| A large variety of symbiotic microorganisms coexist in the mammalian digestive tract,which constitutes a complex ecosystem.Over the past decade,powered by the progress in sequencing technology and new developments in bioinformatics,ample evidence on the relationship between the gut microbiome and host pathology has rapidly accumulated.Currently,many alimentary and extraintestinal diseases are thought to be associated with gut microbiota dysbiosis.Even though most of the samples used were from feces and the appropriateness of using feces as a proxy for other gastrointestinal(GI)segments remained questioned.These findings still elicited scientific and industrial interests in modulating the composition and metabolic signatures of this natural micro-ecosystem,to maintain or promote human nutritional and health status.One of these modulating strategies is dietary regulation.The great influence of diet in shaping gut microbiota has been validated in human populations and laboratory animals.Amongst a wide array of dietary ingredients that are a part of our daily intake,non-digestible carbohydrates are considered as one major factor controlling the community dynamics for the particular fate of these compounds in the mammalian intestine.Historically,some oligomers were termed as prebiotics.Numerous nutrition and clinical surveys have shown beneficial physiological effects of these prebiotic carbohydrates in healthy individuals and in those with acute and chronic diseases,where the prebiotic effects,to a large degree,were attributed to the selective stimulation of the growth or activity of several indigenous health-promoting bacteria(probiotics),such as Bifidobacteria(i.e.,the bifidogenic effect)and Lactobacilli.However,recent researches suggest that the capacity for utilizing prebiotic oligosaccharides is not just limited to the probiotic species.In the complex gut micro-ecosystem,some less-beneficial taxonomic groups,even putrefactive bacteria and potential pathogens,also possess the key genes responsible for the oligosaccharide catabolism and could use these substrates as a sole carbon source for growth.Meanwhile,an increasing number of in vivo investigations exploiting the latest omics technologies further confirmed that multiple taxa,rather than particular species,responded to the prebiotic interventions.Besides,under certain context and doses,the dysregulated fermentation of prebiotic carbohydrates could bring about a series of adverse effects,such as GI discomfort,osmotic and fermentative diarrhea,increasing colonic permeability,impairing the intestinal resistance to pathogen infection,exacerbating the severity of colitis and even inducing icteric hepatocellular carcinoma.Thus,the local and systemic influences of prebiotics on host physiology,directly or through modulating the intestinal microbiome,are subtle and complex and deserve further investigation.Due to limitations in human research,murine models have become crucial in studies of the gut microbiota designed to obtain mechanism insights into different anatomical regions through radical and sometimes even destructive means.Given the fact that a comprehensive characterization of the normal microbiome landscape is a critical prerequisite to understanding and predicting disease-related alterations in microbial communities.In the present study,we first characterized the baseline microbial structure,membership,diversity,and metabolic potential of the GI microbiome inhabiting the length of the rat digest tract.Then through integrating the datasets from other rodents,we further systematically investigated the bacterial biogeography and functional microbiome of the murine gastrointestinal tract(GIT).It is known that the foothold of structure or composition modulation is to augment the probiome and finally optimize the whole intestinal metabolism.However,there is limited data available regarding the impact of prebiotic dosing on the gut metagenome and the functional benefits or potential risks it poses.Hence,we next investigated the effects of two prebiotic oligosaccharides frequently used in pharmaceutical and nutrition care on the microbial metabolism along the longitudinal and radial axes of mice GIT.The functional capacities of the gut microbiome following multiple-dose prebiotic administrations were analyzed and compared via a series of longitudinal and cross-sectional trials.Results are summarized as follows:(?)When comparing the GI microbiota from different murine hosts,the sample points mainly clustered according to the metadata recording host information(adonis:R~2?=?0.25;p?0.001).The rat microbial biogeographic map represented a new reference,distinct from other murine animals.However,when the GI microbiomes of different murine hosts were compared,many functional overlaps were observed.In other words,if opening the envelopes of microbiota and exposing the internal metabolic functions,the entropy increased.This phenomenon implied that although both the biogeographic location and host genotype were prominent driving forces in shaping the gastrointestinal microbiota,the microbiome functions were similar across hosts when observed under similar physicochemical conditions at identical anatomical sites.(?)In contrast to the situations regarding structure(R~2=0.14;p=0.003)and membership(R~2=0.09;p=0.02),the permutational multivariate analysis of variance(PERMANOVA)result revealed that the individual subject was no longer a significant categorical factor(R~2=0.09;p=0.18)with respect to community function.To some extent,this weakened stratification was in line with the HMP results,which showed the taxonomic variety versus metabolic stability within a healthy population.However,when the microbiome was challenged with lactulose,sample points from the same subject were found locally aggregating together.PERMANOVA results further confirmed the significance of these functional agglomeration(lumen:R~2=0.13,p=0.002;mucosa:R~2=0.10,p?0.001).This discrepancy is not surprising because the direct acting point of oligosaccharide driver is specific microorganisms rather than metabolic processes.For different subjects,bacteria possessing key genes for oligosaccharide catabolism may locate in different positions on the pathway network.When stimulated with non-digestible oligosaccharides,the proliferation of these bacteria,along with the production of other induced enzymes,caused inter-subject intestinal metabolism to migrate towards distinct directions.In other words,the prebiotic driving force would smash into the intestinal metabolism and scattered original metabolic homogeneity to a heterogenetic landscape.(?)Community diversity increased from the upper to lower GI segments.Taxonomic stratification in community composition,as well as metabolic heterogeneity in community function,were driven by biogeographic location.In accordance with previously imaged oxygen gradient,aerobic energy metabolism was mainly enriched in the stomach and the core microbiota evolved from aerobic(such as Phyllobacterium,Pseudomonas and Acidovorax)to facultative anaerobic(such as Lactococcus,Staphylococcus,Streptococcus,and Globicatella)to obligatory anaerobic along the gut longitudinal axis.A greater proportion of lactate-producing bacteria(such as Lactobacillus,Turicibacter,and Streptococcus)were found in the stomach and small intestine,where the small-molecule transport and amino acid metabolic activities were prevalent.While anaerobes fermenting carbohydrates and plant aromatic compounds constituted the bulk of the large-intestinal core microbiota,and mucolysis-related metabolism was enriched in the mucosal microbiome.In contrast to the case of the subject factor,the spatially metabolic heterogeneity was reinforced by prebiotic treatment in a dose-related manner.At different sampling sites,the functional variance explained by dietary regulation varied:along the longitudinal axis of the colon,diet-explaining variance decreased from 39.97%(proximal colonic contents)to 32.81%(middle colonic contents)then finally to 26.59%(distal colonic contents);in the distal colonic mucus layer diet explained the least variance(20.83%).These phenomena were probably attributed to the oligosaccharide gradient along the length of the lower digestive tract,where active saccharolytic fermentation gradually exhausted these substrates in the process of intestinal migration.(?)Despite community memberships overlapping to some extent,the co-occurrence networks for the adjacent luminal and mucosal niches in large-intestine showed distinct topological properties.In the lumen,core microbiota formed a relatively sparse network(diameter:8;centralization:0.18;density:0.17)where 28 anaerobic organisms belonging to 3different phyla connected on average to 4.571 neighbors.In the mucus layer,the core population of microbes formed several heterogeneous modules.Notably,15 obligatory anaerobic organisms formed a dense subnetwork(diameter:3;centralization:0.43;density:0.49).Most of the genera in this subnetwork were affiliated to Lachnospiraceae and Ruminococcaceae,with an average of 6.8 neighbors connected to one another.Accordingly,compared with the luminal compartment,the mucosal microbiome was less disturbed by dietary regulation under both low-(12.6%vs.19.8%)and high-dose(26.3%vs.32.2%)treatments.This could be attributed to the richness of endogenous mucin oligosaccharides in these niches,which can buffer the driving force from exogenous dietary oligosaccharides.(?)As prebiotic oligosaccharides can escape host digestion and reach the lower GIT intact,their modulation on gut micro-ecosystem is realized in a direct manner.The effect size of prebiotic administration was related to the molecular structure and intervention dosage of these oligomers.Excessive ingestion of the prebiotics would reduce the diversity of ecosystem services and overturn the trophic balance in the gut.The distribution pattern of COG categories highlighted the dominance of E cluster(amino acid transport and metabolism)after administration.Correspondingly,Bifidobacterium species preferring proteolytic fermentation were in dominant positions,exemplified by the relative abundance of Bifidobacterium adolescentis(E/G=1.128;increasing from 0.86%to 25%)in FOS-high group,and the relative abundances of Bifidobacterium gallicum(E/G=1.363;lumen:64.83%,mucus layer:28.17%)in Lactulose-high group.Meanwhile,the levels of several protein fermentation metabolites such as methanethiol,hydrogen sulfide,phenol,and polyamines,as well as bacterial toxins,showed an increasing trend.On the contrary,in gut metagenomes the abundances ofb-glucuronidase,azoreductase,and urease genes,as well as the abundances of genes involved in indoles,skatole,phenylacetic acid,p-cresol,and secondary bile acid generation decreased.The mechanism behind these effects is speculated as follows:Besides stimulating the intestinal Lactobacilli and Bifidobacteria,prebiotic oligosaccharides could also be utilized by potential pathogens which are usually in low abundance but produce toxins.When the gut symbiotic microorganisms are exposed to excess amounts of prebiotics,the bloom of these detrimental bacteria plus the rapid fermentation of prebiotic oligomers will cause local accumulation of the bacterial toxins and organic acids,which make luminal contents more aggressive.As a defense measure,the intestinal mucosa will be triggered to secrete more mucin.High concentrations of short-chain fatty acids(SCFAs)also will damage the intestinal epithelium,resulting in increased shedding of epithelial cells.These will change the trophic status within the gut and finally break the equilibrium between saccharolytic and proteolytic fermentation,which was reflected in the switch of mucinases mucolytic bacteria used to degrade the mucin glycoprotein. |
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