The intestinal microbiota: from health to disease,and back

Our understanding of the composition and the function of the intestinal microbiota has significantly increased over the past few years. In a series of reviews focusing on the role of the intestinal microbiota in health and disease, we explore recent conceptual and technological advances in this rapidly evolving research arena.     

Antibiotic resistance determinants in the interplay between food and gut microbiota

A complex and heterogeneous microflora performs sugar and lactic acid fermentations in food products. Depending on the fermentable food matrix (dairy, meat, vegetable etc.) as well as on the species composition of the microbiota, specific combinations of molecules are produced that confer unique flavor, texture, and taste to each product. Bacterial populations within such "fermented food microbiota" are often of environmental origin, they persist alive in foods ready for consumption, eventually reaching the gastro-intestinal tract where they can interact with the resident gut microbiota of the host. Although this interaction is mostly of transient nature, it can greatly contribute to human health, as several species within the food microbiota also display probiotic properties. Such an interplay between food and gut microbiota underlines the importance of the microbiological quality of fermented foods, as the crowded environment of the gut is also an ideal site for genetic exchanges among bacteria. Selection and spreading of antibiotic resistance genes in foodborne bacteria has gained increasing interest in the past decade, especially in light of the potential transferability of antibiotic resistance determinants to opportunistic pathogens, natural inhabitants of the human gut but capable of acquiring virulence in immunocompromised individuals. This review aims at describing major findings and future prospects in the field, especially after the use of antibiotics as growth promoters was totally banned in Europe, with special emphasis on the application of genomic technologies to improve quality and safety of fermented foods.     

A role for supplements in optimizing health: the metabolic tune-up

An optimum intake of micronutrients and metabolites, which varies with age and genetic constitution, would tune up metabolism and give a marked increase in health, particularly for the poor, young, obese, and elderly, at little cost. (1) DNA damage. Deficiency of vitamins B-12, folic acid, B-6, C or E, or iron or zinc appears to mimic radiation in damaging DNA by causing single- and double-strand breaks, oxidative lesions or both. Half of the population may be deficient in at least one of these micronutrients. (2) The Km concept. Approximately 50 different human genetic diseases that are due to a poorer binding affinity (Km) of the mutant enzyme for its coenzyme can be remedied by feeding high-dose B vitamins, which raise levels of the corresponding coenzyme. Many polymorphisms also result in a lowered affinity of enzyme for coenzyme. (3) Mitochondrial oxidative decay. This decay, which is a major contributor to aging, can be ameliorated by feeding old rats the normal mitochondrial metabolites acetyl carnitine and lipoic acid at high levels. Many common micronutrient deficiencies, such as iron or biotin, cause mitochondrial decay with oxidant leakage leading to accelerated aging and neural decay.     

Structure and predictive metabolic contribution of intestinal microbiota of Longfin yellowtail (Seriola rivoliana) juveniles in aquaculture systems

Molecular Biology Reports - Seriola rivoliana intestinal microbiota (IM) was characterised under aquaculture conditions through 16S rRNA amplicon sequencing. Specimens of 30 days after...     

Amino acid sequence homology between ligands and their receptors: potential identification of binding sites

Mice were immunized with alpha-bungarotoxin (BGT), a nearly irreversible antagonist of the acetylcholine receptor (AChR), to produce monoclonal antibodies (Mabs). One of the Mabs (JMC2.7) bound not only to BGT, but to the AChR as well. To understand the molecular basis for this novel cross-reaction, the amino acid sequences of these proteins were searched for areas of similarity which might constitute the shared epitope. A number of short segments of sequence homology were found, one of them representing the BGT-binding site of the AChR. Because a portion of BGT resembles that part of the AChR that binds toxin, the self-binding of BGT was evaluated. As shown here, BGT binds specifically to itself to form dimers. In order to extend these observations, other ligand-receptor pairs were examined for sequence homology. The sodium channel and alpha-scorpion toxins were found to have distinct areas of similarity, as do interleukin 2 (IL-2) and the IL-2 receptor. As a general principle, we propose that peptide ligands and their receptors may often share amino acid sequence homology. In fact, the sites of interaction between two proteins may largely be determined by these regions of similarity.     

Neonatal environment exerts a sustained influence on the development of the intestinal microbiota and metabolic phenotype

The postnatal environment, including factors such as weaning and acquisition of the gut microbiota, has been causally linked to the development of later immunological diseases such as allergy and autoimmunity, and has also been associated with a predisposition to metabolic disorders. We show that the very early-life environment influences the development of both the gut microbiota and host metabolic phenotype in a porcine model of human infants. Farm piglets were nursed by their mothers for 1 day, before removal to highly controlled, individual isolators where they received formula milk until weaning at 21 days. The experiment was repeated, to create two batches, which differed only in minor environmental fluctuations during the first day. At day 1 after birth, metabolic profiling of serum by ¹H nuclear magnetic resonance spectroscopy demonstrated significant, systemic, inter-batch variation which persisted until weaning. However, the urinary metabolic profiles demonstrated that significant inter-batch effects on 3-hydroxyisovalerate, trimethylamine-N-oxide and mannitol persisted beyond weaning to at least 35 days. Batch effects were linked to significant differences in the composition of colonic microbiota at 35 days, determined by 16 S pyrosequencing. Different weaning diets modulated both the microbiota and metabolic phenotype independently of the persistent batch effects. We demonstrate that the environment during the first day of life influences development of the microbiota and metabolic phenotype and thus should be taken into account when interrogating experimental outcomes. In addition, we suggest that intervention at this early time could provide ‘metabolic rescue'' for at-risk infants who have undergone aberrant patterns of initial intestinal colonisation.     

Dietary long-chain n-3 PUFA, gut microbiota and fat mass in early postnatal piglet development--exploring a potential interplay

Dietary n-3PUFA and gut bacteria, particularly Bacteroidetes, have been suggested to be related to adiposity. We investigated if n-3PUFA affected fat storage and cecal bacteria in piglets. Twenty-four 4-day-old piglets were allocated to formula rich in n-3PUFA (～3E%) from fish oil (FO) or n-6PUFA from sunflower oil (SO) for 14 days. We assessed body weight, fat accumulation by dual-energy X-ray absorptiometry and microbial molecular fingerprints. Dietary PUFA-composition was reflected in higher erythrocyte n-3PUFA in the FO- than the SO-group (P<0.001). Principal component analysis revealed group differences in the overall microbiotic composition, which involved a larger Bacteroides community in the SO-group (P=0.02). There was no significant difference in body fat percentage and no relationship between fat accumulation and gut Bacteroides. Hence, this study does not support an impact of n-3PUFA or microbiota on fat accumulation during the postnatal maturation period. The impact of dietary PUFA on the gut Bacteroides warrants further investigation.     

Differences in developing intestinal microbiota between allergic and non-allergic infants: a pilot study in Japan

The bacterial compositions of feces were monitored in the first 2 months for 15 infants born in Japan, including eight subjects who developed allergy by the age of 2 years. Primer sets targeting six predominant bacterial groups in the infant intestine, Bacteroidaceae, Enterobacteriaceae, bifidobacteria, enterococci, lactobacilli, and the Clostridium perfringens group, were used for real-time PCR to quantitate each population in the feces. The population of Bacteroidaceae was significantly higher in the allergic group at the ages of 1 month (P=0.03) and 2 months (P=0.05) than in the non-allergic group, while no statistically significant difference was observed for the other bacterial populations.     

Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears

The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C.?perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.     

Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry

Immune function is influenced by the diversity and stability of the intestinal microbiota. A likely trade-off of immune function for growth has been demonstrated in heavier breeds of poultry that have been genetically selected for growth and feed efficiency traits. We investigated the expression of selected innate immune genes and genes encoding products involved in intestinal barrier function to determine whether function changes could be consistently linked to the phenotypic expression of feed conversion ratio (FCR), a common measure of performance within poultry broiler flocks. In addition, we compared individual cecal microbial composition with innate immune gene expression. Samples were utilised from two replicate trials termed P1E1 and P1E2. High (n = 12) and low (n = 12) performing birds were selected based on their individual FCR data from each replicate and combined for microbiota phylogenetic composition and immune gene expression analysis. Toll-like receptor 1 (TLR1La) and zonula occludens 1 (ZO1) were differentially expressed between high- and low-performing broilers. Several taxa were correlated with FCR; of these, unclassified YS2 and ZO1 were also positively correlated with each other. Interactions between taxa and differentially expressed innate immune genes between P1E1 and P1E2 were much greater compared to relationships between high- and low-performing birds. At the level of phylum, reciprocal correlations between tight junction proteins and Toll-like receptors with Bacteroidetes and Firmicutes were evident, as were correlations at the genus level.

     

Amino acid transport systems in animal cells: Interrelations and energization

After summarizing the discrimination of the several transport systems of neutral amino acids in the cell of the higher animal, I discuss here the ways in which 2 dissimilar transport systems interact, so that one tends to run forward for net entry and the other backwards for net exodus. An evaluation of the proposals for energization shows that uphill transport continues when neither alkali-ion gradients nor ATP levels are favorable. Evidence is presented that under these conditions a major contribution is made by another mode of energization, which may depend on the fueling of an oxidoreductase in the plasma membrane. This fueling may involve the export by the mitochondrion of the reducing equivalents of NADH by one of the known shuttles, e.g., the malate-aspartate shuttle. After depletion of the energy reseves in the Ehrilich cell by treating it with dinitrophenol plus iodoacetate concentrative uptake of test amino acids is restoration by pyruvate but in poor correlation with the restoration of alkali-ion gradients and ATP levels. This restoration by pyruvate but not by glucose is highly senstitive to rotenone. A combination of phenazine methosulfate and ascorbate will also produce transport restoration, before either the alkali-ion gradients or ATP levels have begun to rise. The restoration of transport applies to a model amino acid entering by the Na⁺-independent system, as well as to one entering by the principal Na⁺-dependent system, restoration being blocked by ouabain, despite the weak effect of ouabain on the alkali-ion gradients in the Ehrlich cell. Quinacrine terminates very quickly the uptake of model amino acids, before the alkali-ion gradients have begun to fall and before the ATP level has been halved. Quinacrine is also effective in blocking restoration of uphill transport by either pyruvate or the phenazine reagent. Preliminary results show that vesicles prepared from the plasma membrane of the Ehrlich cell quickly reduce cytochrome c or ferricyanide in the presence of NADH, and that the distribution of a test amino acid between the vesicle and its environment is influenced by NADH, quinacrine, and an uncoupling agent in ways consistent with the above proposal, assuming that a majority of the vesicles are everted.     

Molecular link between dietary fibre,gut microbiota and health

Molecular Biology Reports - Natural polysaccharides cellulose, hemicelluloses, inulin etc., galactooligosaccharides (GOS), and fructooligosaccharides (FOS) play a significant role in the...