Clinical effects of antimicrobials and probiotics in combination have been reported, however, little is known about their impact on gut microbiota and its resistome. In this study 16S rRNA gene amplicon, shotgun metagenomics sequencing and antibiotic resistance (ABR) microarray were used on fecal samples of 70 healthy participants, taken at four time points in probiotic (Lactobacillus rhamnosus R0011 and Lactobacillus helveticus R0052) and placebo groups to profile the gut bacterial microbiota and its resistome following administration of amoxicillin-clavulanic acid for one week. Significant shifts in microbiota family composition caused by the antimicrobial in both groups that included decreases in the proportion of Lachnospiraceae, Coriobacteriaceae and unidentified Clostridiales; and notable increases for the proportion of Enterobacteriaceae, Bacteroidaceae and Porphyromonadaceae compared to baseline levels. Resistome showed a corresponding enrichment of ABR genes compared to baseline from such classes as aminoglycosides and beta-lactams that were linked, by in silico inference, to the enrichment of the family Enterobacteriaceae. Despite perturbations caused by short-term antibiotic treatment, both gut microbiota and resistome showed prompt recovery to baseline levels one week after cessation of the antimicrobial. This rapid recovery may be explained by the hypothesis of community resilience.

A commercially available product containing three probiotic bacterial strains (Lactobacillus helveticus R0052, Bifidobacterium longum subsp. infantis R0033, and Bifidobacterium bifidum R0071) was previously shown in animal trials to modulate both T H 1 and T H 2 immune responses. Clinical studies on this combination of bacteria have also shown positive health effects against seasonal winter diseases and rotavirus infection. The goal of this study was to use a well-established in vitro intestinal epithelial (HT-29) cell model that has been shown to constitutively express double-stranded RNA (dsRNA) sensors (Toll-like receptor 3 [TLR3], retinoic acid-inducible gene I, melanoma differentiation-associated gene 5, and dsRNA-activated protein kinase). By using the HT-29 cell model, we wanted to evaluate whether or not this combination of three bacteria had the capacity to immune modulate the host cell response to a dsRNA ligand, poly(I·C). Using a custom-designed, two-color expression microarray targeting genes of the human immune system, we investigated the response of HT-29 cells challenged with poly(I·C) both in the presence and in the absence of the three probiotic bacteria. We observed that the combination of the three bacteria had a major impact on attenuating the expression of genes connected to proinflammatory T H 1 and antiviral innate immune responses compared to that obtained by the poly(I·C)-only challenge. Major pathways through which the multistrain combination may be eliciting its immune-modulatory effect include the TLR3 domain-containing adapter-inducing beta interferon (TRIF), mitogenactivated protein kinase, and NF-B signaling pathways. Such a model may be useful for selecting potential biomarkers for the design of future clinical trials.

While regulatory programs are extensively studied at the level of transcription, elements that are involved in regulation of post-transcriptional processes are largely unknown, and methods for systematic identification of these elements are in early stages. Here, using a novel computational framework, we have integrated sequence information with several functional genomics data sets to characterize conserved regulatory programs of trypanosomatids, a group of eukaryotes that almost entirely rely on post-transcriptional processes for regulation of mRNA abundance. This analysis revealed a complex network of linear and structural RNA elements that potentially govern mRNA abundance across different life stages and environmental conditions. Furthermore, we show that the conserved regulatory network that we have identified is responsive to chemical perturbation of several biological functions in trypanosomatids. We have further characterized one of the most abundant regulatory RNA elements that we discovered, an AU-rich element (ARE) that can be found in 3′ untranslated region of many trypanosomatid genes. Using bioinformatics approaches as well as in vitro and in vivo experiments, we have identified three ELAV-like homologs, including the developmentally critical protein TbRBP6, which regulate abundance of a large number of trypanosomatid ARE-containing transcripts. Together, these studies lay out a roadmap for characterization of mechanisms that modulate development and metabolic pathways in trypanosomatids.

Genome-wide transcriptional analysis in intestinal epithelial cells (IEC) can aid in elucidating the impact of single versus multi-strain probiotic combinations on immunological and cellular mechanisms of action. In this study we used human expression microarray chips in an in vitro intestinal epithelial cell model to investigate the impact of three probiotic bacteria, Lactobacillus helveticus R0052 (Lh-R0052), Bifidobacterium longum subsp. infantis R0033 (Bl-R0033) and Bifidobacterium bifidum R0071 (Bb-R0071) individually and in combination, and of a surface-layer protein (SLP) purified from Lh-R0052, on HT-29 cells’ transcriptional profile to poly(I:C)-induced inflammation. Hierarchical heat map clustering, Set Distiller and String analyses revealed that the effects of Lh-R0052 and Bb-R0071 diverged from those of Bl-R0033 and Lh-R0052-SLP. It was evident from the global analyses with respect to the immune, cellular and homeostasis related pathways that the co-challenge with probiotic combination (PC) vastly differed in its effect from the single strains and Lh-R0052-SLP treatments. The multi-strain PC resulted in a greater reduction of modulated genes, found through functional connections between immune and cellular pathways. Cytokine and chemokine analyses based on specific outcomes from the TNF-α and NF-κB signaling pathways revealed single, multi-strain and Lh-R0052-SLP specific attenuation of the majority of proteins measured (TNF-α, IL-8, CXCL1, CXCL2 and CXCL10), indicating potentially different mechanisms. These findings indicate a synergistic effect of the bacterial combinations relative to the single strain and Lh-R0052-SLP treatments in resolving toll-like receptor 3 (TLR3)-induced inflammation in IEC and maintaining cellular homeostasis, reinforcing the rationale for using multi-strain formulations as a probiotic.

This information is current as Proinflammatory Responses Induced − α Secretome and TNF-Serovar Typhimurium Salmonella enterica R0011 in the Attenuation of rhamnosus Lactobacillus Secretome Components from

Probiotic supplementation plays a key role in maintaining intestinal homeostasis due to its ability to modulate gut microbiota. Although their potential as potent antioxidants have previously been explored, their ability to affect the redox status in the gut lumen of healthy subjects or those with gastrointestinal (GI) disorders remains unclear. In our study, we assessed the ability of single strain and multispecies probiotic supplementation to cause a change in the redox status of normal fecal water and in Clostridium (C.) difficile-infected fecal water using a simulated gastrointestinal model. Changes in redox status were assessed by ferric-reducing antioxidant power (FRAP), 2’,2’-diphenyl-1-picrylhydrazyl (DPPH), and iron and copper chelation assays. The findings from our study showed that in normal fecal water, probiotic supplements, apart from Lactobacillus (L.) rhamnosus R0011, showed a significant increase in iron chelation (p < 0.05), which was associated with lower FRAP and copper chelation. In C. difficile-infected fecal water, all probiotic supplements showed a significant increase in FRAP (p < 0.05) and were associated with increased copper chelation. The DPPH assay showed no treatment effect in either fecal water. These findings suggest that C. difficile mediates dysregulation of redox status, which is counteracted by probiotics through ferric-reducing ability and copper chelation.

Clostridium (C.) difficile-infection (CDI), a nosocomial gastrointestinal disorder, is of growing concern due to its rapid rise in recent years. Antibiotic therapy of CDI is associated with disrupted metabolic function and altered gut microbiota. The use of probiotics as an adjunct is being studied extensively due to their potential to modulate metabolic functions and the gut microbiota. In the present study, we assessed the ability of several single strain probiotics and a probiotic mixture to change the metabolic functions of normal and C. difficile-infected fecal samples. The production of short-chain fatty acids (SCFAs), hydrogen sulfide (H 2 S), and ammonia was measured, and changes in microbial composition were assessed by 16S rRNA gene amplicon sequencing. The C. difficile-infection in fecal samples resulted in a significant decrease (p < 0.05) in SCFA and H 2 S production, with a lower microbial alpha diversity. All probiotic treatments were associated with significantly increased (p < 0.05) levels of SCFAs and restored H 2 S levels. Probiotics showed no effect on microbial composition of either normal or C. difficile-infected fecal samples. These findings indicate that probiotics may be useful to improve the metabolic dysregulation associated with C. difficile infection.Probiotics, defined as live microorganisms that impart beneficial effects on the host when given in adequate quantities [11], have shown beneficial effects in the GI tract such as improving metabolic function [12][13][14][15], counteracting infections [16][17][18], regulating immune function, decreasing GI disorder symptoms [16,[19][20][21], and potentially lowering the risk of developing colon cancer [22]. Most of the probiotics utilized to date are usually from the Lactobacilli, Bifidobacteria, and yeast (Saccharomyces) groups. The efficacy and proposed mechanisms of action of these microbes in regulating intestinal microbiota functions are generally strain-specific. Some probiotic strains are thought to produce antimicrobial metabolites such as bacteriocins, to lower the pH by generating hydrogen peroxide and SCFAs, or to restrict pathogenic growth by competing for essential nutrients and adherence onto the gut mucosal barrier [18,[23][24][25][26][27]. Several probiotics may reduce CDI-associated diarrhea and prevent primary CDI formation using some of the abovementioned mechanisms, but perhaps predominantly by inhibiting the adhesion of C. difficile in the intestine [28,29]. In the case of Saccharomyces (S.) boulardii, the mechanism was shown to involve the proteolytic hydrolysis of the CD enterotoxins A and B [30]. Although the Lactobacillus (L.) rhamnosus GG strain and S. boulardii have been studied the most in the context of CDI-associated diarrhea [9,31], several other strains such as Bifidobacterium (B.) longum and L. acidophilus CL1285 have also shown efficacy against antibiotic-associated diarrhea [32][33][34][35]. Furthermore, strains such as L. plantarum 299v have been shown to enhance microbial function in CDI patients recei...

BackgroundConstipation is a frequent problem in adults with Prader–Willi syndrome. Certain probiotics have been shown to improve transit and gastrointestinal symptoms of adults with functional constipation. The aim of this study is to determine the effect of daily consumption of Bifidobacterium animalis ssp. lactis B94 (B. lactis B94) on stool frequency, stool form, and gastrointestinal symptoms in adults with Prader–Willi syndrome.MethodsAdults with Prader–Willi syndrome (18–75 years old, n = 36) will be recruited and enrolled in a 20-week, randomized, double-blind, placebo-controlled, crossover study. Study subjects will be randomized to B. lactis B94 or placebo each for a 4-week period, preceded by a 4-week baseline and followed by 4-week washouts. Subjects will complete daily records of stool frequency and stool form (a proxy of transit time). Dietary intake data also will be collected. Stools, one in each period, will be collected for exploratory microbiota analyses.DiscussionTo our knowledge, this is the first randomized controlled trial evaluating the effectiveness of B. lactis in adults with Prader–Willi syndrome. The results of this study will provide evidence of efficacy for future clinical trials in patient populations with constipation.Trial registrationClinicalTrials.gov (NCT03277157). Registered on 08 September 2017.Electronic supplementary materialThe online version of this article (10.1186/s13063-018-2648-x) contains supplementary material, which is available to authorized users.