Effects of antibiotic therapy on the gastrointestinal microbiota and the influence ofLactobacillus casei

Alteration of Gut Microbiota in Alzheimer's Disease and Their Relation to the Cognitive Impairment

BACKGROUND

Dysbiosis of gut microbiota has been reported to be enrolled in the pathogenesis of Alzheimer's disease (AD). However, there is a lack of relevant studies on this topic in Egyptian patients with AD.

OBJECTIVE

To investigate different species of gut microbiota in Egyptian patients with AD and correlate microbiota bacterial abundance with clinical data.

METHODS

The study included 25 patients with AD and 25 healthy volunteers as age and sex-matched controls. Clinical data was taken for each patient, including medical history and examination; Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) were assessed for each participant. Bacterial DNA was extracted from stool, and abundance quantified via qPCR using 16S rRNA group-specific primers.

RESULTS

Akkermansia, Enterobacteria, Bacteroidetes, Bacillus cereus, Prevotella, and Clostridium cluster IV were more abundant in the AD group than in the control group, although there was significantly less abundance of Bifidobacterium spp., Firmicutes, and Actinobacteria in patients with AD than in controls, whereas no such significance was found for lactic acid bacteria between both groups. Lactic acid bacteria and Prevotella abundance was negatively correlated with cognitive impairment (p = 0.03 with MMSE, and p = 0.03 with MoCA). Prevotella abundance was positively correlated with age of onset and duration of illness and negatively correlated with smoking and coronary heart disease (p = 0.007, p = 0.03, p = 0.035, and p = 0.047, respectively).

CONCLUSION

The current work highlighted a significant relationship between AD and gut microbiota dysbiosis. A higher abundance of Prevotella species and lactic acid bacteria was correlated with cognition.

Changes in the Diversity and Composition of Gut Microbiota of Red-Crowned Cranes (Grus japonensis) after Avian Influenza Vaccine and Anthelmintic Treatment

Gut microbiota homeostasis is important for host health and well-being; however, drugs may affect the composition and function of the gut microbiota. Red-crowned cranes are a vulnerable species. Treatment of red-crowned cranes with avian influenza vaccines and anthelmintics has played pivotal roles in therapeutic management in zoos. To investigate the changes in the diversity and composition of gut microbiota after the avian influenza vaccine and anthelmintic treatment, we used 16S rRNA sequencing to obtain and compare the bacterial community composition before and after the treatment. The alpha diversity of the gut microbiota of red-crowned cranes decreased on the day of the treatment and then fluctuated over time. The composition of gut microbiota tended to be similar in the short term after the treatment, as supported by the beta diversity hierarchical cluster analysis. Only 3, 8, and 72 operational taxonomic units (OTUs) of the three individuals were shared among the five groups before and after treatment. The relative abundance of Firmicutes significantly increased to 99.04% ± 0.28% on the day of the treatment, in which the relative abundance of Lactobacillus was 93.33% ± 5.85%. KEGG pathways analysis indicated that the main function of the gut microbiota is involved in metabolism, and the present study indicates that the gut microbiota of red-crowned cranes is resilient to the avian influenza vaccine and anthelmintic, even disordered in the short term, and could recover over time. More individual experimentation and functional potential in metabolism are needed in the future to support animal disease control and optimal management in the zoo.

Changes in the gut microbiota diversity of brown frogs (Rana dybowskii) after an antibiotic bath

Background

Captive amphibians frequently receive antibiotic baths to control bacterial diseases. The potential collateral effect of these antibiotics on the microbiota of frogs is largely unknown. To date, studies have mainly relied on oral administration to examine the effects of antibiotics on the gut microbiota; in contrast, little is known regarding the effects of bath-applied antibiotics on the gut microbiota. The gut microbiota compositions of the gentamicin, recovery, and control groups were compared by Illumina high-throughput sequencing, and the functional profiles were analysed using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, the relationship between the structure and predicted functional composition of the gut microbiota was determined.

Results

The alpha diversity indices were significantly reduced by the gentamicin bath, illustrating that this treatment significantly changed the composition of the gut microbiota. After 7 days, the gut microbiota of the recovery group was not significantly different from that of the gentamicin group. Forty-four indicator taxa were selected at the genus level, comprising 42 indicators representing the control group and 2 indicators representing the gentamicin and recovery groups. Potential pathogenic bacteria of the genera Aeromonas, Citrobacter, and Chryseobacterium were significantly depleted after the gentamicin bath. There was no significant positive association between the community composition and functional composition of the gut microbiota in the gentamicin or control frogs, indicating that the functional redundancy of the gut bacterial community was high.

Conclusions

Gentamicin significantly changed the structure of the gut microbiota of R. dybowskii, and the gut microbiota exhibited weak resilience. However, the gentamicin bath did not change the functional composition of the gut microbiota of R. dybowskii, and there was no significant correlation between the structural composition and the functional composition of the gut microbiota.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-03044-z.

Probiotics for the prevention of antibiotic-associated diarrhoea: a systematic review and meta-analysis

OBJECTIVE

To evaluate existing evidence for the use of probiotics in preventing antibiotic-associated diarrhoea (AAD) in adults.

DESIGN

Systematic review and meta-analysis of randomised controlled trials (RCTs).

DATA SOURCES

We performed a literature search of the electronic databases CINAHL Plus, EMBASE, MEDLINE (Ovid) and Web of Science from database inception to May 2021 as well as hand searching of trial registries and reference lists of related reviews.

STUDY SELECTION

Two reviewers identified whether RCTs met the following inclusion criteria: adult population to whom antibiotics were administered; a probiotic intervention; a placebo, alternative dose, alternative probiotic strain or no treatment control; and incidence of AAD as the outcome.

DATA EXTRACTION AND SYNTHESIS

Two reviewers independently collected data and assessed risk of bias using preconstructed data extraction forms. We used a random effects model for all analyses. Subgroup analyses were performed to evaluate species-specific and dose-specific response.

RESULTS

Forty-two studies (11,305 participants) were included in this review. The pooled analysis suggests that co-administration of probiotics with antibiotics reduces the risk of AAD in adults by 37% (risk ratio (RR)=0.63 (95% CI 0.54 to 0.73), p<0.00001). The overall quality of the evidence using the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) criteria was found to be moderate. In subgroup analyses, high dose compared with low dose of the same probiotic demonstrated a positive protective effect (RR 0.54 (95% CI 0.38 to 0.76), p<0.01), and only certain species, mainly of the lactobacillus and bifidobacteria genera, were found to be effective. Studies with a low baseline AAD risk did not show any difference in risk but studies with moderate or high baseline AAD risk demonstrated a significant risk reduction.

CONCLUSIONS

Probiotics are effective for preventing AAD. Secondary analyses of higher dosages and certain species have shown increased effectiveness. Our results may not be applicable in clinical scenarios of lower baseline AAD risk.

Perils and pitfalls of probiotic quasi-experimental studies for primary prevention of Clostridioides difficile infection: A review of the evidence

BACKGROUND

Primary prevention of Clostridioides (Clostridium) difficile infections (CDI) is an important but challenging infection control goal for hospitals and health care facilities. Enhanced infection control protocols have reduced CDI rates, but the problem persists and administration of probiotics to patients at risk could be very useful if shown to be safe and effective. Randomized controlled trials are largely impractical for primary prevention CDI trials due to large required study sizes and quasi-experimental studies are becoming more frequent as a method to assess this problem.

OBJECTIVE

Our goal is to review the published quasi-experimental studies adding probiotics to their infection control protocols to reduce CDI and determine the strengths and limitations for this type of study design.

METHODS

The literature was searched using PubMed, Google Scholar, Medline and Cochrane Databases and gastrointestinal meeting abstracts from January 2000 to January 2020 for quasi-experimental intervention studies testing various probiotics for the primary prevention of CDI.

RESULTS

We found 28 studies with 7 different types of probiotics (10 studies implementing a hospital-wide intervention, 6 studies targeting 1-3 wards, and 12 studies on either sustainability, cost-effectiveness or subgroup analysis). Some probiotics demonstrated a significant reduction in CDI rates; all four of the probiotic types given only on specific wards and 3 of the 4 probiotics given facility-wide. However, this type of study design was influenced by numerous factors which must be carefully accounted for in the analysis.

CONCLUSIONS

Some probiotics may be an effective addition to infection control protocols to prevent C. difficile infections, but careful study design considerations are needed.

Marine polysaccharides from Gelidium pacificum Okamura and Cereus sinensis reveal prebiotic functions

Many marine polysaccharides as prebiotics can promote host health by modulating gut microbiota. This study investigated the beneficial effects of purified marine plant-derived Gelidium pacificum Okamura polysaccharide (GPOP-1) and marine animal-derived Cereus sinensis polysaccharide (CSP-1) on normal mice by modulating gut microbiota. The composition and diversity of gut microbiota were evaluated using 16S rRNA high-throughput sequencing. The results showed that GPOP-1 and CSP-1 altered the composition of the gut microbiota and promoted the growth of beneficial bacteria. At the genus level, GPOP-1 increased the relative abundance of Bacteroides, Phascolarctobacterium, and decreased the relative abundance of Ruminococcus, Helicobacter, Allobaculum, Dorea and AF12. While CSP-1 increased the relative abundance of Coprococcus, Adlercreutzia, Roseburia, Phascolarctobacterium, and decreased the relative abundance of Bacteroides, Ruminococcus and Oscillospira. The changes in the gut microbiota may affect the body weight, immune organ index and the production of short-chain fatty acids in normal mice. Compared to the normal control group, GPOP-1 decreased average weight gain while CSP-1 increased average weight gain. Furthermore, both GPOP-1 and CSP-1 significantly increased thymus and spleen indexes and total short chain fatty acids production in mice. In summary, GPOP-1 and CSP-1 exerted prebiotic effects on normal mice.

The role of probiotics on the roadmap to a healthy microbiota: a symposium report

The ninth International Yakult Symposium was held in Ghent, Belgium in April 2018. Keynote lectures were from Professor Wijmenga on using biobanks to understand the relationship between the gut microbiota and health; and Professor Hill on phage-probiotic interactions. Session one included talks from Professor Plӧsch on epigenetic programming by nutritional and environmental factors; Professor Wilmes on the use of "omics" methodologies in microbiome research and Professor Rescigno on the gut vascular barrier. Session two explored the evidence behind Lactobacillus casei Shirota with Dr Nanno explaining the plasticity in immunomodulation that enables the strain to balance immune functions; Dr Macnaughtan outlining its potential therapeutic use in cirrhosis and Professor Nishida detailing effects in subjects under stress. The third session saw Professor Marchesi describing that both the host genes and the gut microbiota can play a role in cancer; Professor Bergheim highlighting crosstalk between the gut and the liver and Professor Cani describing the relationship between the gut microbiota and the endocrine system. The final session explored probiotic mechanisms, with Professor Lebeer dissecting the challenges in conducting mechanistic studies; Professor Wehkamp describing the mucosal defence system and Professor Van de Wiele detailing methods for modelling the gut microbiota in vitro.

Bacillus strains as human probiotics: characterization, safety, microbiome, and probiotic carrier

Both spore and vegetative forms of Bacillus species have been used as probiotics, and they have high stability to the surrounding atmospheric conditions such as heat, gastric conditions, and moisture. The commercial Bacillus probiotic strains in use are B. cereus, B. clausii, B. coagulans, B. licheniformis, B. polyfermenticus, B. pumilus, and B. subtilis. These strains have antimicrobial, anticancer, antioxidant, and vitamin production properties. However, Bacillus probiotics can also produce toxins and biogenic amines and transfer antibiotic resistance genes; therefore, their safety is a concern. Studies on the microbiome using probiotic Bacillus strains are limited in humans. Most microbiome research has been conducted in chicken, mouse, and pig. Some Bacillus probiotics are used as fermentation starters in plant and soybean and dietary supplement of baking foods as a probiotic carrier. This review summarizes the characterization of Bacillus species as probiotics for human use and their safety, microbiome, and probiotic carrier.

Effects of a probiotic drink containing Lactobacillus casei strain Shirota on dental plaque microbiota

Objective

To investigate the effects of a probiotic drink containing Lactobacillus casei strain Shirota on dental plaque microbiota.

Methods

Caries-free young adults were administered a probiotic drink containing L. casei Shirota (Yakult) three times on day 1, then once daily for 28 days. Dental plaque samples were collected and analysed by 16S rRNA sequencing before (day 1), during (day 2), and one day following intervention (day 30).

Results

Out of samples from 10 included participants, 256 814 sequences passed through quality control, clustered into 170–234 different ‘species-level’ phylotypes. Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria were the most abundant phyla. Dental plaque microbiota composition significantly changed at different taxonomic levels following probiotic consumption. At genus level, the relative abundance of Veillonella and Kingella increased significantly following intervention, while that of Leptotrichia reduced significantly during intervention, but recovered to baseline level at day 30. Alpha diversity and overall structure of the dental plaque microbiota was not significantly impacted by the probiotic.

Conclusion

Yakult intake changed the abundance of some bacteria related to caries, suggesting that the change of composition may be beneficial to oral health, while the overall microbiota structure remained unaffected.

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets

Administrating antibiotics to young piglets may have short- and long-term consequences on the gut microbiota. We hypothesised that these consequences may be alleviated by concurrent probiotic administration. The study objective was to investigate the effect of administrating gentamicin and a mixture of Bacillus (B.) licheniformis, B. subtilis and B. amyloliquefaeceans spores on the gut microbiota of piglets pre- and post-weaning. Twenty-four sows and their litters were randomly allocated to four treatment groups receiving; a) Bacillus spore mixture (six B. subtilis, two B. amyloliquefaeceans, and one B. licheniformis) fed to sows and piglets (PRO); b) gentamicin (5 mg per day) administered to piglets on day 4, 5, and 6 of age (AB); c) Bacillus spore mixture fed to sows and piglets, and gentamicin to piglets (PRO+AB); or d) no administration of probiotics or antibiotics (CTRL). Faecal and digesta samples were collected repeatedly during the study. Selected samples were subjected to 16S rRNA gene sequencing, culture counts, and organic acid, biogenic amine and tissue gene expression analysis. Treatment had a significant effect on the faecal microbial community composition on day 28 and 42, and colonic community on day 28. Faecal species richness (observed and estimated) and Shannon index, and colonic species richness, were higher in AB compared to PRO piglets on day 28, and were not significantly different from day 42. PRO piglets had the highest faecal concentration of iso-butyric acid on day 7 and a higher butyric acid concentration compared to CTRL piglets. We conclude that gentamicin and Bacillus spores influence the gut microbial diversity of piglets, although administration of gentamicin did not result in dysbiosis as hypothesised.

Primary prevention of Clostridium difficile infections with a specific probiotic combining Lactobacillus acidophilus, L. casei, and L. rhamnosus strains: assessing the evidence

Clostridium difficile infection (CDI) has become the leading healthcare-associated infection and cause of outbreaks around the world. Although various innovative treatments have been developed, preventive strategies using multi-faceted infection control programmes have not been successful in reducing CDI rates. The major risk factor for CDI is the disruption of the normally protective gastrointestinal microbiota, typically by antibiotic use. Supplementation with specific probiotics has been effective in preventing various negative outcomes, including antibiotic-associated diarrhoea and CDI. However, a consensus of which probiotic strains might prevent CDI has not been reached and meta-analyses report high degrees of heterogeneity when studies of different probiotic products are pooled together. We searched the literature for probiotics with sufficient evidence to assess clinical efficacy for the prevention of CDI and focused on one specific probiotic formulation comprised of three lactobacilli strains (Lactobacillus acidophilus CL1285, Lactobacillus casei LBC80R, Lactobacillus rhamnosus CLR2, Bio-K+) for its ability to prevent CDI in healthcare settings. A literature search on this probiotic formulation was conducted using electronic databases (PubMed, Google Scholar), abstracts from infectious disease and infection control meetings, and communications from the probiotic company. Supporting evidence was found for its mechanisms of action against CDI and that it has an excellent safety and tolerability profile. Evidence from randomized controlled trials and facility-level interventions that administer Bio-K+ show reduced incidence rates of CDI. This probiotic formulation may have a role in primary prevention of healthcare-associated CDI when administered to patients who receive antibiotics.

Bacterial Diversity in Traditional Doogh in Comparison to Industrial Doogh

Forty-four samples of traditional Doogh and yoghurt were collected from 13 regions of 4 provinces in west of Iran (13 area) and analyzed using molecular methods including PCR, denaturing gradient gel electrophoresis (DGGE) of 16S rDNA, and sequencing. Moreover, collected samples as well as samples from industrially Doogh were analyzed with quantitative real-time PCR (RT-PCR). Analyzed 16S rRNA gene sequences of Doogh samples could be allocated to the presence of Lactobacillus spp. The typical yoghurt starter culture bacteria included four different Lactobacillus species with possible probiotic properties, L. acidophilus, L. helveticus, L. kefiranofaciens, and L. amylovorus. DGGE of traditional Doogh and yoghurt and RT-PCR of traditional Doogh and yoghurt and also industrial Doogh samples demonstrated that traditional Doogh and yoghurt show a higher abundance of total bacteria and lactobacilli and a higher bacterial diversity, respectively. Considering diversity and higher probiotic bacteria content in traditional Doogh, consumers’ healthiness in tribes and villages could be promoted with these indigenous products.

The association of type II diabetes with gut microbiota composition

It is known that type 2 diabetes (T2D) in humans could be linked to the composition of gut microbiota. The aim of this study was to evaluate three faecal bacterial species, including Bacteroides fragilis, Bifidobacterium longum and Faecalibacterium prausnitzii in patients with T2D. This case control study included 18 patients with T2D and 18 matched persons without diabetes. The concentrations of B. fragilis, B. longum and F. prausnitzii were determined by quantitative Real-Time PCR. Quantitative PCR analysis revealed that the gut bacterial composition in patients with T2D was partially different from that in the healthy individuals. Faecalibacterium prausnitzii was significantly lower in patients with T2D (P-value = 0.038). Bacteroides fragilis was under-represented in the microbiota of the group with diabetes, but its difference between two groups was not significant (P-value = 0.38). No difference was observed for B. longum community between the both groups (P-value = 0.99). Characterization of specific species of intestinal microbiota shows some compositional changes in patients with T2D. The results may be valuable for developing strategies to control type 2 diabetes by modifying the intestinal microbiota. Long-term studies with emphasis on other bacterial groups are suggested to clarify the association of T2D with gut microbiota.

Primary prevention of Clostridium difficile infections - how difficult can it be?

C. difficile infections (CDI) have been a challenging disease to treat, much less to prevent, for decades. Efforts for primary prevention have mainly focused on improving infection control practices, but CDI outbreaks continue to plague healthcare facilities. Areas covered: A literature search from 1970-December 2016 found 13 facility-level and 2 patient-level strategies that were evidence-based. The aim of this manuscript is to assess the current state of the literature on primary prevention of CDI and offer insights into which strategies may be more effective. Expert commentary: The strongest evidence for primary prevention is based on multi-faceted infection control bundles, while there is promising moderate evidence involving facility-wide use of specific probiotics. Moderate-level evidence was found for patient-level use of specific probiotics and low level evidence for vaccines. Future suggestions include use of consistent outcome metrics, measurements of implementation compliance and program sustainability.

Nutritional advice for community patients: insights from a panel discussion

This article describes the conclusions of an expert panel that discussed four case studies; these were examples of patients typically encountered by nurses working in the community. The panel considered the nutritional and lifestyle advice that could be given by nurses relating to conditions such as irritable bowel syndrome (IBS), depression, chronic fatigue syndrome, vulnerability to common infections, elderly care, recurrent urinary tract infection, antibiotic use, and risk of type 2 diabetes. A general conclusion was the importance of motivational interviewing techniques in achieving full understanding of patients' concerns and to determine the best health strategy. As well as specific guidance appropriate for each disorder, a range of information sources for both health professionals and patients are listed in the paper. The panel noted that, although general nutritional advice can be given by nurses working at GP surgeries and in the community, patients should always be referred to registered dietitians or nutritionists if significant dietary changes are considered.

Microbiota and epigenetic regulation of inflammatory mediators in type 2 diabetes and obesity

Metabolic syndrome is associated with alterations in the structure of the gut microbiota leading to low-grade inflammatory responses. An increased penetration of the impaired gut membrane by bacterial components is believed to induce this inflammation, possibly involving epigenetic alteration of inflammatory molecules such as Toll-like receptors (TLRs). We evaluated changes of the gut microbiota and epigenetic DNA methylation of TLR2 and TLR4 in three groups of subjects: type 2 diabetics under glucagon-like peptide-1 agonist therapy, obese individuals without established insulin resistance, and a lean control group. Clostridium cluster IV, Clostridium cluster XIVa, lactic acid bacteria, Faecalibacterium prausnitzii and Bacteroidetes abundances were analysed by PCR and 454 high-throughput sequencing. The epigenetic methylation in the regulatory region of TLR4 and TLR2 was analysed using bisulfite conversion and pyrosequencing. We observed a significantly higher ratio of Firmicutes/ Bacteroidetes in type 2 diabetics compared to lean controls and obese. Major differences were shown in lactic acid bacteria, with the highest abundance in type 2 diabetics, followed by obese and lean participants. In comparison, F. prausnitzii was least abundant in type 2 diabetics, and most abundant in lean controls. Methylation analysis of four CpGs in the first exon of TLR4 showed significantly lower methylation in obese individuals, but no significant difference between type 2 diabetics and lean controls. Methylation of seven CpGs in the promoter region of TLR2 was significantly lower in type 2 diabetics compared to obese subjects and lean controls. The methylation levels of both TLRs were significantly correlated with body mass index. Our data suggest that changes in gut microbiota and thus cell wall components are involved in the epigenetic regulation of inflammatory reactions. An improved diet targeted to induce gut microbial balance and in the following even epigenetic changes of pro-inflammatory genes may be effective in the prevention of metabolic syndrome.