NORMAL BACTERIAL POPULATIONS OF THE INTESTINE AND THEIR RELATION TO INTESTINAL FUNCTION

Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens

BACKGROUND

The gut microbiota plays an essential role in maintaining gut homeostasis and improving performance, with the composition of microbial communities visibly differing across different laying stages in hens and significantly correlating with egg production. To gain further insights into the association between microbial community characteristics and laying periods in Hy-Line variety brown and Isa brown laying hens, we conducted a 16S rRNA amplicon sequencing survey.

RESULTS

Our result revealed the diversity of bacteria in the early laying period was commonly higher than peak, and in Hy-Line variety brown laying hens were generally higher than Isa brown. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) revealed that the structure and composition of the gut microbiota of laying hens exhibited significant differences among different groups. Phylum Firmicutes, Bacteroidota, Proteobacteria, and Fusobacteriota were found that dominant in the host's feces. Therein, the abundance of Fusobacteriota was higher in the peak period than in the early period, while the abundance of Cyanobacteria in the early period was higher in two breeds of hens. Furthermore, random forest based on machine learning showed that there were several distinctly abundant genera, which can be used as potential biomarkers to differentiate the different groups of laying periods and breeds. In addition, the prediction of biological function indicated the existing discrepancy in microbial function among the microbiota of four groups.

CONCLUSIONS

Our findings offer new insights into the bacterial diversity and intestinal flora composition of different strains of laying hens during various laying periods, contributing significantly to the improvement of production performance and the prevention of chicken diseases.

Small Intestinal Bacterial Overgrowth-Pathophysiology and Its Implications for Definition and Management

The concept of small intestinal bacterial overgrowth (SIBO) arose in the context of maldigestion and malabsorption among patients with obvious risk factors that permitted the small bowel to be colonized by potentially injurious colonic microbiota. Such colonization resulted in clinical signs, symptoms, and laboratory abnormalities that were explicable within a coherent pathophysiological framework. Coincident with advances in medical science, diagnostic testing evolved from small bowel culture to breath tests and on to next-generation, culture-independent microbial analytics. The advent and ready availability of breath tests generated a dramatic expansion in both the rate of diagnosis of SIBO and the range of associated gastrointestinal and nongastrointestinal clinical scenarios. However, issues with the specificity of these same breath tests have clouded their interpretation and aroused some skepticism regarding the role of SIBO in this expanded clinical repertoire. Furthermore, the pathophysiological plausibility that underpins SIBO as a cause of maldigestion/malabsorption is lacking in regard to its purported role in irritable bowel syndrome, for example. One hopes that the application of an ever-expanding armamentarium of modern molecular microbiology to the human small intestinal microbiome in both health and disease will ultimately resolve this impasse and provide an objective basis for the diagnosis of SIBO.

Investigating the human jejunal microbiota

Descriptions of the small intestinal microbiota are deficient and conflicting. We aimed to get a reliable description of the jejunal bacterial microbiota by investigating samples from two separate jejunal segments collected from the luminal mucosa during surgery. Sixty patients with morbid obesity selected for elective gastric bypass surgery were included in this survey. Samples collected by rubbing a swab against the mucosa of proximal and mid jejunal segments were characterized both quantitatively and qualitatively using a combination of microbial culture, a universal quantitative PCR and 16S deep sequencing. Within the inherent limitations of partial 16S sequencing, bacteria were assigned to the species level. By microbial culture, 53 patients (88.3%) had an estimated bacterial density of < 1600 cfu/ml in both segments whereof 31 (51.7%) were culture negative in both segments corresponding to a bacterial density below 160 cfu/ml. By quantitative PCR, 46 patients (76.7%) had less than 104 bacterial genomes/ml in both segments. The most abundant and frequently identified species by 16S deep sequencing were associated with the oral cavity, most often from the Streptococcus mitis group, the Streptococcus sanguinis group, Granulicatella adiacens/para-adiacens, the Schaalia odontolytica complex and Gemella haemolysans/taiwanensis. In general, few bacterial species were identified per sample and there was a low consistency both between the two investigated segments in each patient and between patients. The jejunal mucosa of fasting obese patients contains relatively few microorganisms and a core microbiota could not be established. The identified microbes are likely representatives of a transient microbiota and there is a high degree of overlap between the most frequently identified species in the jejunum and the recently described ileum core microbiota.

COLIGENTA treatment of small intestinal bacterial overgrowth. Results of an open study

PURPOSE

The treatment of small intestinal overgrowth (SIBO) varies according to the center. The present study aimed to evaluate the efficacy of COLIGENTA, an association of colimycin and gentamycin, on SIBO symptomatology and breath test normalization PATIENTS AND METHODS: In this prospective cross-sectional open study, 150 patients with functional bowel disorders and SIBO diagnosed by lactulose hydrogen breath test (LHBT) underwent COLIGENTA oral treatment. A new HLBT was performed 4 weeks after the first HLBT.

RESULTS

The patients were mainly female (74%), with a mean age of 47.4 ± 16.2 years and a body mass index of 26.2 ± 5.9 kg/m². After treatment, a decrease of expired hydrogen concentration (P<0.001) was found in the entire population. Improvement of gastrointestinal symptoms was found in 129 patients (86%), while the breath test's normalization was found in 62 patients (42%). Logistic regression showed that normalization of bowel symptoms was not associated with demographics, clinical, or hydrogen breath concentration. In contrast, normalization of LHBT was associated with an increase of breath hydrogen concentration at time 100 min during the first test (P = 0.003; OR=1.072; 95%CI= [1.023-1.123]).

CONCLUSION

The present study shows that 10-days of COLIGENTA treatment has a high SIBO clinical improvement rate and can be used as the first or second treatment line.

[NSAID enteropathy]

Nonsteroidal anti-inflammatory drugs (NSAIDs) are one of the most commonly used drugs in the world, and their side effects are very high. First of all, these are NSAID gastropathy, but in the long term, 5070% of NSAIDs cause damage to the small intestine (NSAID enteropathy), sometimes with serious consequences. To date, no drugs have been proposed with proven effectiveness to prevent this side effect. Apparently, this is not due to the fully clarified mechanism of pathogenesis. The most promising is the hypothesis of the participation of individual representatives of microflora in the development of enteropathy. Therefore, modulating the intestinal flora with the help of probiotics can be the basic therapeutic strategy for the prevention and treatment of such damage.

Microbiota Plays a Key Role in Non-Steroidal Anti-Inflammatory Drug-Induced Small Intestinal Damage

BACKGROUND

Non-steroidal anti-inflammatory drugs (NSAIDs) damage the small intestine by causing multiple erosions and ulcers. However, to date, no established therapies and prophylactic agents are available to treat such damages. We reviewed the role of intestinal microbiota in NSAID-induced intestinal damage and identified potential therapeutic candidates.

SUMMARY

The composition of the intestinal microbiota is an important factor in the pathophysiology of NSAID-induced small intestinal damage. Once mucosal barrier function is disrupted due to NSAID-induced prostaglandin deficiency and mitochondrial malfunction, lipopolysaccharide from luminal gram-negative bacteria and high mobility group box 1 from the injured epithelial cells activate toll-like receptor 4-signaling pathway and nucleotide-binding oligomerization domain-like receptor family, pyrin domain-containing 3 inflammasome; this leads to the release of proinflammatory cytokines such as tumor necrosis factor-α and interleukin-1β. Proton pump inhibitors (PPIs) are often used for the prevention of NSAID-induced injuries to the upper gastrointestinal tract. However, several studies indicate that PPIs may induce dysbiosis, which may exacerbate the NSAID-induced small intestinal damage. Our recent research suggests that probiotics and rebamipide could be used to prevent NSAID-induced small intestinal damage by regulating the intestinal microbiota. Key Messages: Intestinal microbiota plays a key role in NSAID-induced small intestinal damage, and modulating the composition of the intestinal microbiota could be a new therapeutic strategy for treating this damage.

Association between symptoms of irritable bowel syndrome and methane and hydrogen on lactulose breath test

Whether hydrogen and methane gas produced during lactulose breath test (LBT) are associated with symptoms of irritable bowel syndrome (IBS) is not determined. We aimed to investigate whether hydrogen and methane on LBT are associated with IBS symptoms. Sixty-eight IBS patients meeting the Rome III criteria for IBS, and 55 healthy controls, underwent LBT. The IBS subjects recorded their customary gastrointestinal symptoms on a questionnaire using visual analogue scales. LBT positivity was defined to be above 20 ppm rise of hydrogen or 10 ppm rise of methane within 90 min. Gas amounts produced during LBT were determined by calculating area under the curve of hydrogen and methane excretion. Symptom severity scores were not different between the LBT (+) IBS and LBT (-) IBS subjects and also between methane producers and non-methane producers. Gas amounts produced during LBT were not associated with IBS symptoms, except a weak correlation between total gas amounts and a few IBS symptoms such as bloating (r = 0.324, P = 0.039), flatulence (r = 0.314, P = 0.046) and abdominal pain (r = 0.364, P = 0.018) only in LBT (+) IBS. In conclusion, hydrogen and methane gas on LBT are not useful for predicting the customary symptoms and subtypes of IBS.

Pilot study of probiotic dietary supplementation for promoting healthy kidney function in patients with chronic kidney disease

INTRODUCTION

Uremic syndrome consists of nitrogenous waste retention, deficiency in kidney-derived hormones, and reduced acid excretion, and, if untreated, may progress to coma and eventual death. Previous experience suggests that oral administration of a probiotic formulation of selected microbial strains may extend renoprotection via intraintestinal extraction of toxic waste solutes in patients with chronic kidney disease (CKD)stages 3 and 4. This report presents preliminary data from a pilot study.

METHODS

This was a 6-month prospective, randomized, double-blind, placebo-controlled crossover trial of a probiotic bacterial formulation conducted in four countries, at five institutions, on 46 outpatients with CKD stages 3 an nd 4: USA (n=10), Canada (n=113), Nigeria (n=115), and Argentina (n=8). Outcomes were compared using biochemical parameters:blood urea nitrogen (BUN), serum creatinine, and uric acid. General well-being was assessed as a secondary parameter by a quality of life (QQOL) questionnaire on a subjective scale of 1-10.

RESULTS

Oral ingestion of probiotics (90 billion colony forming units [CFUs]/day) was well tolerated and safe during the entire trial period at all sites. BUN levels decreased in 29 patients (63%, P<0.05), creatinine levels decreased in 20 patients (43%, no statistical significance), and uric acid levels decreased in 15 patients (33%, no statistical significance). Almost all subjects expressed a perceived substantial overall improvement in QOL (86%, P<0.05).

CONCLUSION

The main outcomes of this preliminary trial include a significant reduction of BUN, enhanced well-being, and absence of serious adverse effects, thus supporting the use of the chosen probiotic formulation for bowel-based toxic solute extraction. QOL and BUN levels showed statistically significant differences in outcome (P<0.05) between placebo and probiotic treatment periods at all four sites (46 patients). A major limitation of this trial is the small sample size nd elated inconsistencies.

The pathogenesis of gastrointestinal bacterial overgrowth

The normal indigenous intestinal microflora consists of about 10(15) bacteria that under physiological conditions reside mainly in the lower gastrointestinal tract. Bacterial overgrowth implies abnormal bacterial colonization of the upper gut, resulting from failure of specific defense mechanisms restricting colonization under physiological conditions. At present two types of bacterial overgrowth with defined pathogenesis can be distinguished: (1) gastric overgrowth with upper respiratory tract microflora resulting from selective failure of the gastric acid barrier, and (2) gastrointestinal overgrowth with Gram-negative bacilli (enteric bacteria) resulting from failure of intestinal clearance. Helicobacter pylori-induced gastritis of the oxyntic mucosa is the main cause of acquired failure of the gastric acid barrier, which is common among the healthy elderly. Intestinal clearance may fail as the result of impaired intestinal peristalsis or anatomical abnormalities that alter luminal flow. Impaired peristalsis is associated with conditions interfering with intestinal neuromuscular function including myopathic, neuropathic, autoimmune, infectious, inflammatory, metabolic, endocrine, and neoplastic diseases. Anatomical abnormalities are mainly the result of gastrointestinal surgery, intestinal diverticula or fistula. Combined failure of intestinal clearance and the gastric acid barrier results in more severe colonization with Gram-negative bacilli. Gram-negative bacilli are uncommon in the upper gut of otherwise healthy individuals with gastric hypochlorhydria, being acquired (H. pylori) or drug-induced. Significant bacterial overgrowth with Gram-negative bacilli is a rational in the search for an explanation to optimize clinical management. The clinical significance of colonization with upper respiratory tract microflora remains unclear. Translocation of live bacteria, their metabolic products, or antigens from a small bowel colonized by Gram-negative bacilli play a role in the pathogenesis of spontaneous bacterial peritonitis in hepatic disease and in certain types of sepsis, indicating that further studies can point to new patient populations with potential benefit from medical treatment.

ASSOCIATION OF GERMFREE MICE WITH BACTERIA ISOLATED FROM NORMAL MICE

Germfree mice were given food contaminated with pure cultures of various bacterial species isolated from ordinary healthy mice. The cultures were given singly, or in association, or consecutively at weekly intervals. Whatever the technique of administration, the lactobacilli and anaerobic streptococci immediately established themselves throughout the gastrointestinal tract, and became closely associated with the walls of the organs. In contrast, the organisms of the bacteroides group were found in large numbers only in the large intestine. Within a week after exposure, the populations of these three bacterial species reached levels similar to those found in ordinary mice. They remained at these characteristic levels throughout the period of observation (several months). Their presence resulted in a progressive decrease in the size of the cecum which eventually became normal in gross appearance. Coliform bacilli multiplied extensively and persisted at high levels in all parts of the gastrointestinal tract of germfree mice, even after these had become colonized with lactobacilli, anaerobic streptococci and bacteroides. However, the coliform population fell precipitously within a few days after the animals were fed the intestinal contents of healthy pathogen-free mice.

Vitamin B12 synthesis by human small intestinal bacteria

In man, physiological amounts of vitamin B12 (cyanocobalamin) are absorbed by the intrinsic factor mediated mechanism exclusively in the ileum. Human faeces contain appreciable quantities of vitamin B12 or vitamin B12-like material presumably produced by bacteria in the colon, but this is unavailable to the non-coprophagic individual. However, the human small intestine also often harbours a considerable microflora and this is even more extensive in apparently healthy southern Indian subjects. We now show that at least two groups of organisms in the small bowel, Pseudomonas and Klebsiella sp., may synthesise significant amounts of the vitamin.

Microorganisms responsible for controlling the populations of Escherichia coli and enterococcus and the consistency of cecal contents in the chicken

A study was made to clarify what kinds of intestinal organisms might be responsible for controlling the populations of Escherichia coli and Streptococcus faecalis var. liquefaciens in the cecum and the consistency of the cecal of chickens. Germ-free chickens were inoculated orally with various mixtures of bacterial cultures alone or in combination, different dilutions of the cecal contents of chickens, different dilutions of the cecal contents treated by healing or with chloroform, the supernatant of diluted cecal contents, and dilutions of human feces. Factors controlling the E. Coli populations, enterococcal populations, and consistency of the cecal contents were shown to be independent of one another. The ecosystem controlling the E. coli or enterscoccal population was more complex than that controlling the consistency of the cecal contents. The former was composed of anaerobic and facultatively anaerobic bacteria isolated and heat- or chloroform-resistance organisms, and the latter of heat- or chloroform-resistance alone, which were inferred not to prevailing in the cecal contents of chickens. Discussion is made on ecological systems controlling flora.

Stagnant loop syndrome resulting from small-bowel irradiation injury and intestinal by-pass

Stagnant or blind-loop syndrome includes vitamin B12 malabsorption, steatorrhea, and bacterial overgrowth of the small intestine. A case is presented to demonstrate this syndrome occurring after small-bowel irradiation injury with exaggeration postenterocolic by-pass. Alteration of normal small-bowel flora is basic to development of the stagnant-loop syndrome. Certain strains of bacteria as Bacteriodes and E. coli are capable of producing a malabsorption state. Definitive therapy for this syndrome developing after severe irradiation injury and intestinal by-pass includes antibiotics. Rapid symptomatic relief from diarrhea and improved malabsorption studies usually follow appropriate antibiotic therapy. Recolonization of the loop(s) with the offending bacterial species may produce exacerbation of symptoms. Since antibiotics are effective, recognition of this syndrome is important. Foul diarrheal stools should not be considered a necessary consequence of irradiation injury and intestinal by-pass.

Biology of the bifidobacteria

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Efficiency of Various Intestinal Bacteria in Assuming Normal Functions of Enteric Flora After Association with Germ-Free Mice

Strictly anaerobic and facultatively anaerobic bacteria were isolated from the intestinal tract of normal mice. Germ-free mice were associated with mixtures of varying complexity of pure cultures of these bacteria. The development of normal features in these animals was then determined on the basis of the following criteria: (i) size of the cecum, (ii) size of the Escherichia coli population in the cecum, (iii) histology of the intestinal tract, and (iv) development of a mucosa-associated flora in stomach and large intestine. Germ-free mice contaminated with cecal contents from conventional mice were used as controls to establish normal values for these parameters. Some strictly anaerobic bacteria could be implanted into germ-free mice only after prior implantation of an E. coli strain. E. coli was found in large numbers in stomach and cecum of mice monocontaminated with this organism. Use of restraining devices indicated that the E. coli population in the stomach was maintained by coprophagy and did not contribute significantly to the size of the cecal population. A mixture of 50 strictly anaerobic bacteria plus 80 facultative anaerobes rendered recipient animals normal with respect to the criteria tested. Other, less complex bacterial mixtures reduced the cecal size and the intestinal E. coli population to levels intermediate between those found in normal and germ-free mice. With all bacterial mixtures tested, the intestinal E. coli population decreased, if at all, within a period of about 10 days after introduction of other bacteria, and remained stable thereafter. This suggests that the intestinal E. coli population is controlled by a mechanism which reduces population size without affecting the growth rate.

Bacteria, bile, and the small bowel

Microbial populations of the small bowel and bile salt metabolism were studied in 15 patients with lesions of the stomach and small intestine. These types of microorganism could be correlated with the site and extent of stasis in the small bowel and the presence of a normally functioning stomach. The presence of obligate anaerobes (bacteroides) and free bile acids could be correlated with areas of stagnation. When these abnormalities were detected throughout the small bowel, steatorrhoea was also noted. However, bacteroides and free bile acids in localized regions of either proximal or distal small bowel were generally associated with normal faecal fat excretion. Vitamin B(12) malabsorption appeared to be related to the total number of bacteria colonizing the small bowel rather than to any specific type of microorganisms. The effect of antibiotics on intestinal function and bacteriology was studied in three patients. In one patient, the broad-spectrum antibiotic tetracycline was effective in eradicating an abnormal bacterial flora. In the other two, lincomycin, which is specifically effective in eradicating the anaerobic flora, restored intestinal function to normal.

Intestinal malabsorption in childhood

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Vitamin K Compounds in Bacteria That Are Obligate Anaerobes

A naphthoquinone-dependent strain of Bacteroides melaninogenicus has been used in a microbiological assay to survey bacteria for compounds of the vitamin K group. Organisms known to contain vitamin K, as well as several bacteria that are obligate anaerobes, produced substances which satisfied the naphthoquinone requirement of the assay organism. Vitamin K was chemically isolated from strains of Bacteroides melaninogenicus, Bacteroides fragilis, and Veillonella alcalescens.