Mucosally associated bacterial flora of the human colon: quantitative and species specific differences between normal and inflamed colonic biopsies

Drug Disposition in the Lower Gastrointestinal Tract: Targeting and Monitoring

The increasing prevalence of colonic diseases calls for a better understanding of the various colonic drug absorption barriers of colon-targeted formulations, and for reliable in vitro tools that accurately predict local drug disposition. In vivo relevant incubation conditions have been shown to better capture the composition of the limited colonic fluid and have resulted in relevant degradation and dissolution kinetics of drugs and formulations. Furthermore, drug hurdles such as efflux transporters and metabolising enzymes, and the presence of mucus and microbiome are slowly integrated into drug stability- and permeation assays. Traditionally, the well characterized Caco-2 cell line and the Ussing chamber technique are used to assess the absorption characteristics of small drug molecules. Recently, various stem cell-derived intestinal systems have emerged, closely mimicking epithelial physiology. Models that can assess microbiome-mediated drug metabolism or enable coculturing of gut microbiome with epithelial cells are also increasingly explored. Here we provide a comprehensive overview of the colonic physiology in relation to drug absorption, and review colon-targeting formulation strategies and in vitro tools to characterize colonic drug disposition.

The effect of storage at ambient temperature on the feline fecal microbiota

BACKGROUND

Feline fecal microbiota analyses can potentially be impacted by a variety of factors such as sample preparation, sequencing method and bioinformatics analyses. Another potential influence is changes in the microbiota from storage of samples prior to processing. This study examined the effect of ambient temperature exposure on the feline fecal microbiota composition. Fecal samples were collected from 12 healthy cats, within 15 min after defecation. Samples were aliquoted and the first aliquot was frozen at -80 °C within 1 hour of defecation. Remaining aliquots were maintained at ambient temperature (20 to 23 °C) and frozen at -80 °C at 6, 12, 24, 36, 48, 72 and 96 h after collection. DNA was extracted from all aliquots, and polymerase chain reaction (PCR). The PCR products were sequenced with next-generation sequencing (Illumina MiSeq).

RESULTS

No significant differences were observed in alpha and beta biodiversity indexes, as well as relative abundance of different taxa over time (P > 0.05 for all tests between time points). Principal coordinate analyses demonstrated that samples cluster mainly by cat, with no significant differences between time points (AMOVA, P > 0.05; HOMOVA, P > 0.05). Linear discriminant analysis effect size method was performed and failed to detect any enriched taxa, between time points. Random forest algorithm analysis indicated homogeneity across time points.

CONCLUSIONS

Although existing evidence from human fecal storage studies is contradictory, a recent study in companion animals agreed with the current study, demonstrating that maintenance of feline fecal samples at ambient temperature for up to 4 days has no effect on the bacterial membership and structure.

Lactobacillus-produced exopolysaccharides and their potential health benefits: a review

Lactic acid bacteria, such as those of the Lactobacillus genus, naturally reside within the microbiota of the human body and have long been used as starter cultures and probiotic enhancers in fermented foods, such as fermented drinks, yoghurts and cheeses. Many of the beneficial qualities of these bacteria have traditionally been associated with the bacteria themselves, however, a recent spate of studies have demonstrated a wide variety of biological effects exhibited by lactobacilli-produced exopolysaccharides which could, theoretically, confer a range of local and systemic health benefits upon the host. In this review, we discuss the production of exopolysaccharides within the Lactobacillus genus and explore their potential as beneficial bioactive compounds.

Intestinal microbial dysbiosis and colonic epithelial cell hyperproliferation by dietary α-mangostin is independent of mouse strain

Beverages and supplements prepared from mangosteen fruit are claimed to support gut health and immunity, despite the absence of supporting evidence from clinical trials. We recently reported that α-mangostin (α-MG), the most abundant xanthone in mangosteen fruit, altered the intestinal microbiome, promoted dysbiosis, and exacerbated colitis in C57BL/6J mice. The objective of this study was to determine whether induction of dysbiosis by dietary α-MG is limited to the C57BL/6J strain or represents a more generic response to chronic intake of the xanthone on the gut microbiota of mice. C3H, Balb/c, Nude FoxN1^nu, and C57BL/6J mice, each demonstrating unique microbiomes, were fed standard diet or diet containing 0.1% α-MG for four weeks. Dietary α-MG significantly altered the cecal and colonic microbiota in all four strains of mice, promoting a reduction in generally assumed beneficial bacterial groups while increasing the abundance of pathogenic bacteria. Consumption of α-MG was associated with reduced abundance of Firmicutes and increased abundance of Proteobacteria. The abundance of Lachnospiraceae, Ruminococcaceae, and Lactobacillaceae was reduced in α-MG-fed mice, while that of Enterobacteriaceae and Enterococcaceae was increased. Dietary α-MG also was associated with increased proliferation of colonic epithelial cells, infiltration of immune cells, infiltration of immune cells and increased fluid content in stool. These results suggest that ingestion of pharmacologic doses of xanthones in mangosteen-containing supplements may adversely alter the gut microbiota and should be used with caution.

Dietary α-mangostin, a xanthone from mangosteen fruit, exacerbates experimental colitis and promotes dysbiosis in mice

SCOPE

Ulcerative colitis (UC) is a chronic inflammatory disease of the colon. α-Mangostin (α-MG), the most abundant xanthone in mangosteen fruit, exerts anti-inflammatory and antibacterial activities in vitro. We evaluated the impact of dietary α-MG on murine experimental colitis and on the gut microbiota of healthy mice.

METHODS AND RESULTS

Colitis was induced in C57BL/6J mice by administration of dextran sulfate sodium (DSS). Mice were fed control diet or diet with α-MG (0.1%). α-MG exacerbated the pathology of DSS-induced colitis. Mice fed diet with α-MG had greater colonic inflammation and injury, as well as greater infiltration of CD3(+) and F4/80(+) cells, and colonic myeloperoxidase, than controls. Serum levels of granulocyte colony-stimulating factor, IL-6, and serum amyloid A were also greater in α-MG-fed animals than in controls. The colonic and cecal microbiota of healthy mice fed α-MG but no DSS shifted to an increased abundance of Proteobacteria and decreased abundance of Firmicutes and Bacteroidetes, a profile similar to that found in human UC.

CONCLUSION

α-MG exacerbated colonic pathology during DSS-induced colitis. These effects may be associated with an induction of intestinal dysbiosis by α-MG. Our results suggest that the use of α-MG-containing supplements by patients with UC may have unintentional risk.

Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease

BACKGROUND

Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition without any known cause or cure. An imbalance in normal gut biota has been identified as an important factor in the inflammatory process.

METHODS

Fifty-eight biopsies from Crohn's disease (CD, n = 10), ulcerative colitis (UC, n = 15), and healthy controls (n = 16) were taken from a population-based case-control study. Automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphisms (T-RFLP) were used as molecular tools to investigate the intestinal microbiota in these biopsies.

RESULTS

ARISA and T-RFLP data did not allow a high level of clustering based on disease designation. However, if clustering was done based on the inflammation criteria, the majority of biopsies grouped either into inflamed or noninflamed groups. We conducted statistical analyses using incidence-based species richness and diversity as well as the similarity measures. These indices suggested that the noninflamed tissues form an intermediate population between controls and inflamed tissue for both CD and UC. Of particular interest was that species richness increased from control to noninflamed tissue, and then declined in fully inflamed tissue.

CONCLUSIONS

We hypothesize that there is a recruitment phase in which potentially pathogenic bacteria colonize tissue, and once the inflammation sets in, a decline in diversity occurs that may be a byproduct of the inflammatory process. Furthermore, we suspect that a better knowledge of the microbial species in the noninflamed tissue, thus before inflammation sets in, holds the clues to the microbial pathogenesis of IBD.

Bioecological control of inflammatory bowel disease

It is today generally accepted, that the intestinal bacterial flora is deeply involved in the pathogenesis of human inflammatory bowel diseases (IBDs), although the exact presence of unwanted or lack of specific crucial bacteria are not yet known. Westerners lack to large extent important immunomodulatory and fibre-fermenting lactic acid bacteria (LAB), bacteria which are present in all with a more primitive rural lifestyle. Acute reduction of flora is observed in disease, including IBD, as well as in mental and physical stress. Some observations suggest the mucosa has lost its ability of holding back the pathogenic flora and prevent close contacts between resident microflora and the epithelial surface. Among the manifestations of IBD are increased inflammation and coagulability, impaired cellular membrane function, exaggerated nitric oxide production and impaired short-chain fatty acid production. Animal studies suggest, in addition to reduced flora, an intimate association with immunostimulatory DNA, malfunctioning trifoil factors, increased splanchnic metabolism and reduced availability of natural antioxidants. Treatment with plant fibres, antioxidants and sometimes probiotics have had limited success. The most dramatic effects are seen in the few cases where total faecal replacement (TFR) has been tried. The general experience this far is that the best effects are obtained with compositions of probiotics rather than with single LAB treatments.

Lupin kernel fiber consumption modifies fecal microbiota in healthy men as determined by rRNA gene fluorescent in situ hybridization

BACKGROUND

Changes in the composition of gastrointestinal microbiota by dietary interventions using pro- and prebiotics provide opportunity for improving health and preventing disease. However, the capacity of lupin kernel fiber (LKFibre), a novel legume-derived food ingredient, to act as a prebiotic and modulate the colonic microbiota in humans needed investigation.

AIM OF THE STUDY

The present study aimed to determine the effect of LKFibre on human intestinal microbiota by quantitative fluorescent in situ hybridization (FISH) analysis.

DESIGN

A total of 18 free-living healthy males between the ages of 24 and 64 years consumed a control diet and a LKFibre diet (containing an additional 17-30 g/day fiber beyond that of the control-incorporated into daily food items) for 28 days with a 28-day washout period in a single-blind, randomized, crossover dietary intervention design.

METHODS

Fecal samples were collected for 3 days towards the end of each diet and microbial populations analyzed by FISH analysis using 16S rRNA gene-based oligonucleotide probes targeting total and predominant microbial populations.

RESULTS

Significantly higher levels of Bifidobacterium spp. (P = 0.001) and significantly lower levels of the clostridia group of C. ramosum, C. spiroforme and C. cocleatum (P = 0.039) were observed on the LKFibre diet compared with the control. No significant differences between the LKFibre and the control diet were observed for total bacteria, Lactobacillus spp., the Eubacterium spp., the C. histolyticum/C. lituseburense group and the Bacteroides-Prevotella group.

CONCLUSIONS

Ingestion of LKFibre stimulated colonic bifidobacteria growth, which suggests that this dietary fiber may be considered as a prebiotic and may beneficially contribute to colon health.

Probiotics as flourishing benefactors for the human body

This article provides a comprehensive review of the beneficial effects of various strains of probiotics in preventing and treating certain diseases. Currently, changed lifestyles as well as the increased use of antibiotics are significant factors challenging the preservation of a healthy intestinal microflora. The concept of probiotics is to restore and uphold a microflora advantageous for the human body. Probiotics are found in a number of fermented dairy products, infant formula, and dietary supplements. In the presence of prebiotics, which are nondigestible food ingredients favorable for probiotic growth, their survival in the intestine is ameliorated.

Probiotics and chronic disease

In today's climate, changed lifestyles and the increased use of antibiotics are significant factors that affect the preservation of a healthy intestinal microflora. The concept of probiotics is to restore and maintain a microflora advantageous to the human body. Probiotics are found in a number of fermented dairy products, infant formula, and dietary supplements. Basic research on probiotics has suggested several modes of action beneficial for the human body and clinical research has proven its preventive and curative features in different intestinal and extraintestinal diseases. Chronic diseases cause considerable disablement in patients and represent a substantial economic burden on healthcare resources. Research has demonstrated a crucial role of nutrition in the prevention of chronic disease. Thus, positive, strain-specific effects of probiotics have been shown in diarrheal diseases, inflammatory bowel diseases, irritable bowel syndrome, and Helicobacter pylori-induced gastritis, and in atopic diseases and in the prevention of cancer. As the majority of probiotics naturally inhabit the human intestinal microflora, their use has been regarded as very safe. However, in view of the range of potential benefits on health that might be achieved by the use of some probiotic bacteria, major and thorough evaluation is still necessary. In conclusion, probiotics act as an adjuvant in the prevention and treatment of a wide variety of chronic diseases.

Mucosal bacteria in ulcerative colitis

Ulcerative colitis (UC) is an acute and chronic inflammatory bowel disease of unknown aetiology, although bacterial species belonging to the normal colonic microbiota are known to be involved in its initiation and maintenance. Several organisms have been linked to the disease; however, mucosa-associated bacteria are more likely to be involved than their luminal counterparts, due to their close proximity to the host epithelium. Comparative bacteriological analyses were done on rectal biopsies to investigate differences in mucosal bacteria in patients with UC and healthy controls. Complex bacterial communities were found in both groups, with significant reductions in bifidobacterial numbers in UC, which suggested that they might have a protective role in the disease. Accordingly, a therapy for treating UC was designed, with the aim of modifying the mucosal microbiota to increase bifidobacterial colonisation and reduce inflammation. Ranges of mucosal and faecal bifidobacteria were tested for their substrate preferences and their abilities to survive under a variety of environmental conditions. A synbiotic comprising a probiotic (Bifidobacterium longum) isolated from healthy rectal mucosa combined with a prebiotic (oligofructose-enriched inulin - Synergy 1) was developed. The treatment was used in a randomised controlled trial involving eighteen patients with active UC, for a period of 1 month. Rectal biopsies were collected at the beginning and end of the study. Bacteriological analysis and transcription levels of epithelium-related immune markers were assessed. Results demonstrated that short-term synbiotic treatment resulted in increased bifidobacterial colonisation of the rectal mucosa and induced significant reductions in the expression of molecules that control inflammation in active UC.

Molecular characterization of rectal mucosa-associated bacterial flora in inflammatory bowel disease

BACKGROUND

Colorectal bacteria may play a role in the pathogenesis of inflammatory bowel disease (IBD). To test the hypothesis that, in affected patients, the numbers of potentially protective mucosal bacteria might be reduced and pathogenic species increased, we compared rectal mucosa-associated flora in patients with IBD and normal controls.

METHODS

Snap-frozen rectal biopsies taken at routine diagnostic colonoscopy from 33 patients with ulcerative colitis, 6 patients with Crohn's disease, and 14 controls with normal colonoscopy were processed, and individual bacterial groups were counted using fluorescent in situ hybridization.

RESULTS

Bacteria were mostly found apposed to the epithelial surface and within crypts. Epithelium-associated counts of bifidobacteria in active [median 15/mm of epithelial surface (range, 4-56), n = 14] and quiescent ulcerative colitis [26/mm (range, 11-140), n = 19] were lower than in controls [56/mm (range, 0-144), n = 14; P = 0.006 and P = 0.03, respectively]. Conversely, epithelium-associated Escherichia coli counts were higher in active [82/mm (range, 56-136)] than inactive ulcerative colitis [6/mm (range, 0-136), P = 0.0001] or controls [0/mm (range, 0-16), P < 0.0001]. Epithelium-associated clostridia counts were also higher in active [3/mm (range, 0-9)] than inactive colitis [0/mm (range, 0-9), P = 0.03] or controls [0/mm (range, 0-1); P = 0.0007]. Epithelium-associated E. coli counts were higher in Crohn's disease [42/mm (range, 3-90), n = 6] than controls (P = 0.0006). E. coli were also found as individual bacteria and in clusters in the lamina propria in ulcerative colitis and Crohn's disease but in none of the controls (P < 0.01). Numbers of Lactobacillus and Bacteroides showed no differences between patient groups.

CONCLUSIONS

The reduction in mucosa-associated bifidobacteria and increase in E. coli and clostridia in patients with IBD supports the hypothesis that an imbalance between potentially beneficial and pathogenic bacteria may contribute to its pathogenesis.

Chemotaxonomic analysis of bacterial populations colonizing the rectal mucosa in patients with ulcerative colitis

The etiology of ulcerative colitis (UC) is unknown, but evidence links it to bacteria belonging to the normal colonic microbiota. The aims of this study were to characterize bacteria colonizing the rectal epithelium, and to investigate whether significant differences existed in UC. Rectal biopsy specimens were obtained via endoscopy from 9 patients with active colitis and 10 patients without inflammatory bowel disease. Complex bacterial communities colonized the rectal mucosa in all subjects. Overall, 72 bacterial taxa (18 genera) were detected. Twenty species were common to both groups, but only differences in bifidobacteria were statistically significant (P=.005). Peptostreptococci were only detected in patients with UC. Microscopy showed that bacteria in mucosal biofilms often occurred in microcolonies. Interindividual variations in mucosal biofilms made it difficult to assign a role for specific bacteria in UC etiology. However, differences in bifidobacteria and peptostreptococci may implicate these organisms in this disease.

Lactobacillus plantarum 299: beneficial in vitro immunomodulation in cells extracted from inflamed human colon

BACKGROUND AND AIM

The present study determined the pattern of cytokine secretion (interleukin [IL]-1beta, tumor necrosis factor [TNF]-alpha, interferon [IFN]-gamma and IL-10) and their cellular sources in mononuclear cells isolated from colonic mucosa from normal and ulcerative colitis (UC) in response to probiotic and pathogenic bacteria.

METHODS

Mononuclear cells were extracted from normal and active UC colonic mucosa and incubated with pure sonicates of probiotic, commensal, and pathogenic bacteria. Cytokine secretion was measured in culture supernatant and intracellular cytokine staining measured using fluorescent-activated cytometry.

RESULTS

In mononuclear cells isolated from normal mucosa, significant increases in mean IL-1beta were observed with enteropathogenic Escherichia coli (286.3 +/- 138.7 pg/mL P < 0.05) and E. coli (440.5 +/- 194.0 pg/mL P < 0.01) compared with unstimulated control cells (16.7 +/- 4.8 pg/mL). In contrast, mononuclear cells isolated from active UC mucosa produced significant increases in mean IL-1beta in response to stimulation with Salmonella dublin (230.5 +/- 38.8 pg/mL P < 0.05), enteropathogenic E. coli (231.7 +/- 45.3 pg/mL P < 0.05) and E. coli (465.4 +/- 60.2 pg/mL P < 0.001) compared with unstimulated control cells (60.7 +/- 17.1 pg/mL). Escherichia coli also produced significant mean increases of TNF-alpha and IFN-gamma compared with unstimulated control cells. No significant increases in IL-1beta, TNF-alpha or IFN-gamma were observed with Lactobacillus plantarum in cells derived from normal or inflamed mucosa. Strikingly, incubation of L. plantarum with mononuclear cells isolated from active UC mucosa resulted in significant increases of mean IL-10 (327 +/- 53.5 pg/mL, P < 0.05) compared with unstimulated control cells (29.7 +/- 13.2 pg/mL). Intracellular cytokine staining confirmed T-cell and macrophage IL-10 production after L. plantarum stimulation.

CONCLUSIONS

Lactobacillus plantarum demonstrates beneficial immunomodulatory activity by increasing IL-10 synthesis and secretion in macrophages and T-cells derived from the inflamed colon. This may provide a mechanism through which probiotic bacteria ameliorate inappropriate inflammation and induce tolerance.

Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis

AIM

The aim of this study was to characterize the bacterial community adhering to the mucosa of the terminal ileum, and proximal and distal colon of the human digestive tract.

METHODS AND RESULTS

Pinch samples of the terminal ileum, proximal and distal colon were taken from a healthy 35-year-old, and a 68-year-old subject with mild diverticulosis. The 16S rDNA genes were amplified using a low number of PCR cycles, cloned, and sequenced. In total, 361 sequences were obtained comprising 70 operational taxonomic units (OTU), with a calculated coverage of 82.6%. Twenty-three per cent of OTU were common to the terminal ileum, proximal colon and distal colon, but 14% OTU were only found in the terminal ileum, and 43% were only associated with the proximal or distal colon. The most frequently represented clones were from the Clostridium group XIVa (24.7%), and the Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides) cluster (27.7%).

CONCLUSION

Comparison of 16S rDNA clone libraries of the hindgut across mammalian species confirms that the distribution of phylogenetic groups is similar irrespective of the host species. Lesser site-related differences within groups or clusters of organisms, are probable.

SIGNIFICANCE AND IMPACT

This study provides further evidence of the distribution of the bacteria on the mucosal surfaces of the human hindgut. Data contribute to the benchmarking of the microbial composition of the human digestive tract.

Probiotics in health and disease in the pediatric patient

Probiotics are truly a timeless concept. Initially standard components of the human diet, potentially beneficial bacteria and yeast have been eliminated systematically through modern methods of preparing and preserving foods. Although the concept of probiotics is not new, the science of probiotics is in its infancy. Only recently have techniques been developed to identify, culture, and produce the probiotics that are suitable for medical use consistently. Furthermore, the potential uses for these organisms may extend far beyond what originally was thought. In no way should probiotics be thought of as a panacea for the diseases described earlier; however, when used appropriately, they represent a potentially beneficial adjunct to other proved therapies and have the added benefit of providing a stabilizing influence on the delicate balance between the ecosystem that consists of the human and its flora.

Pre-, pro- and synbiotics

Approximately 70% of the immune system is localized in the gastrointestinal tract. The saliva and gastrointestinal secretions, as well as flora (probiotics) and supplied fibres (prebiotics), are important for optimal function. Probiotic bacteria have been shown to influence the immune system through several molecular mechanisms. Pre-, pro- and synbiotics (products produced by fermentation) offer both protection against and cure of a variety of endemic and acute diseases. This review summarizes the present experience in various forms of diarrhoea, inflammatory bowel disease, and Helicobacter infections, in intensive care patients and in connection with extensive surgery.

Assessment of adhesion properties of novel probiotic strains to human intestinal mucus

Potential new probiotic strains Lactobacillus brevis PELI, L. reuteri ING1, L. rhamnosus VTT E-800 and L. rhamnosus LC-705 were assessed for their adhesion properties using the human intestinal mucus model. The effect on the adhesion of exposure to acid and pepsin and to milk were tested to simulate gastric and food processing conditions, and the effect of different growth media on adhesion was tested. The properties of the four strains were compared to the well-investigated probiotic L. rhamnosus strain GG. Three of the tested strains showed significant adhesion properties in the mucus model, while L. brevis PELI had intermediate adhesion and L. rhamnosus LC-705 adhered poorly. Pretreatment with different milks decreased the adhesion and low pH and pepsin treatment reduced the adhesion of all tested strains except L. rhamnosus LC-705. No competitive exclusion of pathogenic Salmonella typhimurium or Escherichia coli SfaII was observed. The results indicate that major differences exist between tested proposed probiotic strains. The growth media and the food matrix significantly affect the adhesive ability of the tested strains. This has previously not been taken into account when selecting novel probiotic strains.