (ACHIM) is a feasible model for the human gut microbiota and naturally inhibits Salmonella infection. By mimicking Salmonella infection in vitro using ACHIM, we observed a large reduction of Salmonella growth by the ACHIM itself. Treatments with phage and antibiotic further inhibited Salmonella growth. However, phage treatment had less impact on the nontargeted bacteria in ACHIM than the antibiotic treatment did. Phage treatment has high specificity when combating Salmonella infection and offers a noninvasive alternative to antibiotic treatment.

IMPORTANCE Antibiotic-resistant bacteria are a global threat. Therefore, alternative approaches for combatting bacteria, especially antibiotic-resistant bacteria, are urgently needed. Using a human gut microbiota model, we demonstrate that bacteriophages (phages) are able to substantially decrease pathogenic Salmonella without perturbing the microbiota. Conversely, antibiotic treatment leads to the eradication of close to all commensal bacteria, leaving only antibiotic-resistant bacteria. An unbalanced microbiota has been linked to many diseases both in the gastrointestinal tract or “nonintestinal” diseases. In our study, we show that the microbiota provides a protective effect against Salmonella. Since phage treatment preserves the healthy gut microbiota, it is a feasible superior alternative to antibiotic treatment. Furthermore, when combating infections caused by pathogenic bacteria, gut microbiota should be considered.

Author Video: An author video summary of this article is available.

Clostridium difficile, the Difficult "Kloster" Fuelled by Antibiotics

Clostridium difficile is normally present in low numbers in a healthy adult gastro-intestinal tract (GIT). Drastic changes in the microbial population, e.g., dysbiosis caused by extensive treatment with antibiotics, stimulates the growth of resistant strains and the onset of C. difficile infection (CDI). Symptoms of infection varies from mild diarrhea to colitis (associated with dehydration and bleeding), pseudomembranous colitis with yellow ulcerations in the mucosa of the colon, to fulminant colitis (perforation of the gut membrane), and multiple organ failure. Inflamed epithelial cells and damaged mucosal tissue predisposes the colon to other opportunistic pathogens such as Clostridium perfringens, Staphylococcus aureus, Klebsiella oxytoca, Candida spp., and Salmonella spp. This may lead to small intestinal bacterial overgrowth (SIBO), sepsis, toxic megacolon, and even colorectal cancer. Many stains of C. difficile are resistant to metronidazole and vancomycin. Vaccination may be an answer to CDI, but requires more research. Success in treatment with probiotics depends on the strains used. Oral or rectal fecal transplants are partly effective, as spores in the small intestine may germinate and colonize the colon. The effect of antibiotics on C. difficile and commensal gut microbiota is summarized and changes in gut physiology are discussed. The need to search for non-antibiotic methods in the treatment of CDI and C. difficile-associated disease (CDAD) is emphasized.

Effects of medicines used to treat gastrointestinal diseases on the pharmacokinetics of coadministered drugs: a PEARRL Review

Objectives

Drugs used to treat gastrointestinal diseases (GI drugs) are widely used either as prescription or over-the-counter (OTC) medications and belong to both the 10 most prescribed and 10 most sold OTC medications worldwide. The objective of this review article is to discuss the most frequent interactions between GI and other drugs, including identification of the mechanisms behind these interactions, where possible.

Key findings

Current clinical practice shows that in many cases, these drugs are administered concomitantly with other drug products. Due to their metabolic properties and mechanisms of action, the drugs used to treat gastrointestinal diseases can change the pharmacokinetics of some coadministered drugs. In certain cases, these interactions can lead to failure of treatment or to the occurrence of serious adverse events. The mechanism of interaction depends highly on drug properties and differs among therapeutic categories. Understanding these interactions is essential to providing recommendations for optimal drug therapy.

Summary

Interactions with GI drugs are numerous and can be highly significant clinically in some cases. While alterations in bioavailability due to changes in solubility, dissolution rate, GI transit and metabolic interactions can be (for the most part) easily identified, interactions that are mediated through other mechanisms, such as permeability or microbiota, are less well-understood. Future work should focus on characterising these aspects.

Helicobacter pylori and gut microbiota in multiple sclerosis versus Alzheimer's disease: 10 pitfalls of microbiome studies

Alteration of microbiota has been associated with intestinal, inflammatory, and neurological diseases. Abundance of "good bacteria" such as Bifidobacterium, or their products have been generally believed to be beneficial for any diseases, while "bad bacteria" such as pathogenic Helicobacter pylori are assumed to be always detrimental for hosts. However, this is not the case when we compare and contrast the association of the gut microbiota with two neurological diseases, multiple sclerosis (MS) and Alzheimer's disease (AD). Following H. pylori infection, pro-inflammatory T helper (Th)1 and Th17 immune response are initially induced to eradicate bacteria. However, H. pylori evades the host immune response by inducing Th2 cells and regulatory T cells (Tregs) that produce anti-inflammatory interleukin (IL)-10. Suppression of anti-bacterial Th1/Th17 cells by Tregs may enhance gastric H. pylori propagation, followed by a cascade reaction involving vitamin B₁₂ and folic acid malabsorption, plasma homocysteine elevation, and reactive oxygen species induction. This can damage the blood-brain barrier (BBB), leading to accumulation of amyloid-β in the brain, a hallmark of AD. On the other hand, this suppression of pro-inflammatory Th1/Th17 responses to H. pylori has protective effects on the hosts, since it prevents uncontrolled gastritis as well as suppresses the induction of encephalitogenic Th1/Th17 cells, which can mediate neuroinflammation in MS. The above scenario may explain why chronic H. pylori infection is positively associated with AD, while it is negatively associated with MS. Lastly, we list "10 pitfalls of microbiota studies", which will be useful for evaluating and designing clinical and experimental microbiota studies.

Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome

Analysis of the human microbiome continues to reveal new and previously unrealized associations between microbial dysbiosis and disease. Novel approaches to bacterial identification using culture-independent methods allow practitioners to discern the presence of alterations in the taxa and diversity of the microbiome and identify correlations with disease processes. While some of these diseases that have been extensively studied are well-defined in their etiology and treatment methods (colorectal cancer), others have provided much more significant challenges in both diagnosis and treatment. One such condition, chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), has several etiological and potentiating contributions from infection, inflammation, central nervous system (CNS) changes, stress, and central sensitization-all factors that play important roles in the crosstalk between the human body and its microbiome. No singular cause of CP/CPPS has been identified and it is most likely a syndrome with multifactorial causes. This heterogeneity and ambiguity are sources of significant frustration for patients and providers alike. Despite multiple attempts, treatment of chronic prostatitis with monotherapy has seen limited success, which is thought to be due to its heterogeneous nature. Phenotypic approaches to both classify the disease and direct treatment for CP/CPPS have proven beneficial in these patients, but questions still remain regarding etiology. Newer microbiome research has found correlations between symptom scores and disease severity and the degree of dysbiosis in urine and gut (stool) microbiomes in these patients as compared to un-afflicted controls. These findings present potential new diagnostic and therapeutic targets in CP/CPPS patients.

Antibiotic prescription and food allergy in young children

Background

To assess the relationship between any systemic antibiotic prescription within the first year of life and the presence of an ICD-9-CM diagnosis code for food allergy (FA).

Methods

This was a matched case–control study conducted using South Carolina Medicaid administrative data. FA cases born between 2007 and 2009 were matched to controls without FA on birth month/year, sex, race/ethnicity. Conditional logistic regression was used to model the adjusted odds ratio (aOR) of FA diagnosis. All models were adjusted for presence of asthma, wheeze, or atopic dermatitis.

Results

A total of 1504 cases and 5995 controls were identified. Receipt of an antibiotic prescription within the initial 12 months of life was associated with FA diagnosis in unadjusted and adjusted models (aOR 1.21; 95 % CI 1.06–1.39). Compared to children with no antibiotic prescriptions, a linear increase in the aOR was seen with increasing antibiotic prescriptions. Children receiving five or more (aOR 1.64; 95 % CI 1.31–2.05) antibiotic prescriptions were significantly associated with FA diagnosis. The strongest association was noted among recipients of cephalosporin and sulfonamide antibiotics in both unadjusted and adjusted models.

Conclusions

Receipt of antibiotic prescription in the first year of life is associated with FA diagnosis code in young children after controlling for common covariates. Multiple antibiotic prescriptions are more strongly associated with increases in the odds of FA diagnosis.