Mucosal dendritic cell diversity in the gastrointestinal tract

The discovery of dendritic cells (DCs) in skin by Paul Langerhans in 1868 identified a cell type which has since been recognized as a key link between innate and adaptive immunity. DCs originate from bone marrow and disseminate through blood to all tissues in the body, and distinct DC subpopulations have been identified in many different tissues. DC diversity is apparent throughout all mucosal surfaces of the body, but the focus of this review article is DC diversity throughout the gastro-intestinal tract (GIT). DC subpopulations have been well characterized in the oral cavity and small intestine, but DC characterization in other regions, such as the esophagus and stomach, is limited. Substantial research has focused on DC function during disease, but understanding the regulation of inflammation and the induction of acquired immune responses requires combined phenotypic and functional characterization of individual DC subpopulations. Furthermore, little is known regarding mucosal DC subpopulations in the GIT of the neonate and how these DC populations change following colonization by commensal microflora. The current review will highlight mucosal DC diversity and discuss factors that may influence mucosal DC differentiation.     

普氏蹄蝠胃肠道菌群的多样性

【目的】研究普氏蹄蝠(Hipposideros pratti)胃肠道菌群多样性及致病菌的种类。【方法】采用Mi Seq高通量测序技术,通过对16S r RNA基因V1-V2区基因进行测序,研究普氏蹄蝠胃肠道细菌的群落组成。应用MG-RAST V3.3.6分析和统计样品序列和操作分类单元(OTU)数目,分析胃肠道菌群物种丰度,并进行聚类分析。【结果】从普氏蹄蝠胃和肠道中分别获得144 998条和275 274条原始序列以及48 332条和91 758条有效序列,分属于894个和756个操作分类单元。胃中菌群丰度指数Chao指数(1 490)和ACE指数(2 221)分别低于肠道菌群的Chao指数(2 051)和ACE指数(3 556);Shannon多样性指数(2.405)低于肠道(2.407);Simpson多样性指数(0.168)高于肠道(0.151)。系统进化分析表明胃肠中的细菌主要分布在6个门,均以变形菌门(Proteobacteria)(胃中占56.4%,肠中占46.0%)和厚壁菌门(Firmicutes)(胃中占40.7%,肠中占49.2%)为优势菌门。胃肠道中丰度在0.1%以上的属有24个,胃中优势类群为乳球菌属(Lactococcus)和哈夫尼菌属(Hafnia),分别占整个菌群的26.1%和21.0%;肠道中优势类群为肠球菌属(Enterococcus)和沙门氏菌属(Salmonella),分别占整个菌群的15.2%和12.7%。普氏蹄蝠胃肠道中的优势菌群均为人类的致病菌或者条件致病菌。【结论】普氏蹄蝠携带有大量人类致病菌。因此,应注意防止向人类传播。     

Within‐host evolution versus immigration as a determinant of Escherichia coli diversity in the human gastrointestinal tract

When a human host harbors two or more strains of Escherichia coli, the second strain is more likely to be a member of the same phylogroup rather than a different phylogroup. This outcome may be the consequence of a within host evolution event or an independent immigration/establishment event. To determine the relative importance of these two events in determining E. coli diversity in a host, a collection of multiple E. coli isolates recovered from each of 67 patients undergoing colonoscopies was used. Whole genome sequence data were available for one example of every REP‐fingerprint type identified in a patient. Sequence type (ST) and single‐nucleotide polymorphism (SNP) analyses revealed that 83% of strains observed in the host population were a consequence of immigration/establishment events. Restricting the analysis to hosts harboring two or more strains belonging to the same phylogroup revealed that in about half of these cases, the presence of a second strain belonging to the same phylogroup was the consequence of an independent immigration/establishment event. Thus, the results of this study show that despite hosts being exposed to a diversity of E. coli via their food, factors related to the host also determine what E. coli strains succeed in establishing.     

Mutualistic rhizobia reduce plant diversity and alter community composition

Mutualistic interactions can be just as important to community dynamics as antagonistic species interactions like competition and predation. Because of their large effects on both abiotic and biotic environmental variables, resource mutualisms, in particular, have the potential to influence plant communities. Moreover, the effects of resource mutualists such as nitrogen-fixing rhizobia on diversity and community composition may be more pronounced in nutrient-limited environments. I experimentally manipulated the presence of rhizobia across a nitrogen gradient in early assembling mesocosm communities with identical starting species composition to test how the classic mutualism between nitrogen-fixing rhizobia and their legume host influence diversity and community composition. After harvest, I assessed changes in α-diversity, community composition, β-diversity, and ecosystem properties such as inorganic nitrogen availability and productivity as a result of rhizobia and nitrogen availability. The presence of rhizobia decreased plant community diversity, increased community convergence (reduced β-diversity), altered plant community composition, and increased total community productivity. These community-level effects resulted from rhizobia increasing the competitive dominance of their legume host Chamaecrista fasciculata. Moreover, different non-leguminous species responded both negatively and positively to the presence of rhizobia, indicating that rhizobia are driving both inhibitory and potentially facilitative effects in communities. These findings expand our understanding of plant communities by incorporating the effects of positive symbiotic interactions on plant diversity and composition. In particular, rhizobia that specialize on dominant plants may serve as keystone mutualists in terrestrial plant communities, reducing diversity by more than 40 %.     

Nitrogenase diversity and activity in the gastrointestinal tract of the wood-eating catfish Panaque nigrolineatus

The Amazonian catfish, Panaque nigrolineatus, consume large amounts of wood in their diets. The nitrogen-fixing community within the gastrointestinal (GI) tract of these catfish was found to include nifH phylotypes that are closely related to Clostridium sp., Alpha and Gammaproteobacteria, and sequences associated with GI tracts of lower termites. Fish fed a diet of sterilized palm wood were found to contain nifH messenger RNA within their GI tracts, displaying high sequence similarity to the nitrogen-fixing Bradyrhizobium group. Nitrogenase activity, measured by acetylene reduction assays, could be detected in freshly dissected GI tract material and also from anaerobic enrichment cultures propagated in nitrogen-free enrichment media; nifH sequences retrieved from these cultures were dominated by Klebsiella- and Clostridium-like sequences. Microscopic examination using catalyzed reporter deposition-enhanced immunofluorescence revealed high densities of nitrogenase-containing cells colonizing the woody digesta within the GI tract, as well as cells residing within the intestinal mucous layer. Our findings suggest that the P. nigrolineatus GI tract provides a suitable environment for nitrogen fixation that may facilitate production of reduced nitrogen by the resident microbial population under nitrogen limiting conditions. Whether this community is providing reduced nitrogen to the host in an active or passive manner and whether it is present in a permanent or transient relationship remains to be determined. The intake of a cellulose rich diet and the presence of a suitable environment for nitrogen fixation suggest that the GI tract microbial community may allow a unique trophic niche for P. nigrolineatus among fish.     

Assimilation of water and dietary ions by the gastrointestinal tract during digestion in seawater-acclimated rainbow trout

Recent studies focusing on the consequences of feeding for ion and water balance in freshwater fish have revealed the need for similar comparative studies in seawater fish. A detailed time course sampling of gastrointestinal (GI) tract contents following the ingestion of a single meal of a commercial diet revealed the assimilation of both water and dietary ions (Na⁺, Cl^?, K⁺, Ca²⁺, Mg²⁺) along the GI tract of seawater-acclimated rainbow trout (Oncorhynchus mykiss) which had been fasted for 1 week. Consumption of the meal did not change the drinking rate. There was a large secretion of fluid into the anterior intestine and caecae (presumably bile and/or pancreatic secretions). As a result, net assimilation (63%) of the ingested water along the GI tract was lower than generally reported for fasted trout. Mg²⁺ was neither secreted into nor absorbed from the GI tract on a net basis. Only K⁺ (93% assimilated) and Ca²⁺ (43% assimilated) were absorbed in amounts in excess of those provided by ingested seawater, suggesting that dietary sources of K⁺ and Ca²⁺ may be important to seawater teleosts. The oesophagus–stomach served as a major site of absorption for Na⁺, Cl^?, K⁺, Ca²⁺, and Mg²⁺, and the anterior intestine and caecae as a major site of net secretion for all of these ions, except Cl^?. Despite large absorptive fluxes of these ions, the ionic composition of the plasma was maintained during the digestion of the meal. The results of the present study were compared with previous work on freshwater-acclimated rainbow trout, highlighting some important differences, but also several similarities on the assimilation of water and ions along the gastrointestinal tract during digestion. This study highlights the complicated array of ion and water transport that occurs in the intestine during digestion while revealing the importance of dietary K⁺ and Ca²⁺ to seawater-acclimated rainbow trout. Additionally, this study reveals that digestion in seawater-acclimated rainbow trout appears to compromise intestinal water absorption.     

Genomic diversity of cultivable Lactobacillus populations residing in the neonatal and adult gastrointestinal tract

The objective of this study was to investigate the cultivable Lactobacillus population in adult and infant faecal material to identify strains shared across a number of individuals. A range of lactobacilli isolated on Lactobacillus-selective agar from faeces of 16 infants and 11 adults were genetically fingerprinted and further characterized by 16S rRNA gene sequencing. The relatedness of all the Lactobacillus strains isolated to known species was also determined both genetically and phenotypically. This study revealed that the human intestine is initially colonized by only a few (1-2) different cultivable strains whereas in adults the pattern becomes more complex with a higher diversity of strains. The adult samples contained three genetically distinct Lactobacillus strains in some cases, while infant samples generally harboured only one dominant Lactobacillus strain. Moreover, the species in general appeared to differ with Lactobacillus rhamnosus and Lactobacillus casei/paracasei found mainly in adults, whereas Lactobacillus gasseri and Lactobacillus salivarius were more commonly isolated in infant samples. The data reaffirm the differences in Lactobacillus populations both between individual subjects and between the infant and adult, with an overall change in the diversity and complexity from early stages of life to adulthood.     

The genetic diversity of lactic acid producing bacteria in the equine gastrointestinal tract

Seventy-two lactic acid producing bacterial isolates (excluding streptococci) were cultured from the gastrointestinal tract of six horses. Two of the horses were orally dosed with raftilose to induce lactic acidosis and laminitis while the remaining four were maintained on a roughage diet. Near complete 16S rDNA was amplified by PCR from the genomic DNA of each isolate. Following RFLP analysis with the restriction enzymes MboI, HhaI and HinfI, the PCR products from the 18 isolates that produced L- and/or D-lactate were subsequently cloned and sequenced. DNA sequence analysis indicated that the majority of the isolates were closely related to species within the genus Lactobacillus, including Lactobacillus salivarius, Lactobacillus mucosae and Lactobacillus delbrueckii. Four isolates were closely related to Mitsuokella jalaludinii. Lactic acid producing bacteria (LAB) from the equine gastrointestinal tract was dominated by representatives from the genus Lactobacillus, but also included D-lactate-producing bacteria closely related to M. jalaludinii. Identification and characterization of LAB from the equine gastrointestinal tract should contribute to our understanding and management of fermentative acidosis, ulceration of the stomach and laminitis.     

Effect of condensed tannins on bacterial diversity and metabolic activity in the rat gastrointestinal tract

The effect of dietary condensed tannins (proanthocyanidins) on rat fecal bacterial populations was ascertained in order to determine whether the proportion on tannin-resistant bacteria increased and if there was a change in the predominant bacterial populations. After 3 weeks of tannin diets the proportion of tannin-resistant bacteria increased significantly (P < 0.05) from 0.3% +/- 5.5% to 25.3% +/- 8.3% with a 0.7% tannin diet and to 47.2% +/- 5.1% with a 2% tannin diet. The proportion of tannin-resistant bacteria returned to preexposure levels in the absence of dietary tannins. A shift in bacterial populations was confirmed by molecular fingerprinting of fecal bacterial populations by denaturing gradient gel electrophoresis (DGGE). Posttreatment samples were generally still distinguishable from controls after 3.5 weeks. Sequence analysis of DGGE bands and characterization of tannin-resistant isolates indicated that tannins selected for Enterobacteriaceae and Bacteroides species. Dot blot quantification confirmed that these gram-negative bacterial groups predominated in the presence of dietary tannins and that there was a corresponding decrease in the gram-positive Clostridium leptum group and other groups. Metabolic fingerprint patterns revealed that functional activities of culturable fecal bacteria were affected by the presence of tannins. Condensed tannins of Acacia angustissima altered fecal bacterial populations in the rat gastrointestinal tract, resulting in a shift in the predominant bacteria towards tannin-resistant gram-negative Enterobacteriaceae and Bacteroides species.     

Sensation in the gastrointestinal tract

There are similarities between sensation in the gastrointestinal tract (GI tract) and somatic sensation. This review concentrates on parasympathetic (vagal) components of GI sensation rather than the sympathetic (splanchnic) elements. A wide range of enteroceptors have been described over the whole length of the gut which subserve several different sensory modalities. Fibres from these enteroceptors project to the medulla, primarily to the nucleus of the solitary tract. In the medulla there is considerable integration of afferent information from different parts of the GI tract. Regulatory peptides are present both in the brain and in the GI tract. It is likely that these peptides may play a role in the modulation of sensory information in the medulla. Parallels may be drawn at a receptor level between somatic sensation and sensation in the GI tract. More centrally, sensory mechanisms relating to the gut seem less highly organized than in somatic sensation. This reduced influence of the central nervous system in GI tract sensation may be explained by the presence in the gut of a highly sophisticated intrinsic nervous system, the enteric nervous system, which pre-programmes many of the functions of the GI tract.     

Rates of fermentative digestion in the howler monkey, Alouatta palliata (primates: ceboidea)

1. Caecal material of wild howler monkeys was analyzed by gas chromatography for evidence of fermentation activity and rates of production and absorption of volatile fatty acids. 2. Results showed a high rate of production of acetic acid and lesser production of propionic, butyric and isobutyric acids. The VFA content of the blood was increase in passage through the caecal vascular system. 3. We estimate that howler monkeys may obtain as much as 31% of their required daily energy from fermentation end products. 4. Energy rich fatty acids may be of particular importance to howlers when they are living on diets high in leaves, which have high cell wall contents and low contents of nonstructural carbohydrates.     

Biofuels generation from sweet sorghum: fermentative hydrogen production and anaerobic digestion of the remaining biomass

The present study focuses on the exploitation of sweet sorghum biomass as a source for hydrogen and methane. Fermentative hydrogen production from the sugars of sweet sorghum extract was investigated at different hydraulic retention times (HRT). The subsequent methane production from the effluent of the hydrogenogenic process and the methane potential of the remaining solids after the extraction process were assessed as well. The highest hydrogen production rate (2550 ml H(2)/d) was obtained at the HRT of 6h while the highest yield of hydrogen produced per kg of sorghum biomass was achieved at the HRT of 12h (10.4l H(2)/kg sweet sorghum). It has been proved that the effluent from the hydrogenogenic reactor is an ideal substrate for methane production with approximately 29l CH(4)/kg of sweet sorghum. Anaerobic digestion of the solid residues after the extraction process yielded 78l CH(4)/kg of sweet sorghum. This work demonstrated that biohydrogen production can be very efficiently coupled with a subsequent step of methane production and that sweet sorghum could be an ideal substrate for a combined gaseous biofuels production.     

Prostaglandins: effects on the gastrointestinal tract

Several prostaglandins have been shown to exert five major gastrointestinal actions. Inhibition of gastric acid secretion, orally and parenterally. Antiulcer activity (they prevent gastric and duodenal ulcers produced experimentally in animals, and they accelerate the rate of healing of duodenal ulcers in humans). Cytoprotection for the stomach, the small and the large intestine. Cytoprotection is defined as the property of many prostaglandins to protect the mucosa of the stomach and intestine from becoming inflamed and necrotic when this mucosa is exposed to noxious agents. Cytoprotection is separate from, and unrelated to, inhibition of gastric secretion. In humans, certain prostaglandins of the E type given at very low doses prevent gastric bleeding produced by aspirin and indomethacin. Stimulation of intestinal secretion, through increase of cyclic AMP formation. Stimulation of smooth muscle contraction. Certain prostaglandins are likely to be beneficial in the treatment of gastric ulcers, stress ulcers, duodenal ulcers, and perhaps gastritis and certain forms of inflammatory bowel disease.     

Taste receptors in the gastrointestinal tract. V. Acid sensing in the gastrointestinal tract

Luminal acidity is a physiological challenge in the foregut, and acidosis can occur throughout the gastrointestinal tract as a result of inflammation or ischemia. These conditions are surveyed by an elaborate network of acid-governed mechanisms to maintain homeostasis. Deviations from physiological values of extracellular pH are monitored by multiple acid sensors expressed by epithelial cells and sensory neurons. Acid-sensing ion channels are activated by moderate acidification, whereas transient receptor potential ion channels of the vanilloid subtype are gated by severe acidosis. Some ionotropic purinoceptor ion channels and two-pore domain background K(+) channels are also sensitive to alterations of extracellular pH.     

Growth media in anaerobic fermentative processes: The underestimated potential of thermophilic fermentation and anaerobic digestion

Fermentation and anaerobic digestion of organic waste and wastewater is broadly studied and applied. Despite widely available results and data for these processes, comparison of the generated results in literature is difficult. Not only due to the used variety of process conditions, but also because of the many different growth media that are used. Composition of growth media can influence biogas production (rates) and lead to process instability during anaerobic digestion. To be able to compare results of the different studies reported, and to ensure nutrient limitation is not influencing observations ascribed to process dynamics and/or reaction kinetics, a standard protocol for creating a defined growth medium for anaerobic digestion and mixed culture fermentation is proposed. This paper explains the role(s) of the different macro- and micronutrients, as well as the choices for a growth medium formulation strategy. In addition, the differences in nutrient requirements between mesophilic and thermophilic systems are discussed as well as the importance of specific trace metals regarding specific conversion routes and the possible supplementary requirement of vitamins. The paper will also give some insight into the bio-availability and toxicity of trace metals. A remarkable finding is that mesophilic and thermophilic enzymes are quite comparable at their optimum temperatures. This has consequences for the trace metal requirements of thermophiles under certain conditions. Under non-limiting conditions, the trace metal requirement of thermophilic systems is about 3 times higher than for mesophilic systems.     

Membrane receptors in the gastrointestinal tract

This review focusses on the roles that membrane receptors and their transducers play in the physiology and pathology of the gastrointestinal tract. The multifactorial: factorial regulation of mucosal growth and function is discussed in relation to the heterogeneity of exocrine and endocrine populations that originate from progenitor cells in stomach and intestine.