Gastrointestinal Tract Ecosystem Research Articles

СУБПОПУЛЯЦИОННЫЙ СОСТАВ ИНТРАЭПИТЕЛИАЛЬНЫХ ЛИМФОЦИТОВ У ПАЦИЕНТОВ С БОЛЕЗНЬЮ КРОНА

Crohn’s disease is an autoimmune inflammatory bowel disease characterized with the chronic relapsing-remitting inflammation, mainly in the terminal parts of the small intestine and colon, as a result of a genetic predisposition or environmental factors influence. It is associated with impaired bacterial clearance and changes in immunological parameters what resulted in disruption of the gastrointestinal tract ecosystem, formed by the microbiome and non-living components such as mucus, food metabolites or additives. Intraepithelial lymphocytes of the gastrointestinal tract play an important role in mucosal immunity and their phenotype and functional profile is largely determined by the microbiome composition and environmental factors affecting it (diet, smoking, seasonal changes, air pollution, hygiene, etc.). In this investigation the changes in intraepithelial lymphocytes phenotype of small and large intestine were shown in patient with Crohn’s disease as well as the correlation of intraepithelial lymphocytes phenotype with clinical data was established. Obtained data may be used as a hallmark of immune inflammation in the gut and make intraepithelial lymphocytes as ideal candidate for targeting in further immunoregulation of mucosal adaptive immune response against autoantigens.

Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization

Primary bile acids (BAs) are a collection of host-synthesized metabolites that shape physiology and metabolism. BAs transit the gastrointestinal tract and are subjected to a variety of chemical transformations encoded by indigenous bacteria. The resulting microbiota-derived BA pool is a mediator of host-microbiota interactions. Bacterial bile salt hydrolases (BSHs) cleave the conjugated glycine or taurine from BAs, an essential upstream step for the production of deconjugated and secondary BAs. Probiotic lactobacilli harbor a considerable number and diversity of BSHs; however, their contribution to Lactobacillus fitness and colonization remains poorly understood. Here, we define and compare the functions of multiple BSHs encoded by Lactobacillus acidophilus and Lactobacillus gasseri Our genetic and biochemical characterization of lactobacilli BSHs lend to a model of Lactobacillus adaptation to the gut. These findings deviate from previous notions that BSHs generally promote colonization and detoxify bile. Rather, we show that BSH enzymatic preferences and the intrinsic chemical features of various BAs determine the toxicity of these molecules during Lactobacillus growth. BSHs were able to alter the Lactobacillus transcriptome in a BA-dependent manner. Finally, BSHs were able to dictate differences in bacterial competition in vitro and in vivo, defining their impact on BSH-encoding bacteria within the greater gastrointestinal tract ecosystem. This work emphasizes the importance of considering the enzymatic preferences of BSHs alongside the conjugated/deconjugated BA-bacterial interaction. These results deepen our understanding of the BA-microbiome axis and provide a framework to engineer lactobacilli with improved bile resistance and use probiotics as BA-altering therapeutics.

Insights into the gastrointestinal tract microbiomes of Indian population

Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.

Homeostasis and dysbiosis of the gut microbiome in health and disease

The human gastrointestinal tract (GIT) harbors taxonomically and functionally complex microbial ecosystem. The composition of the microbial species in the GIT ecosystem varies among individuals and throughout development. Both environmental factors as well as host genetics influence the composition and homeostasis of GIT microbiome. Intrinsic GIT microbiome can be characterized in terms of diversity, richness, dynamics and resilience. In healthy individual, microbial communities maintain homeostatic equilibrium and are resistant against perturbations. The resilience and resistance to perturbations of the GIT microbial ecosystem are robust but not absolute. Several factors can affect the homeostatic equilibrium of GIT microbiome and lead to dysbiotic microbiome configuration. Taxonomic and/or functional dysbiosis in the GIT microbiome is associated with numerous health disorders like inflammatory bowel disease (IBD), malnutrition, metabolic disorders, asthma and neurodegenerative diseases. In this review, we discuss our current understanding of homeostasis and dysbiosis of the microbial ecology in the human gut and health disorders that are associated with the microbiome dysbiosis.

Exopolysaccharides Produced by Lactobacillus rhamnosus KL 53A and Lactobacillus casei Fyos Affect Their Adhesion to Enterocytes.

Probiotics promote and help to maintain beneficial microbiota composition of the gastrointestinal tract ecosystem and have a positive impact on the host’s health. Production of exopolysaccharides is an important feature of probiotic lactobacilli. It increases the chance of their survival in the gastrointestinal tract and promotes adhesion to the epithelium; therefore, exopolysaccharides are important for the process of colonization. Two lactic acid bacteria strains were used in this study: Lactobacillus rhamnosus KL 53A and Lactobacillus casei Fyos. Exopolysaccharides were isolated from bacterial cells and their monosaccharide composition was examined using liquid chromatography. The influence of exopolysaccharides on lactobacilli adhesion to enterocytes was studied after deglycosylation of the bacterial cells and incubation with the selected intestinal microbiota strains that metabolize polysaccharides – Faecalibacterium prausnitzii DSM 17677 and Blautia luti DSM 14534. Both deglycosylation and incubation with polysaccharide metabolizing strains influenced the ability of probiotic strains to adhere to enterocytes. Enzymatic deglycosylation decreased adhesion efficiency of L. rhamnosus KL 53A; however, co-incubation of both lactobacillus strains with F. prausnitzii DSM 17677 resulted in an increase of their adhesion efficiency. Exopolysaccharides are important adhesins of Lactobacillus spp. that influence their ability to colonize gut epithelium. Other members of gut microbiota can modify the adhesion property in situ; therefore the composition and metabolic state of commensal bacteria may influence their probiotic action.

An update discussion on the current assessment of the safety of veterinary antimicrobial drug residues in food with regard to their impact on the human intestinal microbiome.

The human gastrointestinal tract ecosystem consists of complex and diverse microbial communities that have now been collectively termed the intestinal microbiome. Recent scientific breakthroughs and research endeavours have increased our understanding of the important role the intestinal microbiome plays in human health and disease. The use of antimicrobial new animal drugs in food-producing animals may result in the presence of low levels of drug residues in edible foodstuffs. There is concern that antimicrobial new animal drugs in or on animal-derived food products at residue-level concentrations could disrupt the colonization barrier and/or modify the antimicrobial resistance profile of human intestinal bacteria. Therapeutic doses of antimicrobial drugs have been shown to promote shifts in the intestinal microbiome, and these disruptions promote the emergence of antimicrobial-resistant bacteria. To assess the effects of antimicrobial new animal drug residues in food on human intestinal bacteria, many national regulatory agencies and international committees follow a harmonized process, VICH GL36(R), which was issued by a trilateral organization of the European Union, the USA, and Japan called the International Cooperation on Harmonization of Technical Requirements for Veterinary Medicinal Products (VICH). The guidance describes a general approach currently used by national regulatory agencies and international committees to assess the effects of antimicrobial new animal drug residues in animal-derived food on human intestinal bacteria. The purpose of this review is to provide an overview of this current approach as part of the antimicrobial new animal drug approval process in participating countries, give insights on the microbiological endpoints used in this safety evaluation, and discuss the availability of new information. Copyright © 2016 John Wiley & Sons, Ltd.

Experimental Induction of <i>Escherichia coli</i> Diarrhoea in Weaned Piglets

Escherichia coli diarrhoea is a multifactorial condition which usually occurs during the post-weaning and is responsible for economic losses in pig production. One approach, to evaluate if substitute of antibiotic in vivo is effective in controlling postweaning diarrhea in the gastrointestinal tract ecosystem, is to use an appropriate disease model. However, there are still many criticisms related to the incidence and the severity of the diarrhoea in the experimental conditions. The aim of the study was to set up an Escherichia coli challenge model in order to induce a significant percentage of diarrhoea in weaned piglets for the evaluation of innovative compounds in vivo. A total of 35 piglets, weaned at 33±2 days were randomized into 3 groups: control (CG), infected 1 (IG1) and infected 2 (IG2). One day after arrival piglets of IG1 and IG2 were orally inoculated with 3.7 × 108 CFU of Escherichia coli O149. All piglets were fed a high protein ration for 3 days. Daily health status and faeces were recorded by a point scale individually. Challenge strains in faecal samples were evaluated by polymerase chain reaction, serotyping and biochemical identification. Diarrhoea was observed in 96.67% (58.6% severe; 41.4% mild) of all infected piglets and occurred on average 1.3 days after the challenge. The CG group presented one piglet with a transient mild diarrhoea. The E. coli challenge significantly affected the consistency and color of faeces (P E. coli O149, mainly hemolytic (88%), was isolated in 56% of faecal samples and the 70% of piglets with severe diarrhoea shed E. coli O149 in the faeces. Zootechnical parameters did not show significant differences. The experimental conditions described in this study allowed to effectively induce diarrhoea in weaned piglets. In conclusion a multifactorial approach (infectious, nutritional and management) is necessary to reproduce in vivo diarrhea in piglets.

The use of probiotics for critically ill patients in hospitals

This article is based on a review of published literature, mainly from 2005 to 2008. Several reports demonstrate statistically signifi cant benefi cial health effects of probiotic supplementation, especially for the treatment of rotavirus-associated diarrhoea. The following main topics have been reviewed: bacterial translocation from the gut and infectious disease; virulence factors including toxicity; metabolic functions including host storage, platelet aggregation, deconjugation of bile acids, and degradation of mucin. Furthermore, resistance to antimicrobials, with emphasis on the location of the genes involved, has been reviewed. Studies concerning probiotic supplementation in hospital patients suffering from acute pancreatitis, antibiotic-associated diarrhoea, including Clostridium difficile infection, and non-alcoholic fatty liver disease are reviewed. Supplementation with probiotic bacteria in critically ill children, e.g. in intensive care, is also discussed. The use of probiotics for patients with diarrhoea, Helicobacter pylori infection and infl ammatory bowel disease is mentioned, as well as for patients with AIDS, urogenital infections, and small intestinal bacterial overgrowth. Particular attention has been paid to a large Dutch study (PROPATRIA), which showed increased mortality in patients with acute pancreatitis who were given enteral nutrition to which probiotics had been added, compared with enteral nutrition alone. Similarities in some acquired resistance genes between probiotic microorganisms and other bacteria of human origin suggest the transfer of resistance genes between commensal microorganisms in the complex gastrointestinal tract ecosystem. Intake of probiotic microorganisms that carry transferable antimicrobial resistance genes may increase the risk of the transfer of such genes to the resident microbiota in patients. Although some benefi cial effects have been reported in some patient groups, we conclude that the adverse effects that have been observed are well documented, thus indicating that caution should be observed in administering probiotic bacteria to critically ill patients. Key words: Prebiotics , microbiota , PROPATRIA

Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis

The microbial community structure of pig manure slurry (PMS) was determined with comparative analysis of 202 bacterial, 44 archaeal and 33 eukaryotic small subunit (SSU) rDNA partial sequences. Based on a criterion of 97% of sequence similarity, the phylogenetic analyses revealed a total of 108, eight and five phylotypes for the Bacteria, Archaea and Eukarya lineages, respectively. Only 36% of the bacterial phylotypes were closely related (⩾97% similarity) to any previously known sequence in databases. The bacterial groups most often represented in terms of phylotype and clone abundance were the Eubacterium (22% of total sequences), the Clostridium (15% of sequences), the Bacillus–Lactobacillus–Streptococcus subdivision (20% of sequences), the Mycoplasma and relatives (10% of sequences) and the Flexibacter–Cytophaga–Bacteroides (20% of sequences). The global microbial community structure and phylotype diversity show a close relationship to the pig gastrointestinal tract ecosystem whereas phylotypes from the Acholeplasma–Anaeroplasma and the Clostridium purinolyticum groups appear to be better represented in manure. Archaeal diversity was dominated by three phylotypes clustering with a group of uncultured microorganisms of unknown activity and only distantly related to the Thermoplasmales and relatives. Other Archaea were methanogenic H 2/CO 2 utilisers. No known acetoclastic Archaea methanogen was found. Eukaryotic diversity was represented by a pluricellular nematode, two Alveolata, a Blastocystis and an Entamoebidae. Manure slurry physico-chemical characteristics were analysed. Possible inhibitory effects of acetate, sulphide and ammonia concentrations on the microbial anaerobic ecosystem are discussed.

The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533.

Lactobacillus johnsonii NCC 533 is a member of the acidophilus group of intestinal lactobacilli that has been extensively studied for their "probiotic" activities that include, pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into its physiology and identify genes potentially involved in interactions with the host, we sequenced and analyzed the 1.99-Mb genome of L. johnsonii NCC 533. Strikingly, the organism completely lacked genes encoding biosynthetic pathways for amino acids, purine nucleotides, and most cofactors. In apparent compensation, a remarkable number of uncommon and often duplicated amino acid permeases, peptidases, and phosphotransferase-type transporters were discovered, suggesting a strong dependency of NCC 533 on the host or other intestinal microbes to provide simple monomeric nutrients. Genome analysis also predicted an abundance (>12) of large and unusual cell-surface proteins, including fimbrial subunits, which may be involved in adhesion to glycoproteins or other components of mucin, a characteristic expected to affect persistence in the gastrointestinal tract (GIT). Three bile salt hydrolases and two bile acid transporters, proteins apparently critical for GIT survival, were also detected. In silico genome comparisons with the >95% complete genome sequence of the closely related Lactobacillus gasseri revealed extensive synteny punctuated by clear-cut insertions or deletions of single genes or operons. Many of these regions of difference appear to encode metabolic or structural components that could affect the organisms competitiveness or interactions with the GIT ecosystem.

The Application of Ecological Principles and Fermentable Fibers to Manage the Gastrointestinal Tract Ecosystem

Because diet can influence the structure and functions of the gastrointestinal tract, there are opportunities for using diet as a “management tool” to affect the resident microbiota. Fermentable fibers increase the densities of beneficial bacteria and stimulate growth and functions of the healthy intestine. Recent findings show that after acute diarrhea, the use of an oral electrolyte solution with the fermentable fiber oligofructose accelerates recovery of beneficial bacteria, reduces the relative abundance of detrimental bacteria, stimulates mucosal growth and enhances digestive and immune functions. This review will focus on how the principles of stream ecology can be applied to better understand the distribution of bacteria along the length of the gastrointestinal tract, the effect of diarrhea on the gastrointestinal ecosystem and how fermentable fibers can be used as a “management tool” to promote gastrointestinal health in normal states and during recovery from diarrhea.

Ribosomal efficiency and growth rates of freshly isolated Escherichia coli strains originating from the gastrointestinal tract

It has been previously reported that for natural Escherichia coli isolates from the ECOR collection, there were differences in the ribosomal efficiencies and there was a direct correlation between growth rate and the ribosome efficiency (R-factor). The aim of this study was to determine whether strains freshly isolated (i.e. subcultured <5 times) from the gastrointestinal tract ecosystem also exhibited this correlation. Eleven E. coli and two Enterobacter spp. isolates from either humans, pigs, rats or a mammoth were investigated. Considerable variability in the R-factor was noted using an in vitro translation assay, however no consistent correlation between the R-factor and growth rate was noted.