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PubMed1986

Influence of light and natural microbiota of the Butrón river on E. coli survival.

The survival of an E. coli strain in water samples from the Butrón river has been studied. The input of E. coli cells in the aquatic system breaks down the established balance among the components of the natural microbiota: E. coli becomes the object of the active protozoal predation whereas the autochtonous heterotrophic community become alternative preys. As a result of this new situation, the natural microbiota increases but returns to the initial values once the E. coli cells have been removed from the system. The effect of the temperature of incubation on the survival is exerted through the effect of this parameter on the predatory activity of the protozoa. Light has a lethal and direct action on the E. coli cells, the effect of this parameter is even superior to that of predation.

Animals↗
PubMed1982

Effects of oil and gas well-drilling fluids on the biomass and community structure of microbiota that colonize sands in running seawater.

Well-drilling fluid and a number of the known components (barite, clay, Aldacide, Surflo, and Dowicide, were tested for effects on the biomass and community structure of the microbiota that colonize marine sands exposed for eight weeks to running ambient seawater. Shading the microbiota from light depressed the microflora without a significant effect on the biomass, while well-drilling fluids layered on the surface or mixed with the sand significantly increased a component of the bacteria and the microfauna as reflected in changes in the fatty acid composition. There were some shading effects from the surface layering of well-drilling fluids as reflected in the fatty acids from the microflora when compared to the sands mixed with well-drilling fluids. Barite had essentially no effect on the biomass or community structure while clays increased nearly all of the biomass indicators for the bacteria as well as the microfauna; the clay overlay mirrors the effect of the drilling fluids. Aldacide shifted the bacterial composition, depressing the proportions of microbes containing the cyclopropane fatty acids and the anaerobic pathways of desaturation. Concentrations of 1 and 15 microgram/L increased the bacterial biomass as reflected in the total lipid (16:0) and extractable lipid phosphate coupled with a decrease in the total microeukaryotes. Surflo increased the biomass and shifted the bacterial community structure at concentrations between 4 and 800 microgram/L. The lowest level also stimulated the microfauna. Dowicide at 100 microgram/L increased the bacteria forming cis-vaccenic acid and the microfauna similar to low concentrations of Surflo.

Fatty Acids↗
PubMed2006

Comparison of antagonistic ability against enteropathogens by G+ and G- anaerobic dominant components of human fecal microbiota.

To confirm if anaerobic G+-components are those responsible for the function of colonization resistance, obligate anaerobic G+- and G- -bacteria from normal dominant microbiota of human feces were isolated from three successive collections and then used in in vitro assays for antagonism against two enteropathogenic bacteria. The production of inhibitory diffusible compounds was determined on supplemented BHI agar and MRS agar media for G- - and G+-bacteria, respectively. Salmonella enterica subsp. enterica serovar Typhimurium and Shigella sonnei were used as indicators. G+-bacteria presented a higher overall antagonistic frequency against both pathogenic bacteria (57 and 64 % for S. enterica serovar Typhimurium and S. sonnei, respectively) when compared to G+-microorganisms but with a quite elevated variation between volunteers (0-100 %) and collection samples (40-72 and 40-80 % for S. enterica sv. Typhimurium and S. sonnei, respectively). On the other hand, only three among 143 G- -isolates tested showed antagonistic activity. The results showed that, at least in vitro, obligate anaerobic G+-components of the dominant human fecal microbiota present a higher potential for antagonism against the enteropathogenic models tested than do G- -bacteria.

Adult↗
PubMed2002

Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis).

To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.

Animals↗
PubMed2005

Using phospholipid fatty acid technique to study short-term effects of the biological control agent Pseudomonas fluorescens DR54 on the microbial microbiota in barley rhizosphere.

The biological control agent (BCA) Pseudomonas fluorescens DR54 was applied to seeds (experiment 1) or roots (experiment 2) of barley growing in microcosms, while noninoculated plants served as controls. The fate of the BCA and its effects on the rhizosphere microbial community was evaluated in microcosms destructively sampled at days 2, 4, 6, and 9 after inoculation. In both experiments the number of P. fluorescens DR54 cells decreased immediately after application as enumerated by immunostaining and microscope direct counting. Substrate-induced respiration (SIR) was taken as a measurement of the active microbial biomass, while indicators of the total microbiota (and main taxonomic groups) were obtained using the phospholipid fatty acid (PLFA) technique. In experiment 1, these parameters were unaffected by the relatively small number of BCA cells applied, whereas in experiment 2, the larger BCA input resulted in an enhanced level of both SIR and PLFAs from Gram-negative bacteria (which included the BCA itself). However, at day 9 after inoculation, treatments with P. fluorescens DR54 and controls were similar in all measured parameters in both experiments. This was also illustrated very clearly by principal component analysis of the PLFA data, which in both experiments were able to discriminate between treatments in the first days after BCA inoculation, thus confirming the sensitivity of this method. Laccase activity has a potential as an indicator of fungal stress, e.g., when challenged with an antifungal BCA. This seemed to be supported in experiment 2, where the activity of this enzyme was enhanced four-fold in the BCA treatment at day 2. Our study shows that under the present conditions, P. fluorescens DR54 disappears from the soil and causes only transient effects on the soil microbiota. It also shows that the PLFA technique is a sensitive and reliable monitoring tool in in situ assessment of BCA nontarget effect on indigenous microorganisms in soil.

Fatty Acids↗
PubMed2005

Suitability of a batch in vitro fermentation model using human faecal microbiota for prediction of conversion of flaxseed lignans to enterolactone with reference to an in vivo rat model.

BACKGROUND: In vitro fermentation models have been used widely for studies of shortchain fatty acid (SCFA) formation from carbohydrates, whereas the suitability of these methods for enterolactone (ENL) formation has received less attention. AIM: The aim was to study the suitability of an in vitro fermentation model for prediction of bioconversion of lignans to ENL, to compare the approach with that of an in vivo rat model and to study the SCFA formation in both models. METHODS: Predigested samples of rye bran (R), flaxseed meal (F) alone, or in combination with rye bran (R&F) and a faecal control were incubated in an in vitro fermentation model using human faecal microbiota. In the in vivo experiment rats consumed a non-fibre control diet (C) or diets supplemented either with rye bran (R), flaxseed meal (F) alone, or with their combination (R&F) for four weeks. Enterodiol (END), ENL and SCFA concentrations were measured from in vitro faecal fermentation samples and from the intestinal contents of rats. Plasma ENL concentrations from rats were also measured. RESULTS: The highest ENL production was found in vitro with the F supplement (areas under curve: 740 +/- 4, 7,500 +/- 400, 2,600 +/- 500 and 1,520 +/- 70 nmol x h for the R, F, R&F supplements and faecal control, respectively). In vivo, the concentration of ENL in caecal digesta from flaxseed meal was significantly (P < 0.05) enhanced by the presence of rye bran (medians 261, 407 and 24 nmol/g in the F, R&F and C groups, respectively). No correlation was found between the models regarding ENL production, possibly due to different responses to the presence of rye bran matrix, differences in microbiota or application of a batch in the in vitro fermentation model. Rye bran supplementation enhanced butyrate production both in vitro and in vivo. CONCLUSION: In vitro fermentation and the in vivo rat models responded differently to the presence of rye bran and no correlation with regard to the ENL formation from flaxseed lignans was observed.

4-Butyrolactone↗
PubMed2002

Vaginal microbiota in healthy pregnant women and prenatal screening of group B streptococci (GBS).

The microbiota of the lower female genital tract was evaluated from vaginal swabs obtained from 623 healthy pregnant women at gestation periods of 35-40 weeks. Isolated and identified microorganisms were expressed as percentages of total samples. As expected, lactobacilli made up the dominant vaginal microbiota (70%). Enterobacteriaceae, mainly Escherichia coli, Klebsiella spp. and Proteus, were present in 38% of the samples, which might reflect the possible contamination of vaginal tract with rectal microorganisms. Candida albicans was present in 10% of healthy pregnant woman assayed. Streptoccocci (Streptococcus sp. and Enterococcus faecalis with 3% and 4%, respectively) and other gram-positive cocci (Staphylococcus sp., 5%), along with other microorgansisms such as Gardnerella vaginalis (5%) and Pseudomonas aeruginosa (2%) may represent a potential infection risk. Streptococcus agalactiae (group B streptococci beta-hemolytic, GBS) was detected in 7% of the samples. GBS infection is a leading cause of neonatal morbidity and mortality in the developed world. Furthermore, GBS was often co-isolated with C. albicans (54.5%) in the samples. A complete and detailed evaluation of the vaginal biota swab, with particular attention to the presence of potential pathogens such as GBS, is a preventive strategy that can provide useful information to obstetricians and gynecologist in managing the last days of pregnancy and delivery.

Adult↗
PubMed1989

Effect of ampicillin-induced alterations in murine intestinal microbiota on the survival and competition of environmentally released pseudomonads.

The environmental release of genetically altered microorganisms has prompted the investigation of their potential health effects by the employment of other-than-human models. Although direct health effects are addressed, this investigation examines primarily some potential indirect health effects associated with environmentally released microorganisms. Indirect effects examined include colonization of the gastrointestinal tract, competition with the resident microbiota, and translocation of the dosed microorganisms to other organs. Pseudomonads used in this study were isolated from a commercial product marketed for environmental PCB degradation. When mice were dosed by gavage with approximately 10(9) ampicillin-resistant pseudomonads, an increase in recovery from the intestinal tract, as compared to untreated animals, was observed 48 hr after dosing. Intestinal survival of Pseudomonas aeruginosa strain BC16 was enhanced 1000-fold and that of P. maltophilia strain BC6, 10-fold. Strains BC17 and BC18 were unaffected. Ampicillin treatment had a significant effect on the relative number of microbiota in the intestine, by selecting primarily for the facultative species. The lactose-fermenting enterobacteria, obligately anaerobic predominantly Gram-negative rods, and total aerobic and anaerobic populations were monitored in the presence and absence of the PCB-degrading pseudomonad. P. aeruginosa strain BC17 and P. maltophilia strain BC6 had a dose effect (p less than 0.05) on the total aerobic and anaerobic populations as well as the lactose-fermenting enterobacteria. These results are similar to those for the mouse isolate control, strain PAMG. P. aeruginosa strain BC18 had a dose effect (p less than 0.05) on the total anaerobic population, including the obligately anaerobic Gram-negative bacilli. No translocation of the dosed strains to the liver, spleen, or lung was observed 48 hr after dosing.

Ampicillin↗
PubMed2004

Antimicrobial susceptibilities of Bacteroides fragilis and Bacteroides thetaiotaomicron strains isolated from clinical specimens and human intestinal microbiota.

Species of Bacteroides fragilis group bacteria are the most prevalent pathogens and have the highest resistance rates to antimicrobial agents among anaerobic bacteria. Infections due to these micro-organisms often originate from patient's own intestinal microbiota. The objective of the study was to determine and compare the susceptibility profiles of clinical and intestinal B. fragilis and B. thetaiotaomicron strains against certain antimicrobials. Isolates were identified by conventional methods and API-20 A. Susceptibility tests were performed according to recommendations of NCCLS (M 11-A4) agar dilution methods. Beta-lactamase production was determined with nitrocefin discs. Forty-five clinical isolates (33 B. fragilis and 12 B. thetaiotaomicron) were from following sites: blood (n:8), intra-abdominal abscess (n:7), soft tissue (n:26), and miscellaneous foci of infection (n:4). Fifty B. fragilis and 60 B. thetaiotaomicron isolates from intestinal microbiota of individuals with no history of antimicrobial treatment within last 30 days were also examined. Beta-lactamase production was detected in 93% of clinical and 99% of intestinal isolates. The organisms including intestinal isolates were uniformly susceptible to metronidazole. The MIC90s of other antibiotics and resistance rates of all clinical isolates to those antibiotics were as follows: 256 microg/mL (93%) for ampicillin, 128 microg/mL (13%) for piperacillin, 64 microg/mL (11%) for cefoxitin, 1 microg/mL (2%) for amoxicillin-clavulanate, 0.5 microg/mL (2%) for imipenem, >256 microg/mL (36%) for clindamycin, 8 microg/mL (2%) for chloramphenicol. Intestinal isolates demonstrated similar resistance rates and MIC90s. Metronidazole, imipenem, amoxicillin-clavulanate seem to be effective drugs against these bacteria in Turkey.

Journal Article↗
PubMed2006

Intestinal microbiota and its effect on the immune system--a nested case-cohort study on prevention of atopy among small children in Trondheim: the IMPACT study.

BACKGROUND: In the past 20-30 years, the prevalence of atopic diseases, particularly among children in the Western world, has increased. It has been suggested that Western lifestyle may have reduced the overall exposure to microbial stimulation early in life. The role of the gut flora in this connection has been studied, but prospective studies are in demand. Within the frame of a comprehensive controlled prospective primary prevention study of atopy and allergic diseases with the aim to reduce the incidence of atopy and allergic diseases among children from birth to six years, a nested case-cohort study is established, "The IMPACT study". AIM: The aim of "The IMPACT study" is to study the impact of gut microbiota composition on cytokine profile development, and on development of atopic disease. DESIGN: Information on risk factors and on disease, together with biological specimens, will be collected prospectively, and analysed in a nested case-cohort design. METHOD: 720 pregnant women are recruited from the control-cohort in the PACT study. The composition of the infant gut microbiota is analysed in stool samples from all children with atopic disease, and randomly selected children sensitized and not sensitized at age 2, at 4, 7, 10 days after birth, and at age 4, 12 and 24 months. 16S rDNA hybridisation technique will be used to specify and quantify the microbial composition in faeces. Cord blood from the same children and venous blood at age 10 days, 4, 12 and 24 months are collected to study the cytokine profile at different ages, in relation to microbial stimulation. Peripheral blood mononuclear cells (PBMC) are stored in liquid nitrogen, and faeces are stored at -80 degrees C. Atopic children will be identified by questionnaire, and the diagnosis confirmed by paediatric examination at age 2 years.

Bifidobacterium↗
PubMed2006

Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection.

The gut microbiotas of zebrafish and mice share six bacterial divisions, although the specific bacteria within these divisions differ. To test how factors specific to host gut habitat shape microbial community structure, we performed reciprocal transplantations of these microbiotas into germ-free zebrafish and mouse recipients. The results reveal that communities are assembled in predictable ways. The transplanted community resembles its community of origin in terms of the lineages present, but the relative abundance of the lineages changes to resemble the normal gut microbial community composition of the recipient host. Thus, differences in community structure between zebrafish and mice arise in part from distinct selective pressures imposed within the gut habitat of each host. Nonetheless, vertebrate responses to microbial colonization of the gut are ancient: Functional genomic studies disclosed shared host responses to their compositionally distinct microbial communities and distinct microbial species that elicit conserved responses.

Animals↗
PubMed2006

Love the one you're with: vertebrate guts shape their microbiota.

Using germ-free animals, Rawls et al. (2006) reveal that the gut of a given host can be colonized by the microbiota of another vertebrate. Remarkably, the recipient host then shapes the composition of the non-native microbiota to more closely resemble that of its native consortium.

Animals↗
PubMed2005

Commensal microbiota alter the abundance and TCR responsiveness of splenic naïve CD4+ T lymphocytes.

The epidemiologic risk of certain systemic immunologic diseases is affected by commensal or environmental microbiota, but the cellular basis of the "hygiene hypothesis" is poorly understood. In this study, we demonstrate that composition of the commensal microbiota affects the functional state of the peripheral naïve (CD62L(hi)CD44(lo)) T lymphocyte populations. Restricted flora (RF) mice (stably colonized with excess nonpathogenic Clostridium sp., and changes in other bacterial and fungal taxa) were distinguished after the neonatal period by a progressive deficiency in absolute numbers of naïve CD4+ and CD8+ T lymphocytes. SPF and RF mice had comparable levels of memory CD4+ and CD8+ T cells. This phenotype was attributable to the altered levels of certain commensals and their products, since germ-free mice had normal absolute numbers of splenic CD4+ and CD8+ T cells and their respective naïve and memory subsets. The naïve CD4+ T cell subset was functionally distinguished in RF mice versus SPF mice by TCR hyperresponsiveness, pro-inflammatory cytokine production, and increased activation-induced cell death. Biochemically, these traits were associated with higher basal phosphorylation of the TCR signaling proteins ZAP-70, Lck, and LAT. These findings indicate that enteric microbial products, through unknown cellular circuitry, influence steps in CD4 T cell differentiation moderating basal TCR signaling and immune responsiveness.

Animals↗
PubMed2005

Trypanosoma cruzi: influence of predominant bacteria from indigenous digestive microbiota on experimental infection in mice.

To verify the influence of some predominant components from indigenous microbiota on systemic immunological responses during experimental Chagas disease, germ-free NIH Swiss mice were mono-associated with Escherichia coli, Enterococcus faecalis, Bacteroides vulgatus or Peptostreptococcus sp. and then infected with the Y strain of Trypanosoma cruzi. All the mono-associations predominantly induced a Th1 type of specific immune response to the infection by T. cruzi. A direct correlation was observed between a higher survival rate and increased IFN-gamma and TNF-alpha production (P<0.05) in E. faecalis-, B. vulgatus-, and Peptostreptococcus-associated mice. Moreover, higher levels of anti-T. cruzi IgG1 and anti-T. cruzi IgG2a were also found in mono-associated animals after infection. On the other hand, with the exception of E. faecalis-associated mice, mono-association induced a lower IL-10 production after infection (P<0.05) when compared with germ-free animals. Interestingly, spleen cell cultures from non-infected germ-free and mono-associated mice spontaneously produced higher levels (P<0.05) of IL-10 than cultures from infected mono-associated mice, except again for E. faecalis-associated animals. In conclusion, the presence of the components of the indigenous microbiota skews the immune response towards production of inflammatory cytokines during experimental infection with T. cruzi in gnotobiotic mice. However, the degree of increase in production of cytokines depends on each bacterial component.

Animals↗
PubMed2005

Modulation of the fecal microbiota by the intake of a Lactobacillus johnsonii La1-containing product in human volunteers.

Lactobacillus johnsonii La1 (La1) is a probiotic strain capable of stimulating the immune system of the host and interfering with gastrointestinal pathogens. This study evaluates how the ingestion of different amounts of La1 influences the main bacterial populations of the fecal microbiota. Eight asymptomatic volunteers participated in the study. After a basal period, they ingested daily 100 mL of a product containing 10(8) CFU mL(-1) of La1 during the first week, 200 mL during the second week and 500 mL during the third week. Fecal samples were obtained at the end of each period and subsequently during 7 weeks. Lactobacilli were determined by culture on MRS agar and La1 colonies were confirmed by ERIC-PCR. The main populations of fecal bacteria were identified by FISH and flow cytometry. At baseline, 37.7% of the total fluorescent bacteria were Eubacterium rectale, 18.3% Fusobacterium prausnitzii, 13.2% Bacteroides, 8.6% Atopobium, 2.30%, Clostridium histolyticum, 2.05% Bifidobacterium and 0.95% Lactobacillus. Fecal excretion of La1 increased during the intake period and decreased during the post-ingestion period, so that no La1 was observed in the stools of the volunteers seven weeks after the intake product has been finished. La1 intake increased the populations of C. histolyticum (p=0.049), Lactobacillus (p=0.056) and Bifidobacterium (p=0.067), and decreased those of F. prausnitzii (p=0.005) while it did not affect Bacteroides, E. rectale and Atopobium populations. These bacterial populations returned to their baseline levels during the post-ingestion period. The regular intake of a La1-containing product beneficially affects the homeostasis of the human fecal microbiota, probably contributing to the health-promoting effects of this probiotic.

Administration, Oral↗
PubMed2006

Antibiotic resistance in the cultivable plaque microbiota of children from different ethnic groups.

The presence of ampicillin-, penicillin-, erythromycin- and tetracycline-resistant bacteria in the dental plaque of White, South Asian and Japanese children was investigated. There was a high prevalence of antibiotic-resistant bacteria in children from diverse ethnic groups. The median percentage of the cultivable plaque microbiota that was resistant to tetracycline was greater in South Asian (2.9%, range 0.1-17.5%) and Japanese (7.7%, range 1.3-56.2%) children than in White children (0.7%, range 0-5.6%), suggesting that ethnic differences exist in the oral load of tetracycline-resistant bacteria (P<0.01). Multiresistant bacteria were frequently isolated, with 42% of isolates exhibiting resistance to two or more antibiotics. This study has demonstrated that antibiotic-resistant bacteria can be readily isolated from the plaque microbiota of children from different ethnic groups.

Anti-Bacterial Agents↗
PubMed2006

Clostridium difficile and Clostridium perfringens species detected in infant faecal microbiota using 16S rRNA targeted probes.

Clostridium perfringens and Clostridium difficile are pathogenic clostridia potentially associated with gastrointestinal infections and allergy in infants. To enable the molecular detection and quantification of these species in the infant gut, two 16S rRNA oligonucleotide probes were developed: Cdif198 for C. difficile and Cperf191 for C. perfringens. We defined the probes in silico using the RDP sequence database. The probes were then validated using FISH combined with flow cytometry and a collection of target and non-target strains, and faecal samples inoculated with dilutions of C. difficile and C. perfringens strains. These new probes were used to assess the composition of the intestinal microbiota of 33 infants of 1.5 to 18.5 months of age, associated with a panel of 8 probes targeting the predominant faecal bacterial groups of humans. The probes designed allowed detection and quantification of the relative proportions of C. difficile (0.5+/-1.0%) and C. perfringens (2.1+/-2.3%) in the microbiota of infants.

Clostridioides difficile↗
PubMed2006

Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota.

Some compounds originating from the human gut microbial metabolism of exogenous and endogenous substrates may have properties that profoundly affect the host's physiological processes. The influence of these metabolites on differences in disease risk among individuals could be mediated by metabolism specific to the gut microbial community composition. In this study, we evaluated the effectiveness of terminal restriction fragment polymorphism (TRFLP) as a biomarker of the fecal microbial community (as a surrogate of gut microbiota) for application in human population-based studies. We tested the effects of experimental conditions on DNA quality, DNA quantity, and TRFLP patterns derived from gut bacterial communities. Genomic DNA was extracted from fecal slurries and the bacterial 16S rDNA genes were amplified and analyzed by TRFLP. We found that the composition of the TRFLP fingerprints varied by different extraction procedure. The best quality and quantity of community DNA extracted from fecal material was obtained by using the QIAamp DNA stool minikit (Qiagen, Valencia, CA) with 95 degrees C incubation and moderate bead beating treatment during the cell-lysis step. Homogenization of fecal samples reduced variation among replicates. Once the TRFLP procedure was optimized, we assessed the methodological and inter-individual variation in gut microbial community fingerprints. The methodological variation ranged from 4.5-8.1% and inter-individual variation was 50.3% for common peaks. In conclusion, standardized TRFLP is a robust, reproducible, and high-throughput method that will provide a useful biomarker for characterizing gut microbiota in human fecal samples.

Adult↗