Normal viral and bacterial flora of the human small and large intestine

Review article: emerging role of the gut microbiome in the progression of nonalcoholic fatty liver disease and potential therapeutic implications

BACKGROUND

Nonalcoholic fatty liver disease (NAFLD) is a prevalent disorder associated with obesity and diabetes. Few treatment options are effective for patients with NAFLD, but connections between the gut microbiome and NAFLD and NAFLD-associated conditions suggest that modulation of the gut microbiota could be a novel therapeutic option.

AIM

To examine the effect of the gut microbiota on pathophysiologic causes of NAFLD and assess the potential of microbiota-targeting therapies for NAFLD.

METHODS

A PubMed search of the literature was performed; relevant articles were included.

RESULTS

The composition of bacteria in the gastrointestinal tract can enhance fat deposition, modulate energy metabolism and alter inflammatory processes. Emerging evidence suggests a role for the gut microbiome in obesity and metabolic syndrome. NAFLD is often considered the hepatic manifestation of metabolic syndrome, and there has been tremendous progress in understanding the association of gut microbiome composition with NAFLD disease severity. We discuss the role of the gut microbiome in NAFLD pathophysiology and whether the microbiome composition can differentiate the two categories of NAFLD: nonalcoholic fatty liver (NAFL, the non-progressive form) vs nonalcoholic steatohepatitis (NASH, the progressive form). The association between gut microbiome and fibrosis progression in NAFLD is also discussed. Finally, we review whether modulation of the gut microbiome plays a role in improving treatment outcomes for patients with NAFLD.

CONCLUSIONS

Multiple pathophysiologic pathways connect the gut microbiome with the pathophysiology of NAFLD. Therefore, therapeutics that effectively target the gut microbiome may be beneficial for the treatment of patients with NAFLD.

Recycling of bowel content: the importance of the right timing

INTRODUCTION

Extracorporeal stool transport (recycling of chyme discharged from the proximal stoma end to the distal end of a high jejunostomy or ileostomy) is thought to be beneficial in preventing malabsoprtion, sodium loss, cholestasis and atrophy of the distal intestine until restoration of the intestinal continuity becomes possible. However little is known about its adverse effects. Our aim was to investigate the microbiological safety of recycling.

MATERIAL AND METHOD

Native samples were taken from the proximal stoma in 5 premature neonates who underwent an ileostomy or a jejunostomy due to necrotising enterocolitis, for qualitative culture. The first sample was drawn immediately after the change of the stoma bag, further samples were sent from the stoma bag at 30, 60, 90, 120, 150, and 180min later. The samples were inoculated by calibrated (10 μl) loops onto blood agar (5% sheep blood), eosin-methylene blue agar and anaerobic blood agar, respectively (Oxoid). The aerobic plates were incubated for 18-20 h at 5% CO2, whereas the anaerobic plates were incubated for 24-48 h in an anaerobic chamber (Concept 400). The bacterial strains were identified to species level by specific biochemical reactions, RapID-ANA II system (Oxoid) and ID32E, Rapid ID 32 Strep ATB automatic system cards (bioMérieux).

RESULTS

The number of colony forming unit (CFU) of Gram-negative bacteria (mainly E. coli) exponentially increased after 30 min and reached 10(5)/ml after 120 min. Gram-positive strains (primarily E. faecalis) were detected after 60 min and CFU increased to 10(5)/ml after 120 min. The number of anaerobic (principally Bacteroides fragilis) CFU started to increase after 120 min. In two cases coagulase negative Staphylococcus strains were isolated the earliest in the chyme. The average of total CFU approached 10(5)/ml after 90 min and exceeded 10(5)/ml after 120 min.

CONCLUSION

The chyme in the stoma bag is colonized by commensal facultative pathogenic enteral/colonic as well as skin flora species after 120 min. Recycling of stoma bag content may be dangerous after 90 min.

The aetiology of diarrhoea in newborn infants

Diarrhoea is a common problem in newborn infants in hospital nurseries. In the past, sporadic diarrhoea was often attributed to dietary indiscretion by the mother, and epidemic diarrhoea was though to be caused by an unknown infectious agent. Techniques with which to locate non-cultivable viruses and untypable enteropathogenic strains of Escherichia coli allow reevaluation of the aetiology of diarrhoea in newborn infants. Preliminary results from Melbourne, Australia, suggest that most diarrhoea in newborn infants is induced by a specific infectious agent. During 1975 the agent most often identified from sporadic and epidemic diarrhoea in hospital nurseries was a reovirus-like particle ("duovirus"). Enterotoxin-producing strains of E. coli were rarely isolated. Future attempts to protect newborn infants from developing diarrhoea must be based on an accurate understanding of the aetiology of this disease.

Small bowel bacterial overgrowth is a common cause of chronic diarrhea

BACKGROUND AND AIMS

Often a cause for chronic non-specific diarrhea (> or =3 stools per day for more than 4 weeks) is not identified. Small bowel bacterial overgrowth (SBO) can occur without morphological damage and remains difficult to diagnose. Often diarrhea is treated empirically with antibiotics with a good response. The aims of the present study were first to investigate the prevalence of SBO in a consecutive series of patients with chronic diarrhea and second to compare the utility of duodenal fluid culture and (14)C-d-xylose breath/lactulose test in diagnosing SBO.

METHODS

In the first study, the cause of chronic diarrhea was prospectively diagnosed in 87 subjects. In the second study, tests of SBO were compared in 18 subjects with chronic diarrhea and 15 subjects with reflux oesophagitis used as control subjects. Duodenal fluid was aspirated at endoscopy and cultured and later a (14)C-d-xylose breath/lactulose test was performed.

RESULTS

In the first study, SBO was present in 48% of those with chronic diarrhea. In the second study, the diarrhea group had an average (range) stool frequency of 5.5 (3-10) per day and had normal duodenal biopsies. A total of 33%, 50%, 67% of subjects had SBO by duodenal culture alone, by a (14)C-d-xylose breath/lactulose test alone and by a combination of both tests, respectively. In the control group, 0%, 13% and 13% had SBO by duodenal culture alone, by (14)C-d-xylose breath/lactulose test alone and by combination of tests, respectively.

CONCLUSION

Small bowel bacterial overgrowth is a common (33-67%) cause of chronic diarrhea.

Frequency of portal and systemic bacteremia in acute appendicitis

BACKGROUND

Acute appendicitis is the most common condition requiring an emergency abdominal operation in childhood. In the present study, we analyzed the frequency of portal and systemic bacteremia in 42 patients with acute appendicitis and determined the microbial agents responsible for an acute appendicitis and for portal and systemic bacteremia.

METHODS

Appendectomies were performed on 50 young patients (5-18 years of age), as well as clinical and bacteriological tests. Six independent samples from each patient isolated from the peripheral vein, superior mesenteric vein, appendix and peritoneum were obtained prior to surgery, during surgery and after surgery for biochemical, immunologic and bacteriologic examination.

RESULTS

Pathohistology confirmed the diagnosis of appendicitis in 42 patients, while in the other eight patients there were no obvious pathologic findings, so they served as a control group. Of 50 patients with a clinical appearance of acute appendicitis, in 19 patients (38%) we detected portal bacteremia in the mesenteric vein, while in only three cases (6%) did we find systemic bacteremia detected from the peripheral vein. Furthermore, bacteriologic analysis revealed that Bacteroides spp. and Escherichia coli were the predominant species isolated.

CONCLUSIONS

The results presented in this paper suggests that portal bacteremia did not influence peripheral blood reactions. Furthermore, in the present study we have found a positive correlation between the smear and bacteremia of the superior mesenteric vein, but not with the bacteremia of systemic blood.

Duodenal microflora in very-low-birth-weight neonates and relation to necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in the neonatal period. Small-bowel overgrowth with aerobic gram-negative bacteria has previously been implicated in the development of NEC. This prospective study performed quantitative bacteriology on 422 duodenal aspirates collected from 122 very-low-birth-weight (<1,500-g) newborns, at the time of routine changing of nasogastric tubes. Isolates of Enterobacteriaceae were typed by repetitive extragenic, palindromic PCR and pulsed-field gel electrophoresis. One or more samples from 50% of these infants yielded gram-negative bacteria, predominantly Escherichia coli, Klebsiella spp., and Enterobacter spp., with counts up to 10(8) CFU/g. The proportion of samples with gram-negative bacteria increased with postnatal age, while the percentage of sterile samples declined. Molecular typing revealed marked temporal clustering of indistinguishable strains. All infants had been fed prior to isolation of gram-negative organisms. Antibiotic use had no obvious effect on colonization with Enterobacteriaceae. There were 15 episodes of suspected NEC (stage I) and 8 confirmed cases of NEC (2 stage II and 6 stage III) during the study period. Duodenal aspirates were collected prior to clinical onset in 13 episodes of NEC. Seven of these yielded Enterobacteriaceae, of which five strains were also isolated from infants without NEC. Very-low-birth-weight infants have high levels of duodenal colonization with Enterobacteriaceae, with evidence of considerable cross-colonization with indistinguishable strains. There was no association between duodenal colonization with particular strains of Enterobacteriaceae and development of NEC.

Acute (ascending) cholangitis

Cholangitis is an infection of an obstructed biliary system, most commonly due to common bile duct stones. Bacteria reach the biliary system either by ascent from the intestine or by the portal venous system. Once the biliary system is colonized, biliary stasis allows bacterial multiplication, and increased biliary pressures enable the bacteria to penetrate cellular barriers and enter the bloodstream. Patients with cholangitis are febrile, often have abdominal pain, and are jaundiced. A minority of patients present in shock with hypotension and altered mentation. There is usually a leukocytosis, and the alkaline phosphatase and bilirubin levels are generally elevated. Noninvasive diagnostic techniques include sonography, which is the recommended initial imaging modality. Standard CT, helical CT cholangiography, and magnetic resonance cholangiography often add important information regarding the type and level of obstruction. Endoscopic sonography is a more invasive means of obtaining high-quality imaging, and endoscopic or percutaneous cholangiography offers the opportunity to perform a therapeutic procedure at the time of diagnostic imaging. Endoscopic modalities currently are favored over percutaneous procedures because of a lower risk of complication. Treatment includes fluid resuscitation and antimicrobial agents that cover enteric flora. Biliary decompression is required when patients do not rapidly respond to conservative therapy. Definitive therapy can be performed by a surgical, percutaneous, or endoscopic route; the last is favored because it is the least invasive and has the lowest complication rate. Overall prognosis depends on the severity of the illness at the time of presentation and the cause of the biliary obstruction.

Gastrointestinal flora and its alterations in critical illness

The normal indigenous flora of the human gastrointestinal tract comprises a remarkably complex yet stable colony of more than 400 separate species, living in a symbiotic relationship with the human host. Stability of that flora is accomplished by multiple mechanisms including gastric acidity, gut motility, bile, products of immune cells in the gut epithelium, and competition between microorganisms for nutrients and intestinal binding sites. The indigenous flora influences multiple aspects of physiologic homeostasis and forms a key component of normal host defenses against infection by exogenous pathogens. Critical illness is associated with striking changes in patterns of microbial colonization, best described in the oropharynx and upper gastrointestinal tract. Pathological colonization occurs with the same species that is predominate in nosocomial infections, and descriptive studies suggest that such colonization is a risk factor for infection. Moreover, prophylactic measures that prevent pathological gut colonization in experimental circumstances reduce rates of nosocomial infection in critically ill patients and, in the case of selective decontamination of the digestive tract, reduce mortality risk. Conventional approaches to infectious diseases have conceptualized microorganisms as inimical and focused on eradicating them as rapidly and fully as possible. Insights from the study of critically ill patients suggest that that relationship is better understood as a symbiotic one and that preservation, rather than elimination, of the indigenous flora provides the greatest promise of clinical benefit to this vulnerable population.

Microflora persistence on duodenojejunal flat or normal mucosa in time after a meal in children

A pathogenic role for high numbers of bacteria in the small intestine had been suggested previously by bacterial counts on luminal aspirates, but these investigations were flawed by the sampling device "contamination" in the mouth and the changing nature of fluent intestinal content. A procedure was developed to sterilize the Watson biopsy capsule with HCl in the upper portion of the duodenum. Bacteria were counted in the mucosal homogenate of the first (diagnostic) duodenojejunal biopsy in 80 untreated celiac children, and in 46 children with irritable bowel syndrome (IBS) in a four-cell, controlled, randomized investigation. Persistence of bacteria on the mucosa for 20 h after the last meal was investigated in 62 subjects, and for 26 h after the last meal in 64 subjects. Bacteria, mainly streptococci and staphylococci, persisted at a concentration of 10(6) per gram of mucosa 20 h after the last meal. The number of bacteria per gram of mucosa was 24 times higher in all 62 children of the 20-h fast groups than in all 64 children of the 26-h fast groups (p < 0.001). The bacteria count in celiac children was 39 times higher in the 20-h fast group than in the 26-h one. This difference was significantly higher than the 11 times difference that was found on the normal mucosa between the 20- and 26-h fast IBS groups (p < 0.001), which was still significant. The number of bacteria on duodenojejunal mucosa depends on nutrient absorption and persists longer than the intermeal interval in these subjects.

Is small bowel bacterial overgrowth of pathogenic significance in persistent diarrhea?

Bacterial overgrowth in the upper small intestine is postulated to cause persistent diarrhea. We compared the fecal and upper intestinal flora in 82 patients with persistent diarrhea aged < or = 36 months and weight-for-length < or = 90% of National Center for Health Statistics standards (NCHS) and 39 non-diarrheal children with age < or = 36 months, nutritionally matched with the patients and residing in the same environment. In the age groups < or = 12 months and > 12 months the duodenal fluid bacterial counts > or = 10(5)/ml were found with similar frequency in patients and controls for aerobic (p = 0.33; p = 0.1) and anaerobic (p = 1.0; p = 1.0) bacteria. However, the duodenal isolation rates of any aerobic bacteria (p < 0.05) without regard to counts and Enterobacteriaceae (p = 0.06) were higher in patients than in controls. Colonization with Enterobacteriaceae was directly correlated with increased stool weight over a 7-day observation period (p < 0.05; p < 0.01). One or more pathogens were isolated in the feces of 58% of the patients and 43.8% of the controls. Enteroadherent E. coli of the localized [EAEC-L] (p < 0.01) and aggregative [EAggEC] (p = 0.22) phenotypes were isolated more commonly from the feces of patients. The duodenal fluid detection rates for Klebsiella were significantly greater (p < 0.01) in patients, while Giardia lamblia was detected more commonly in the duodenal fluid of controls (p < 0.01). The presence of specific pathogens in the feces did not seem to be related to the extent of small bowel colonization.(ABSTRACT TRUNCATED AT 250 WORDS)

Diagnosis of bacterial overgrowth after culturing proximal small-bowel aspirate obtained during routine upper gastrointestinal endoscopy

The purpose of this study was to evaluate the method of obtaining aspirated fluid for culture from the small intestine through a fiberoptic gastrointestinal endoscope for diagnosing small-bowel overgrowth. The study population consisted of 10 healthy volunteers and 26 patients with various gastrointestinal problems referred for routine endoscopic examination. The material to be cultured was obtained under direct visualization approximately 25 to 30 cm distal to the pylorus or from the afferent loop (in Billroth-II patients) with a sterilized sheathed wash pipe passed through the suction channel of the endoscope. Cultures were considered positive for bacterial overgrowth if total counts of organisms were 10(5)/ml or more. All healthy volunteers and 16 of 21 unoperated patients had sterile or insignificant growth, whereas all 5 patients who had Billroth-II operations had positive overgrowth. The endoscopic method for collection of proximal gastrointestinal fluid for culture is simple and can be performed during routine endoscopy.

The diagnosis of small bowel bacterial overgrowth. Reliability of jejunal culture and inadequacy of breath hydrogen testing

The reliability of a single jejunal culture in the diagnosis of small bowel bacterial overgrowth has recently been questioned. Seventy-seven patients thought to have bacterial overgrowth, defined as a jejunal culture yielding at least 10(6) organisms per milliliter of aspirate, took part in the study. Bacterial overgrowth was found in 74% of the patients with predisposing conditions and in 32% of those with no clear causes of bacterial colonization. The intestinal juice of some patients was taken at two different levels of the proximal jejunum, using both the closed- and open-tube systems. Highly significant correlations (rs = 0.90, p less than 0.001) were found between the numbers of bacteria per milliliter at the 2 jejunal levels and between the numbers of bacteria per milliliter of jejunal aspirate obtained from the closed and open tubes (rs = 0.84, p less than 0.001). Compared with the jejunal culture, the gas chromatography of volatile fatty acids in jejunal aspirate and the glucose- and lactulose-hydrogen breath tests showed sensitivities of 56%, 62%, and 68% and specificities of 100%, 83%, and 44%, respectively. This work demonstrates the reliability of jejunal cultures and the inadequacy of breath hydrogen testing in the prediction of positive jejunal cultures. When results of testing for volatile fatty acids in jejunal aspirates are positive, this always indicates the presence of bacterial overgrowth; thus, this procedure would avoid the more complicated, time-consuming, and costly bacteriological analysis of jejunal samples.

Hospital stay and mortality attributed to nosocomial enterococcal bacteremia: a controlled study

A retrospective cohort study of 97 patients identified by prospective hospital-wide surveillance was conducted to determine the length of hospital stay and mortality attributed to hospital-acquired enterococcal bacteremia. The mean duration of hospitalization for cases was 83 days compared with 44 days for matched controls (p = 0.0001). The mortality rate during the study period was 43% among cases and 12% in matched controls (p less than 0.001). Thus the mortality rate attributable to enterococcal bacteremia was 31% and the risk ratio was 4.75. Stepwise discriminant function analysis indicated that the use of vascular catheters and renal dialysis and the presence of immune deficiency were predictors of fatal outcome in cases. Enterococcal bacteremia has become a prominent nosocomial pathogen and is associated with mortality rates well above those expected from the underlying disease.

Effects of sphincteroplasty and endoscopic sphincterotomy on the bacteriologic characteristics of the common bile duct

Forty-five patients with sphincter of Oddi stenosis had specimens of common bile duct cultured during ERCP before either sphincteroplasty or endoscopic sphincterotomy. All had sterile bile before sphincter ablation. Bile was recultured 6 to 36 months later during endoscopy at which time 70 percent of the sphincterotomy and 76 percent of the sphincteroplasty patients had bile colonized principally by enteric organisms. Growth was heavy to moderate in most of the patients and contained few nasopharyngeal organisms. Despite bactobilia, no patient had symptomatic cholangitis, presumably due to excellent drainage of bile. The most likely source of the bactobilia is from direct extension of duodenal organisms into the common bile duct.

Preoperative antibiotics for abdominal gunshot wounds. A prospective, randomized study

In an effort to define the optimal preventive antibiotics for gunshot wounds to the abdomen, 100 consecutive patients were randomized while in the emergency department to receive either combination ampicillin, amikacin, and clindamycin, combination doxycycline and penicillin, or carbenicillin (Groups I, II, and III, respectively). Antibiotics were continued for 5 days in the presence of distal ileal or colonic injury. The study groups were comparable in age, sex, incidence of shock, degree of peritoneal contamination, and abdominal trauma index. The incidence of infection was not statistically different among the groups. Enterobacteriacea were the predominant offenders, although anaerobes were identified in all groups. The critical risk factor was distal ileal or colon injury. This study indicates that a regimen employing a single agent whose spectrum includes both aerobes and anaerobes is as effective as more expensive and potentially toxic multiagent regimens.

Comparison of an open and a closed tube system for collection of jejunal juice

When jejunal juice is obtained by means of open pernasal tubes, the risk of the aspirates being contaminated is presumably high. The present study compares jejunal aspirates obtained from an open and from a closed tube system. Ten patients suspected of having abnormal jejunal flora and five healthy human volunteers were investigated. The pH values of aspirates obtained from the open tubes were significantly lower than the values registered in aspirates from the closed tube system, with a median difference of 0.70 (p less than 0.02). No differences between the two types of aspirate were registered with regard to total number of bacteria, number of bacterial species, lipase, total protein, total amylase or its fractions of pancreatic and salivary isoamylases. For the investigation of pH-sensitive substances in jejunal juice, a closed tube system is therefore recommended, whereas the use of such a device does not seem necessary for the study of bacterial microflora and pancreatic enzymes.

Tube for sampling of uncontaminated small-bowel juice

A tube system for the collection of uncontaminated small-bowel juice is described. It consists of an outer guide tube, its distal end being closed by a membrane, and an inner aspiration tube. When the outer tube is placed at the desired site of aspiration, the membrane is perforated by advancing the sterile inner tube. The device was tested in 90 healthy human volunteers. The procedure was completely or partly unsuccessful in 9 cases (95% confidence limits, 4.7-18.0). Median intubation time was 12 min; range, 5-14 min. The time used for aspiration of 5 ml of intestinal juice varied from 1 to 30 min; median, 10 min. The site of aspiration in jejunum distal to the ligament of Treitz varied from 0 to 14 cm; median, 3 cm. No complications of the procedure were registered.

Upper intestinal bacterial flora during transpyloric feeding

Samples from the pharynx, stomach, duodenum or jejunum, and faeces were collected on 7 days between 1st and 28th day from neonates weighing less than 1.5 kg at birth who were fed by transpyloric tube. These were cultured on selective and non-selective media, and the results were expressed in a semi-quantitative manner. The number of bacterial species and the density of their growth increased with the patient's age; this was particularly noticeable with Gram-negative bacteria and the ratio of Gram-negative to Gram-positive organisms increased steadily in specimens from all sites with increasing age. The upper small intestine was more heavily colonised than the stomach early in life and the microflora present was predominantly faecal in nature. The species isolated from all sites were mainly aerobes or facultative anaerobes; strict anaerobes did not form a significant proportion of the microflora in these infants. Necrotising enterocolitis developed only after heavy jejunal colonisation with Gram-negative bacilli.

Malabsorption secondary to Meckel's diverticulum

This case report of a patient with a large Meckel's diverticulum with associated stagnation and bacterial proliferation demonstrates the resultant metabolic and nutritional alterations that have classically been described with the blind loop syndrome. A lesion as large as the one presented herein has rarely been reported with iron, vitamin B12, and folic acid deficiency anemias secondary to the contaminated small bowel (ileum) syndrome. A discussion of the pathophysiology, diagnosis, and treatment of this disorder and the multiple disease entities incorporated in the contaminated small bowel syndrome are included.

Enterococcal bacteremia: clinical implications and determinants of death

The pathogenicity of the enterococcus remains controversial despite recognition of this organism in inflammatory exudates. A review of 114 patients with 123 bacteremic events with enterococcus from all hospital services was undertaken. A total of 46% were in the perioperative period. The clinical indications for blood culture varied, but only 19 patients had septic shock at the time. Employing three or more associated diseases as a definition, 71 patients were considered chronically ill. The primary sources of bacteremia were commonly urinary tract (22), soft tissue (17), and intra-abdominal (12). An impressive total of 48 patients had no discernible primary focus of infection. Except for the urinary tract, infections tended to be polymicrobial; 51 patients had associated synchronous or metachronous polymicrobial bacteremias. Antibiotic therapy appropriate for enterococcus did not favorably influence outcome. By chi-square analysis, patients with urinary tract and soft tissue infections had significantly better survival rates than the group as a whole, while patients with intra-abdominal sepsis, polymicrobial bacteremia, or an unknown focus of infection did statistically worse. Enterococcal bacteremia results in a high mortality (54%); its frequent identification with other facultative and anaerobic organisms may indicate that it has a synergistic role; the frequency of unexplained bacteremias stimulates speculation that primary bacteremia from the gastrointestinal tract may be a plausible explanation.

The bacterial flora of neonates with congenital abnormalities of the gastro-intestinal tract

The development of the bacterial flora of neonates with congenital abnormalities of the gastro-intestinal tract was studied in 31 infants during the first 10 days of life. Specimens were collected from the umbilicus, mouth and gastro-intestinal tract on the pre-operative day, at operation and on post-operative days 1, 2, 3, 5, 7 and 10. Bacteria were isolated semi-quantitatively on a variety of plain and selective media and identified by conventional methods.Staphylococcus albus was the predominant species isolated from the umbilicus; it was recovered from 24 of the 31 babies. The viridans group of streptococci and Streptococcus salivarius were the commonest species isolated from the mouth; there were no differences between the babies with different abnormalities and treatment with antibiotics had no effect on the bacterial flora. Ten babies were colonized by each species on the pre-operative day, and 25 and 19 respectively by the tenth post-operative day. Anaerobic gram-positive cocci were the predominant oral anaerobes. Bacteria were not isolated from the rectal swabs of babies with tracheo-oesophageal fistula (TOF) or small bowel atresia on the pre-operative days. Post-operatively the predominant faecal isolates from babies with TOF were Str. faecalis, Escherichia coli and Clostridium perfringens. About 80% of the babies with small bowel atresia were colonized by Str. faecalis and Bacteroides vulgatus, 60% each by E. coli, Klebsiella aerogenes and Str. faecium. The five babies with necrotizing enterocolitis were colonized by Str. faecalis, E. coli, Cl. perfringens and Cl. difficile; Bacteroides spp. were not recovered from any of them. The commonest facultative species recovered from babies with large bowel obstruction were Str. faecalis and E. coli. B. vulgatus, Cl. perfringens and Bifidobacterium spp. were the commonest anaerobes and anaerobes outnumbered aerobes. No significant isolates were recovered from the wound swabs and none of the babies developed post-surgical sepsis.

Endoscopic cultures of the proximal gastrointestinal tract

The purpose of this study was to evaluate two methods of obtaining culture material under direct visualization through a fiberoptic upper gastrointestinal endoscope. Collections were made both with a wash pipe and a sterile brush through a sterilized Olympus D panendoscope. Paired aspirate collections were made on 20 occasions from 10 postgastrectomy and six nonoperated patients. Significant bacterial overgrowth was identified equally well by both methods, the the wash tube, which can be reused, is cheaper. The endoscopic method for collecting proximal fluid for culture is simple and can be performed during a routine endoscopy.

Influence of three antimicrobial agents--penicillin, metronidazole, and doxycyclin--on the intestinal microflora of healthy humans

Antimicrobial drugs may affect the normal gut microflora in a potentially harmful manner. The purpose of the present study was to ascertain whether any of several tests could detect drug influence on the intestinal flora of healthy subjects. Jejunal secretions and feces were cultivated aerobically and anaerobically, with measurement of fermentation gas production in tubes supplemented with glucose or lactulose; bacterial bile acid deconjugation was measured with the 14C-GCA test; and pulmonary H2 and CH4 excretion were measured with gas-solid chromatography after lactulose and glucose ingestion in 18 healthy subjects before and after peroral treatment with either penicillin, metronidazole, or doxycyclin. Bacterial numbers and fermentation gas production were unchanged after treatment, as was the bacterial bile acid deconjugating activity. Pulmonary H2 excretion after lactulose ingestion was significantly reduced after penicillin and metronidazole but not after doxycyclin treatment. Pulmonary CH4 disappeared after metronidazole but remained unchanged after penicillin and doxycyclin treatment. It is concluded that pulmonary H2 and CH4 measurement after lactulose ingestion may serve as a sensitive determinant for drug effects on the normal gut microflora.

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.

Microflora of the human small intestine

The human small intestine is normally sterile in nearly one half of North American subjects. In this study the duodenum, jejunum, and ileum were sterile in 82, 69, and 55 per cent of the cases, respectively. Gram-positive cocci were the most frequent finding. E. coli, Enterobacter, and Klebsiella were present in the small bowel in nearly 7, 15, and 35 per cent of duodenal, jejunal, and ileal samples, respecatively. They were present in significant numbers (greater than 1 X 10(5)/ml) in the mid-jejunum in two patients and in the mid-ileum in seven patients (23 per cent). Even with modern anaerobic techniques, anaerobes are scarce in the small bowel; 4 to 6 per cent of persons may have aerotolerant anaerobes like clostridia, but strict anaerobes like bacteroides are rare. Our study provides baseline data for use in interpreting the intestinal bacterial overgrowth associated with certain postoperative disorders.

A bacteriological study of the intestinal mucosa and luminal fluid of adults with acute diarrhoea

Bacteriological studies of jejunal mucosal biopsy specimens and contents were performed on 22 hospitalized adult patients with acute diarrhoea and 24 control normal subjects. None of the washed homogenates of the mucosal specimens were sterile and only one fluid specimen obtained from a control subject was sterile. A definite enteric pathogen was found in only five of the 22 diarrhoea patients. There was no qualitative difference in the bacterial profile of the jejunal mucosa and contents of the diarrhoea patients from that of the control subjects, but there were significant quantitative differences for some bacterial categories. In the control as well as diarrhoea subjects, there was no qualitative difference in the bacterial profile of the jejunal mucosa from that of the fluid, but there were significant quantitative differences for some bacterial categories. The significance of the findings is discussed.

Duodenal microflora: a prospective study in pediatric gastrointestinal disorders

Culture of the duodenal microflora was performed on 96 infants and children with a variety of gastrointestinal disorders. The resident microflora consists predominantly of oral-type microorganisms such as alpha-Streptococci and Neisseria. A fecal-type microflora was found in all 6 infants with post-surgical diarrhea and temporary monosachcaride intolerance; 4 of 22 patients with protracted diarrhea of infancy, 3 of 22 patients with celiac disease, and none of 32 patients with nonspecific diarrhea or 14 others with miscellaneous disorders. Anaerobic microorganisms were seldom isolated. Only 9% of the duodenal cultures were completely sterile, although a further 17 had a quantitative culture less than 5 times 10(4) microorganisms/ml. Small-bowel contamination with fecal-type microorganisms is associated with stasis and disturbance of the normal peristaltic-clearing mechanism. Duodenal culture is essential in any infant with temporary monosaccharide intolerance. It is occasionally useful in other situations where motility may be disturbed.

Bacterial microflora of the upper gastrointestinal tract in infants without diarrhoea

The upper gastrointestinal microflora has been studied by intubation in a group of infants without diarrhoea. The aerobic flora of the nose and throat, and the aerobic and anaerobic flora of the stomach and duodenum have been defined. Prolonged duodenal intubation has been shown to increase the number of coliforms isolated and bacteriological findings after prolonged intubation should therefore be interpreted with care.

Bacterial microflora of the upper gastrointestinal tract in infants with protracted diarrhoea

The aerobic and anaerobic bacterial microflora of the upper gastrointestinal tract in infants with protracted diarrhoea has been described and compared with a group of control infants without diarrhoea. The duodenal juice of patients with protracted diarrhoea was rarely sterile and was characterized by an increase in numbers and types of microorganisms and by the presence of coliforms, particularly Esch. coli. In individual patients the same serotypes of Esch. coli were found throughout the intestinal tract. The presence of Esch. coli in the upper small intestine may be as important to the aetiology of protracted diarrhoea as it is to acute diarrhoea.

The effect of vagotomy and drainage on the small bowel flora

The incidence of small intestinal colonization in unoperated duodenal ulcer patients was low and similar to that in the normal population. The majority of patients seven to 10 days following truncal vagotomy and drainage were colonized whereas none of a control group of patients following simple closure of a perforated duodenal ulcer was colonized. In patients with pyloroplasty, this high incidence fell to control levels on average 18 months postoperatively, but in patients with a gastro-jejunostomy, the incidence remained raised probably due to the presence of the afferent loop. Only two patients developed episodic diarrhoea and there was no obvious association with small bowel colonization.

Biology of the bifidobacteria

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Bacterial flora in the duodenum of patients after biliary fenestration

Fasting duodenal aspirates were studied in 15 patients with a biliary fenestration, 5 patients with a single duodenal diverticulum, 1 patient with a biliary fenestration and duodenal diverticulum, and 11 control subjects. A colonic type of bacterial flora, consisting of coliforms, Clostridium welchii, and Streptococcus faecalis, was found in 10 patients with biliary fenestration, 4 patients with a duodenal diverticulum, the patient with a fenestration and duodenal diverticulum, and in 1 of the control subjects. A high incidence of deconjugation of biles salts (10 out of 15 patients) and of steatorrhoea (8 out of 15 patients) was noted in the patients with biliary fenestration, as well as in those with a duodenal diverticulum (5 and 3 patients out of 5 respectively). Above-normal serum-folate levels were observed in 3 subjects with coliform colonization.

It is possible that vague abdominal symptoms which may be experienced by patients after biliary fenestration, may be due to the presence of an abnormal bacterial flora in the duodenum.

Fecal microflora in health persons in a preindustrial region

Procedures for quantitating the fecal microflora of man were described. Special attention was given to criteria for characterizing the culturable aerobic, Micro-aerophilic, and anaerobic bacteria. Three groups of healthy persons were studied: wholly breast-fed infants (2 to 4 month-olds), weanlings (1 to 2 year-olds), and adults. In breast-fed children, bifidobacteria predominate and outnumber by one or several logs all other culturable bacteria. The fecal flora of wholly breast-fed infants is "simpler" and more numerous [10(11) to 10(12) per g (wet weight) of feces than that of the adult 10(2) to 10(11) per g]. In the adult, gram-negative anaerobic bacilli (bacteroides) outnumber all other groups by a factor of 1 log or more. Weanlings receiving an adult-type diet, but still breast-fed, showed a flora intermediate between that of the wholly breast-fed infant and that of the adult, but more similar to the latter. Anaerobes always constitute the predominant component of the culturable flora of children and adults and are always found in large numbers under conditions of health. The aerobes are significantly less numerous, and vary widely in their number and in the frequency with which they appear in feces.

Partial biliary obstruction with cholangitis producing a blind loop syndrome

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