Microbiocenosis of parietal mucin in gastrointestinal tract of rats with induced disbiosis

Comparative study of qualitative and quantitative characteristics of parietal mucin microbiocenosis in rats with alimentary induced disbiosis was performed. It has been shown that disbiosis was associated with changes in parietal microflora which were observed mainly in colon mucosa. Disbiosis in parietal area, in contrast to central area manifested by changes in quantitative characteristics of microbiocenosis. Results of the study allowed to suppose that parietal mucosal microbiocenosis was more stable than gut one and that this stability was determined by endogenous homeostatic factors of the host.     

Influence of Bacillus cereus on microbiocenosis of gastrointestinal tract in rats

The modifying effect of Bacillus cereus on intestinal microbiocenosis was investigated in eubiotic and disbiotic female rats. Qualitative and quantitative characteristics of gut and mucosal microflora from different parts of rats' intestine were studied before and after intragastral application of B. cereus suspension. The single application of B. cereus suspension resulted in appearance of this bacterium in feces and in parietal mucin from all parts of the intestine. In eubiotic rats compared with disbiotic, B. cereus adhere to parietal mucin much more efficiently and supplanted indigenous microflora. During disbiosis B. cereus sometimes had stimulating effect on the intestinal microbiocenosis. Gut microbiocenosis appeared to be more resistant to B. cereus invasion than mucosal. This fact was considered to be the evidence of higher sensitivity of mucosal microbiocenosis to short-term influence of exogenous microbial factor.     

Comparative study of parietal and lumen microflor in the large intestine in experiments on mice

The methodological aspects of the study of the microflora of the parietal mucous layer (parietal mucin) of the large intestine is discussed; the study is difficult because the mucin layer is thin closely associated with epithelium and the impossibility of the mechanical separation of this layer from the epithelium without damaging the latter is possible. The method of homogenization fails to determine of the composition of parietal mucin proper. Such possibility becomes real after the dissolution of mucin and obtaining the suspension of microbial cells. As experimentally shown in vitro, urea solution, reducing disulfide bonds, effectively depolymerized mucin and exhibited no antibacterial and cytolytic activity. With the use of urea treatment, microflora of parietal mucin of the large intestine was studied on 44 non-inbred mice. This newly developed method was shown to have higher resolution in comparison with the traditional one (homogenization). Some qualitative and quantitative characteristics of the microflora of parietal mucin were established. In the same group of mice the study of fecal microflora was made and compared with microflora of parietal mucin.     

Study of the parietal microflora in the rat intestine

The article deals with the adaptation of the existing method of the isolation of microorganisms from parietal mucin of the intestine of experimental animals (rats) with a view to ensure the methodological uniformity of investigations. The effectiveness of the method of sparing disintegration of parietal mucin taken from the mucous membrane of the gastrointestinal tract, specially developed for human biomaterial, and its adequacy for microbiological investigations of the digestive organs of rats have been confirmed. A certain similarity between the microbiocenosis of the parietal mucin in the intestine of humans and rats has been established.     

The autologous intestinal microflora in the postresuscitation period after acute blood loss in rats

In this work the data obtained in the study of intestinal microbiocenosis in rats on the third day of the postresuscitation period after acute blood loss are presented. The quantitative and qualitative shifts of microflora at different biotopes, such as the wall of the small intestine, the parietal microflora of Peyer's patches, the contents and wall of the large intestine, have been characterized. Some specific features of dysbiotic changes have been revealed in comparison with the shifts of intestinal microflora in cases of dysbacteriosis caused by other reasons. The translocation of different microorganisms, including Bacterium bifidum and lactobacilli, into mesenteric lymph nodes, the liver, the spleen and the blood has been observed.     

Review: Dietary fiber utilization and its effects on physiological functions and gut health of swine

Although dietary fiber (DF) negatively affects energy and nutrient digestibility, there is growing interest for the inclusion of its fermentable fraction in pig diets due to their functional properties and potential health benefits beyond supplying energy to the animals. This paper reviews some of the relevant information available on the role of different types of DF on digestion of nutrients in different sections of the gut, the fermentation process and its influence on gut environment, especially production and utilization of metabolites, microbial community and gut health of swine. Focus has been given on DF from feed ingredients (grains and coproducts) commonly used in pig diets. Some information on the role DF in purified form in comparison with DF in whole matrix of feed ingredients is also presented. First, composition and fractions of DF in different feed ingredients are briefly reviewed. Then, roles of different fractions of DF on digestion characteristics and physiological functions in the gastrointestinal tract (GIT) are presented. Specific roles of different fractions of DF on fermentation characteristics and their effects on production and utilization of metabolites in the GIT have been discussed. In addition, roles of DF fermentation on metabolic activity and microbial community in the intestine and their effects on intestinal health are reviewed and discussed. Evidence presented in this review indicates that there is wide variation in the composition and content of DF among feed ingredients, thereby their physico-chemical properties in the GIT of swine. These variations, in turn, affect the digestion and fermentation characteristics in the GIT of swine. Digestibility of DF from different feed ingredients is more variable and lower than that of other nutrients like starch, sugars, fat and CP. Soluble fractions of DF are fermented faster, produce higher amounts of volatile fatty acid than insoluble fractions, and favors growth of beneficial microbiota. Thus, selective inclusion of DF in diets can be used as a nutritional strategy to optimize the intestinal health of pigs, despite its lower digestibility and consequential negative effect on digestibility of other nutrients.     

Microflora of gastrointestinal tract in patients with chronic cholecystitis

AIM: Assessment of quantitative and qualitative characteristics of gastrointestinal microflora in patients with chronic cholecystitis. MATERIALS AND METHODS: Bacteriological analysis of biopsy samples of esophageal and gastric mucosae as well as stool samples was performed in 10 healthy volunteers and 28 patients with chronic cholecystitis. RESULTS: Opportunistic microorganisms are acquiring greater significance in formation of gastrointestinal microbiocenosis. Significant increase of both isolation rate and density of gastrointestinal tract colonization by staphylococci, enterobacteriae and anaerobic microorganisms was revealed. CONCLUSION: Obtained results showed abnormalities of microbiocenosis of esophageal and gastric mucosae and presence of intestinal disbacteriosis of different degrees of intensity.     

Characteristics of associated microflora of ejaculate from males with gonococcal infections

Species composition and biological properties of aerobic and anaerobic microflora from an ejaculate from males with acute and chronic gonococcal infection and from healthy men were studied. Patients with gonococcal infection were shown to present quantitative and qualitative changes in microbiocenosis of the reproductive tract. Patients with acute gonorrhea displayed decreased species diversity in contrast to healthy persons, while different species of associated with gonococci microbes with high persistent potential, were cultured in patients suffering from a chronic form of infection. The role of revealed pathological biocenosis patterns in developing chronic infection as well as postgonorrheal gonococci-free urethritis is discussed.     

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community beta diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.     

A method for assessing the microflora status of the large intestine using a computer

The qualitative and quantitative composition of the microflora of the large intestine has been studied in 31 healthy adults and in 137 patients with acute viral hepatitides A and B. A set of quantitative tests ensuring the complete characterization of the microbiocenosis under study has been proposed. The results obtained in this investigation have been processed by means of a computer with the use of the principles of numeric taxonomy, thus making it possible to obtain the objective criterion of the state of the microflora of the large intestine, expressed by the similarity index.     

Effect of bioaugmentation and biostimulation on sulfate-reducing column startup captured by functional gene profiling

Sulfate-reducing permeable reactive zones (SR-PRZs) depend upon a complex microbial community to utilize a lignocellulosic substrate and produce sulfides, which remediate mine drainage by binding heavy metals. To gain insight into the impact of the microbial community composition on the startup time and pseudo-steady-state performance, functional genes corresponding to cellulose-degrading (CD), fermentative, sulfate-reducing, and methanogenic microorganisms were characterized in columns simulating SR-PRZs using quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE). Duplicate columns were bioaugmented with sulfate-reducing or CD bacteria or biostimulated with ethanol or carboxymethyl cellulose and compared with baseline dairy manure inoculum and uninoculated controls. Sulfate removal began after ~?15?days for all columns and pseudo-steady state was achieved by Day 30. Despite similar performance, DGGE profiles of 16S rRNA gene and functional genes at pseudo-steady state were distinct among the column treatments, suggesting the potential to control ultimate microbial community composition via bioaugmentation and biostimulation. qPCR revealed enrichment of functional genes in all columns between the initial and pseudo-steady-state time points. This is the first functional gene-based study of CD, fermentative and sulfate-reducing bacteria and methanogenic archaea in a lignocellulose-based environment and provides new qualitative and quantitative insight into startup of a complex microbial system.     

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing

Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.     

Epidemiological assessment of the microbial contamination of the breast milk of healthy women

The qualitative and quantitative composition of the microflora of human milk has been studied. The dynamics of the occurrence of different microorganisms constituting the microflora at different periods of lactation has been established. The connection between the appearance of septic purulent infections in infants and the microbial contamination of milk has been revealed. The presence of Staphylococcus aureus in human milk in an amount of 500 microbial cells/ml has been found to constitute no menace to healthy infants.     

Changes in vaginal microbiocenosis in patients with chronic pelvic inflammatory diseases following antibiotic therapy

The species composition of the vaginal microorganisms in healthy women and in patients with chronic pelvic inflammatory diseases before and after treatment in a gynecological hospital was studied. The study revealed that antibiotic therapy did not lead to complete clinical convalescence. During bacteriological investigation of patients changes in vaginal microbiocenosis, manifested by a decreased number of microbial species, an increased proportion of Escherichia coli, the occurrence of Staphylococcus aureus, a decreased number of Lactobacillus ssp., were observed. Antibiotic therapy aggravated the dysbiotic microbial picture of the vagina.     

Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies

Roman Catacombs are affected by different kinds of biofilms that were extensively investigated in the last 14 years. In particular, the areas far from the lamps are often covered by white biofilms of different extension, consistency and nature. The aim of this paper is to describe the profile of the microbial community present in two areas of the Ocean's Cubiculum (CSC13), characterized by similar alterations described as white biofilms, by using a multistep approach that included direct microscopy observations, culture‐dependent and culture‐independent methodologies through the extraction of DNA and RNA directly from the sampled areas. In addition to this, we extracted the DNA directly from the Petri dishes containing R2A and B4 media after incubation and growth of bacteria. Our results evidenced that a complex bacterial community (mainly constituted by filamentous Actinobacteria, as well as Firmicutes and Proteobacteria) colonizes the two different white biofilms, and its detection, quantitative and qualitative, could be revealed only by different approaches, each method giving different information that only partially overlap.     

Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field

To examine the relationship between plant species composition and microbial community diversity and structure, we carried out a molecular analysis of microbial community structure and diversity in two field experiments. In the first experiment, we examined bacterial community structure in bulk and rhizosphere soils in fields exposed to different plant diversity treatments, via a 16S rRNA gene clone library approach. Clear differences were observed between bacterial communities of the bulk soil and the rhizosphere, with the latter containing lower bacterial diversity. The second experiment focused on the influence of 12 different native grassland plant species on bacterial community size and structure in the rhizosphere, as well as the structure of Acidobacteria and Verrucomicrobia community structures. In general, bacterial and phylum-specific quantitative PCR and PCR-denaturing gradient gel electrophoresis revealed only weak influences of plant species on rhizosphere communities. Thus, although plants did exert an influence on microbial species composition and diversity, these interactions were not specific and selective enough to lead to major impacts of vegetation composition and plant species on below-ground microbial communities.     

Site-specific variation in Antarctic marine biofilms established on artificial surfaces

The community structure and composition of marine microbial biofilms established on glass surfaces was investigated across three differentially contaminated Antarctic sites within McMurdo Sound. Diverse microbial communities were revealed at all sites using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) techniques. Sequencing of excised DGGE bands demonstrated close affiliation with known psychrophiles or undescribed bacteria also recovered from the Antarctic environment. The majority of bacterial sequences were affiliated to the Gammaproteobacteria, Cytophaga/Flavobacteria of Bacteroidetes (CFB), Verrucomicrobia and Planctomycetales. Principal components analysis of quantitative FISH data revealed distinct differences in community composition between sites. Each of the sites were dominated by different bacterial groups: Alphaproteobacteria, Gammaproteobacteria and CFB at the least impacted site, Cape Armitage; green sulfur and sulfate reducing bacteria near the semi-impacted Scott Base and Planctomycetales and sulfate reducing bacteria near the highly impacted McMurdo Station. The highest abundance of archaea was detected near Scott Base (2.5% of total bacteria). Multivariate analyses (non-metric multidimensional scaling and analysis of similarities) of DGGE patterns revealed greater variability in community composition between sites than within sites. This is the first investigation of Antarctic biofilm structure and FISH results suggest that anthropogenic impacts may influence the complex composition of microbial communities.     

Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

Bacterial colonization in the gastrointestinal tracts (GIT) of preweaned calves is very important, since it can influence early development and postweaning performance and health. This study investigated the composition of the bacteria along the GIT (rumen, jejunum, ileum, cecum, and colon) of preweaned bull calves (3 weeks old) using pyrosequencing to understand the segregation of bacteria between the mucosal surface and digesta. Phylogenetic analysis revealed that a total of 83 genera belonging to 13 phyla were distributed throughout the GIT of preweaned calves, with the Firmicutes, Bacteroidetes, and Proteobacteria predominating. Quantitative PCR (qPCR) analysis of selected abundant bacterial genera (Prevotella, Bacteroides, Lactobacillus, and Faecalibacterium) revealed that their prevalence was significantly different among the GIT regions and between mucosa- and digesta-associated communities. Rumens contained the most diverse bacterial population, consisting of 47 genera, including 16 rumen-specific genera, followed by the large intestine and then the small intestine. Bacterial species richness was higher at the mucosal surface than in the local digesta, with the exception of the rumen. The majority of bacteria found on the rumen epithelial surface and within the small intestine could not be identified due to a lack of known genus-level information. Thus, future studies will be required to fully characterize the microbiome during the development of the rumens and the mucosal immune systems of newborn calves. This is the first study to analyze in depth the bacterial composition of the GIT microbiome in preweaned calves, which extends previous findings regarding early rumen colonization and bacterial segregation between mucosa- and digesta-associated microbial communities.     

Changes in colonic mucins of germfree rats in response to the introduction of a "normal" rat microbial flora. Rat colonic mucin.

In order to determine the influence of bacterial colonization on amount and composition of colonic mucins, germfree male AS/Ztm rats were colonized with a rat specific intestinal flora for different times (2, 7, 14, 21, 28, 35, 120 days). The amount of colonic mucins was determined by gel filtration on Sepharose CL-4B; the relative amount of acidic mucins was calculated after ion exchange chromatography. In addition, cecal weight and dry matter of feces were monitored. While germfree and SPF rats revealed similar amounts of colonic mucins (7.0 vs. 7.2 mg mucin/300 g body weight), the initial phase of association was characterized by considerably decreasing values. After four weeks of association, the total amount of colonic mucins had almost equalized in the two groups. The amount of acidic mucins, having decreased during the first three weeks of colonization, rendered values comparable to the SPF mucins after four months of adaptation. Cecomegaly in germfree rats disappeared within the first two days, while solidification of the intestinal content occurred within four months. Mucin losses during initial phase of association are attributed 1. to the disappearance of the cecal mucin pool, and 2. to the mucin degrading activity of some bacterial strains known to be present in the intestinal flora. Further development is conducted by a stimulation of mucin secretion, described to follow the colonization. The initially increased secretion of neutral mucins is attributed to a pronounced release of immature mucin glycoproteins, while the shift to more acidic mucins is considered to result from stimulated secretion as well as from a selective bacterial degradation of neutral mucin components.