ORIGINAL ARTICLE Mucosally associated bacterial flora of the human colon: quantitative and species specific differences between normal and inflamed colonic biopsies Shri Pathmakanthan1, John P. Thornley2 and Chris J. Hawkey1 From the1Department of Gastroenterologyand2Microbiology, University Hospital, Queens Medical Centre, Nottingham NG7 2UH, UK Correspondence to: ShriPathmakanthan, Department of Gastroenterology, University Hospital Queens Medical Centre, Nottingham NG7 2UH, UK. Tel: +44 0115 9249924; Fax: + 44 0115 9422232; e-mail: [email protected] Microbial Ecology in Health and Disease 1999; 11: 169–174 This study quantified and characterised changes to a species level for aerobic and anaerobic bacteria from colonic biopsies of acute ulcerative colitis (UC) comparing them with that of a normal control group. Fresh endoscopic biopsies of the recto – sigmoid region were obtained during flexible sigmoidoscopy from 10 patients suffering an acute attack of UC and a similar number of healthy controls. Quantitative estimation was carried out on selective media for total aerobic, anaerobic, Bacteroides, Bifidobacterium and Lactobacillus spp. (Miles – Misra). Species identification involved gram stain, indole, catalase tests and commercially validated anaerobic, gram-positive and non-enteric fermenting enzyme hydrolysis kits There was a significant quantitative decrease in growth of Lactobacillus spp. in colitic biopsies (p B0.05). Total aerobic speciation revealed 32 different sub-species with 18 of these found only in UC biopsies. Anaerobic speciation revealed 41 different sub-species with a mean 6.7 species in normal and 4.7 in UC patients. Bacteroides thetaiotaomicron was isolated in significantly increased frequency in UC biopsies (8/10) in comparison with normal (4/10). Our data are consistent with the possibility that a reduction in mucosally associated Lactobacillus bacteria in UC permits proliferation of a large number of potentially pathogenic aerobic species and anaerobic predominance of B. thetaiotaomicron. Key words: ulcerative colitis, intestinal flora, Lactobacillus, B. thetaiotaomicron. INTRODUCTION The human colon is the largest ‘microbial organ’ in the body whose primary functions involve the dessication and storage of faeces and water and electrolyte absorption. Recently, great interest has been expressed in the roles played by colonic bacteria in health and disease (1). This is also of growing relevance to idiopathic inflammatory bowel disease, e.g. ulcerative colitis (UC). This is a relapsing and remitting condition of unknown aetiology characterised by extensive and inappropriate inflammation of the colonic mucosa. It is now recognised that commensal colonic bacterial flora not only play important roles in nutrition, metabolic and immune functions, but that their luminal or mucosally associated position may be influential to these functions (2). The interaction between colonic mucosally associated bacteria and the mucus barrier serve to limit the presence and binding of exogenous pathogenic bacteria to the colonic epithelium. It is these bacteria found within and below the mucus layer coating the colonic epithelial cell layer and in the immediate vicinity of the mucosa that are functionally relevant and the probable source of antigenic © Scandinavian University Press 1999. ISSN 0891-060X challenge in UC. Much work in this area has involved the faecal luminal flora, as this material is readily available without need for any invasive procedure. Studies have now demonstrated that differences exist between luminal bacteria and bacterial populations intimately associated with the mucosal surface (3). These studies have quantified the numbers and genera of bacteria present, but few identify these bacteria to species level (4). These studies have also been used to investigate the colonic flora with regard to pharmacological regimens (5). To date, investigations into the colonic bacterial flora in disease have been undertaken with respect to Crohn’s disease (6), cancer and polyp tissue (7) and UC (8). All these studies with the exception of the UC investigations by Poxton et al. and Hartley et al. showed few bacterial flora changes from normal. The UC study undertaken by Hartley et al. (8) showed alterations in the mucosally associated flora at genus level but fell short of speciating these differences or including a ‘normal’ control group. The recent investigations by Poxton et al. (3) which included a control group, concentrated upon alterations within the genus Bacteroides at species level. This study Microbial Ecology in Health and Disease 170 S. Pathmakanthan et al. showed changes in mucosally associated Bacteroides species. It is with these considerations in mind that we chose to specifically examine mucosally associated bacterial flora in acute relapse UC by unprepared flexible sigmoidoscopy. We aimed to quantify and characterise changes to species level for all aerobic species present and a random selection of anaerobic flora and to compare these findings with that of a normal control group. obe Agar supplemented with 4% horse blood and 1% freeze-thaw lysed horse blood for total anaerobic counts (FAA); FAA supplemented with kanamycin 75 mg/ml and vancomycin 2.5 mg/ml (FAAKV) for Bacteroides spp; Rogosa agar (Unipath) for Lactobacillus spp. (RA); Reinforced Clostridial Cotton Blue Agar (RCCBA) for Bifidobacterium. MATERIALS AND METHODS Quantification of both aerobic and anaerobic bacteria employed the Miles – Misra method (9). After complete homogenisation of biopsy, 0.5 ml of the homogenate was transferred to 4.5 ml of brain heart infusion and subsequent preparation of 10-fold dilutions (10 − 1 –10 − 8 cfu/ ml) prepared from this concentration. From each concentration, three separate 5 ml spot volumes were seeded on to the appropriate culture plates for the genus under investigation. These plates were then incubated in the appropriate conditions and colonies counted from 5 ml spots of smallest dilution at 48 and 72 h for aerobic and anaerobic cultures, respectively. Processing of biopsy material Endoscopic biopsies were obtained from patients in whom flexible sigmoidoscopy was being performed in the course of routine clinical care (n=20). Full written consent was obtained from patients and permission for obtaining colonic biopsies was obtained from the hospital ethics committee. Normal controls were obtained from patients undergoing flexible sigmoidoscopy for investigation of haematochezia and familial screening for rectal carcinoma (n= 10). The control group was age and sex matched with the colitic cohort (6 male, 4 female age 18–52 years). Neither control group nor patients with UC had consumed any antibiotic preparation 3 weeks prior to investigation. Flexible sigmoidoscopy allowed examination and biopsy of an unprepared colon without the need for a colonic lavage or enema. This was important as earlier in 6itro experiments in our laboratory had shown an inhibition of bacterial mucosally associated flora in the presence of Picolax (Ferring Pharmaceuticals, Middlesex) but not Klean Prep or Fleet lavage preparations All biopsies were obtained from the recto–sigmoid junction with forceps sterilised in gluteraldehyde (Cidex, Johnson and Johnson, Skipton, Yorkshire) which were rinsed in sterile saline prior to use. Biopsies were gently washed in sterile saline to remove adherent faecal material and immediately transferred with a sterile needle to pre-weighed vials containing 5 ml brain heart infusion broth and 10% glycerol transport medium. This vial was immediately snap-frozen in liquid nitrogen. All bacterial analysis was carried out within 1 week of storage. A representative sample from adjacent mucosa was fixed in formalin for routine histopathology. Frozen vials were transported to an anaerobic cabinet (37°C, N2 80%, H2 10%, CO2 10%) where they were allowed to thaw. Biopsy sample and transport medium (5 ml) were transferred into a ‘Stomacher’ sterile sampling bag (Fischer Scientific, Loughborough, Leicester) and broken up manually. The biopsy homogenate and medium was then pipetted to ensure complete homogenisation. Media The following media were used: Columbia Agar (Unipath) supplemented with 5% horse blood for total counts of aerobic and facultative organisms (BA); Fastidious Anaer- Quantification studies Speciation studies For anaerobic speciation studies, 10 ml of biopsy homogenate was transferred and spread on to BA using a firm 10 ml loop. Following 72 h of anaerobic incubation at 37°C, up to 16 colonies were chosen at random and subsequently re-plated anaerobically and aerobically (to exclude facultative anerobic growth e.g. E. coli ) for single colonies. These were once again anaerobically incubated for 48 h at 37°C and examined for purity. Of these 16 colonies, those successfully replated and purified were subjected to enzyme hydrolysis kits for final identification. Bacterial colonies which demonstrated aerobic growth (all facultative anaerobic E. coli ) were subsequently speciated and analysed aerobically. For aerobic speciation, a similar 10 ml amount from original biopsy homogenate was transferred and spread on to BA for colony identification. Following 48 h of culture in an aerobic incubator, all colonies were subsequently replated and purified. This was possible as much lower numbers of aerobic colonies were found relative to anaerobic growth from both normal and inflamed mucosa allowing complete identification of all colonies to species level. All colonies undergoing species identification underwent gram stain, tests for indole production, catalase activity and oxidase reactions. All colonies were also cross plated in aerobic and anaerobic environments to test for facultative growth. Following replating and purification, anaerobic and aerobic colonies were identified with a commercially validated technology using Anaerobic, Gram-Positive and Non-enteric fermenting enzyme hydrolysis kits (Becton-Dickinson, Identification Systems). Briefly, this methodology consisted of 29 dried biochemical and enzymatic substrates. A pure Mucosally associated bacteria bacterial suspension approximating McFarland standard No 4 was made in the supplied inoculum fluid. These tests were based on microbial utilisation and degradation of specific substrates detected by indicator systems. Enzymatic hydrolysis of fluorogenic substrates containing coumarin derivatives of 4-methylumbelliferone or 7-amino-4-methylcoumarin resulted in increased fluorescence that was detected with a UV light source (10). Chromogenic substrates upon hydrolysis produced colour changes that were detected visually with a standard light source. These ID systems detected the ability of an organism to hydrolyse, degrade, reduce or otherwise utilise a number of substrates with pre-formed enzymes. All reaction results were scored as per the manufacturer’s instruction and entered into a computer database for species identification. All organism identification included recent name changes and was based on Bergey’s manual of determinative bacteriology (9th ed. Williams and Wilkins, Baltimore). 171 Table II Aerobic species that were isolated from both normal and UC samples Bacteria % Isolates in normals % Isolates in UC Escherichia coli Micrococcus spp. Klebsiella oxytoca Gardenella 6aginalis Pantea agglomerans Lactococcus raffinolactis Staphylococcus spp. Stenotrophomonas spp. Bacillus spp. Rothia dentocariosa Acinetobacter Fla6imonas oryzihabitans 38 19 7.1 7.1 4.8 4.8 37.5 1.1 1.1 2.3 0 1.1 4.8 4.8 4.5 0 2.4 2.4 2.4 2.4 1.1 0 6.8 2.3 Statistical analysis Statistics was carried out on SPSS software. For quantitative studies, logged data was analysed using the non paired t-test and the Mann Whitney U Test was used on unlogged data. In speciation studies, The x 2-test was used to compare frequency of isolates between normal and inflamed biopsies. RESULTS Quantification studies Total viable counts of aerobic and anaerobic bacteria isolated from normal and inflamed biopsies are shown in Table I. Average biopsy weight was 5.5 mg. No significant differences were detected between total aerobic and anaerobic counts from normal patients (N) and those with UC. Facultative anaerobes were included in both counts. From 20 biopsy samples, (10 N samples and 10 active UC), Table I Bacteroides spp. predominated in the flora of both N and UC patients (mean: 7.4 × 108 cfu/g and 1.5× 108 cfu/g, respectively). Bacteroides spp. comprised 46 and 42% of the total anaerobic counts from N and UC biopsies, respectively. Bifidobacterium was isolated in all biopsies (mean values, N: 5.3 ×108 cfu/g; UC: 5.6 ×107 cfu/g). Growth on Lactobacillus selective agar (N = 4.8× 108, UC = 1.1× 106) revealed significantly less growth from UC biopsies in comparison to Ns. Speciation studies Every aerobic isolate identified was speciated from N and UC biopsies. This totalled 130 (42 normal, 88 colitic) isolates yielding 32 different sub-species (Table II) Eighteen of these 32 sub-species were found only on UC biopsies (Tables II and III). E. coli was the commonest isolate grown aerobically being present in large amounts in both N and UC patients. Comparison of quantitati6e counts in selecti6e media between normal and UC (cfu/g) Media Biopsy Mean SD p-Value Total anaerobes N UC N UC N UC N UC N UC 1.6×109 3.6×108 7.4×108 1.5×108 5.3×108 5.6×107 4.8×108 1.1×106 6.4×107 2.6×107 92×109 95.1×108 99.6×108 92.1×108 91.5×109 97×107 91×108 92.4×106 96.4×107 92.6×106 ns ns ns ns ns ns ns pB0.05 ns ns Bacteroides Bifidobacterium Lactobacillus Total aerobes N, normal, UC, ulcerative colitis. SD, standard deviation. Table III Percentage of aerobic isolates found only in UC samples Aerobic bacteria only isolated in UC biopsies % Isolated in UC Streptococcus spp. Sphingomonas paucimobilis Corynebacterium spp. Chromobacter 6iolaceum Pseudomonas spp. Corynebacterium aquaticum Oersko6ia spp. Enterococcus faecium Enterobacter agglomerans 8 6.8 5.7 4.5 3.4 3.4 3.4 2.3 2.3 172 S. Pathmakanthan et al. DISCUSSION Table IV Percentage of Bacteroides isolates; UC 6s normal % Isolates in normals % Isolates in UC Total Bacteroides B. 6ulgatus B. splanchnicus B. uniformis B. o6atus B. distasonis B. thetaiotaomicron B. fragilis B. ureolyticus B. gracilis B. capillosus B. caccae B. praecutus 55.7 31.3 15.6 * 14.1 * 9.4 9.4 7.8 57.7 39.3 1.8 1.8 8.9 5.4 32.1 ** 4.7 3.1 3.1 1.6 0 0 1.8 1.8 0 1.8 3.6 1.8 ** pB0.01, * pB0.05. In anaerobic speciation, from the 20 biopsy samples (10 N, 10 UC), 212 isolates (115 N, 97 UC) were successfully purified and identified to represent 41 different sub-species (Tables IV and V). For any individual patient there was a mean 6.7 different anaerobic species in N and 4.7 in UC samples. The principle species were Bacteroides, which were present in every biopsy (Table IV). For any individual patient only a few species of Bacteroides (mean: N = 3.1, UC =2.4; range: N = 1–5, UC =1–4) were isolated. Bacteroides thetaiotaomicron and 6ulgatus were the highest total number of anaerobic isolates identified. B. 6ulgatus was isolated in near equal frequency from normal and inflamed mucosa isolated in 8/10 N patients and 6/10 UC patients. B. thetaiotaomicron was isolated from 8/10 biopsy samples of UC patients with active inflammation but in only 4/10 of N biopsies. Table V Percentage isolation of other anaerobic bacteria cultured from normal and UC biopsies (no significant differences) Anaerobic bacteria Frequency in normal Frequency in UC (%) (%) Bifidobacterium spp. Clostridium spp. Actinomyces spp. Lactobacillus spp. Peptococcus spp. Eubacterium spp. Pre6otella spp. Fusobacterium spp. Mobiluncus spp. Propinibacterium spp. Tissierella spp. 13 7.2 9.6 6.1 5.2 4.3 1.7 1.7 0.9 5.2 4.1 8.2 3.1 0 1 3.1 0.9 0.9 5.2 2.1 0.9 1 The mucosa of the gastrointestinal tract separates 1013 eukaryotic cells from 1014 bacteria with 96 – 99% of this resident bacterial flora consisting of anaerobes and 1 –4% facultative aerobes (gram negative Coliform bacteria, Enterococci, and Proteus, Pseudomonas, Lactobacilli, Candida and other organisms). The predominant cultivable bacteria belong to the genus Bacteroides which accounts for 20 – 30% of the species isolated. This genus constitutes B. fragilis, B. distasonis, B. o6atus, B. thetaiotaomicron, B. 6ulgatus, B. eggerthii, B. uniformis, B. caccae, B. merdae and B. stercoris. B. 6ulgatus is considered the commonest species in this genus and although B. fragilis is less common it is the most prevalent in clinical specimens of blood cultures and wounds (11). Many of the bacteria in the GI tract especially the gram negative rods are opportunist pathogens capable of eliciting injurious, pro-inflammatory responses on interaction with the systemic immune system. It is therefore important to know which species in quality and number are in the most intimate association with the mucosa. UC is a disease where genetic and environmental factors interrelate to induce chronic spontaneously relapsing intestinal inflammation. The clinical features of UC in relapse are similar to those of dysentery and other infectious colitides with luminal bacteria being a pre-requisite for disease development (12). Bacteria are a prerequisite for the development of UC in a susceptible individual and this source of antigen is likely to originate within the mucus sheet adhering to the colonic epithelial cell. This mucus sheet is abnormal in colitics and has been shown to express receptors not usually exposed leading to the potential cultivation of certain potentially pathogenic organisms (13). We avoided the use of any colonic preparation prior to biopsy sampling as preparation for colonoscopy in the form of purgatives, laxatives, anti-microbial agents and enemas has the potential to influence the colonic flora. This was confirmed by earlier in 6itro experiments in our laboratory showing an inhibition of bacterial growth with certain preparations. An earlier study by Poxton et al. had shown that mucosally associated flora of the rectum and the proximal colon are similar indicating that information may be obtained from rectal or sigmoid biopsy samples within range of a flexible or rigid sigmoidoscope (8). The recto – sigmoid junction was especially chosen to avoid any effect rectal steroid or aminosalicylate preparations might have on the rectal mucosa. During flexible sigmoidoscopy it was noted that rectal sparing was observed in some patients who were on steroid enema preparations which may have influenced the quality and quantity of the mucosal flora in biopsies if they were obtained from the rectum. Mucosally associated bacteria All UC patients in this study were also on various preparations of maintenance sulphasalazine. An earlier study involving this drug has concluded that it has little effect on the bacteria colonising the colorectal mucosa (5). The first part of this paper set out to determine quantitative differences between normal and colitic patients. The significantly low numbers of Lactobaccillus in inflamed UC biopsies is an important finding. The reduction in numbers of this particular genus has been reported previously both in an animal model and in biopsy samples of patients with UC (14, 15). Lactic acid bacteria constitute an integral part of the healthy gastrointestinal micro-ecology and are involved in host metabolism with nutritional and therapeutic benefits (16). Their beneficial influence in gastrointestinal disorders and the recent isolation of a broad spectrum anti-microbial substance from some Lactobacilli species demonstrate their protective and stabilising actions in the gastrointestinal tract (17, 18). These quantitative studies also revealed a significant aerobic population resident in mucosally associated flora with aerobic:anerobic ratios of 0.07 and 0.04 in N and UC biopsies, respectively. These ratios are much higher than would be found in faecal samples indicating that aerobic bacteria may have a greater role to play in the homeostasis of this environmental niche. It is important to emphasise that all aerobic growth of biopsies from N and UC biopsies were speciated. These data illustrate a clear increase in range of aerobic organisms found in UC. Although it is not possible to interpret this as a primary or secondary effect, it does illustrate an increase in potentially pathogenic organisms which probably play at least a perpetuating role in the disease process. The sixteen anaerobic isolates from each biopsy sample for speciation were a random representation of the total number of isolates grown. We chose to cultivate anaerobic isolates on non selective blood agar to enable a cross sectional representation of anaerobic flora to be sampled for speciation. Despite the large number of species present in the colon with the potential to colonise the mucosally associated environment, there is clear predominance of Bacteroides spp. mainly 6ulgatus and thetaiotaomicron in N and UC biopsies. Interestingly, B. thetaiotaomicron was more commonly found in acute UC biopsies perhaps indicating that this organism may have a role to play in disease pathogenesis. Similar findings were found in a recent investigation by Poxton et al. (3). It is tempting to speculate that a lack of lactobacillus found in UC biopsies shown in the first set of quantitative data may allow a combination of B. thetaiotaomicron and potentially pathogenic aerobic species to alter the characteristics of the bacterial environment adjacent to the mucosa towards one of an increasingly pro-inflammatory nature. 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