Dietary glycated protein modulates the colonic microbiota towards a more detrimental composition in ulcerative colitis patients and non-ulcerative colitis subjects

Aim:  To investigate the effect of native, heated and glycated bovine serum albumin (BSA) on the ulcerative colitis (UC) and non-UC colonic microbiota in vitro .
Methods and Results:  Continuous flow culture (CFC) models of the human colonic microbiota inoculated with faeces from UC and non-UC volunteers were maintained on BSA as growth substrate. Changes in bacterial populations and short-chain fatty acids were determined. UC and non-UC microbiota differed significantly in microbial populations, with elevated numbers of sulfate-reducing bacteria (SRB) and clostridia in the microbiota from UC patients. Compared with native BSA, glycated BSA modulated the gut microbiota of UC patients in vitro towards a more detrimental community structure with significant increases in putatively harmful bacteria (clostridia, bacteroides and SRB; P  < 0·009) and decreases in dominant and putatively beneficial bacterial groups (eubacteria and bifidobacteria; P  < 0·0004). The levels of beneficial short-chain fatty acids were significantly decreased by heated or glycated BSA, but were increased significantly by native BSA.
Conclusion:  The UC colonic microbiota maintained in CFC was significantly modified by glycated BSA.
Significance and Impact of the Study:  Results suggest that dietary glycated protein may impact upon the composition and activity of the colonic microbiota, an important environmental variable in UC.     

On the relationship between sialomucin and sulfomucin expression and hydrogenotrophic microbes in the human colonic mucosa

The colonic mucus layer is comprised primarily of acidomucins, which provide viscous properties and can be broadly classified into sialomucins or sulfomucins based on the presence of terminating sialic acid or sulfate groups. Differences in acidomucin chemotypes have been observed in diseases such as colorectal cancer and inflammatory bowel disease, and variation in sialo- and sulfomucin content may influence microbial colonization. For example, sulfate derived from sulfomucin degradation may promote the colonization of sulfate-reducing bacteria (SRB), which through sulfate respiration generate the genotoxic gas hydrogen sulfide. Here, paired biopsies from right colon, left colon, and rectum of 20 subjects undergoing routine screening colonoscopies were collected to enable parallel histochemical and microbiological studies. Goblet cell sialo- and sulfomucins in each biopsy were distinguished histochemically and quantified. Quantitative PCR and multivariate analyses were used to examine the abundance of hydrogenotrophic microbial groups and SRB genera relative to acidomucin profiles. Regional variation was observed in sialomucins and sulfomucins with the greatest abundance of each found in the rectum. Mucin composition did not appear to influence the abundance of SRB or other hydrogenotrophic microbiota but correlated with the composition of different SRB genera. A higher sulfomucin proportion correlated with higher quantities of Desulfobacter, Desulfobulbus and Desulfotomaculum, relative to the predominant Desulfovibrio genus. Thus, acidomucin composition may influence bacterial sulfate respiration in the human colon, which may in turn impact mucosal homeostasis. These results stress the need to consider mucus characteristics in the context of studies of the microbiome that target intestinal diseases.     

Differential analysis of protein expression of Bifidobacterium grown on different carbohydrates

We observed recently that colonic fermentation of lactose might be a major factor in the pathophysiology of lactose intolerance. Proteomic techniques could be helpful in interpreting the metabolic pathways of lactose fermentation. The objective of this study was to explore proteomic methodologies for studying bacterial lactose metabolism that can be used to detect and identify proteins associated with the onset of intolerance symptoms. Differential expression of cytoplasmic proteins of Bifidobacterium animalis, Bifidobacterium breve and Bifidobacterium longum grown on different carbohydrates (lactose, glucose, galactose) was analyzed with surface-enhanced laser desorption ionization-time of flight (SELDI-TOF) MS and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). After fractionation by SDS-PAGE, differentially-expressed proteins were identified with LC-MS/MS. The three strains grown on the same carbohydrate or the same strain grown on glucose or lactose showed differences in SELDI-TOF MS protein profiles. Differences in protein expression were observed in B. breve grown on glucose, galactose or lactose as analyzed with SDS-PAGE. With LC-MS/MS, proteins from Bifidobacterium were identified, which included enzymes for metabolism of lactose, glucose and galactose. In conclusion, the applied techniques can discern differences in protein expression of bacteria metabolizing different carbohydrates. These techniques are promising in studying metabolism of lactose and other substrates in a complex bacterial ecosystem such as the colonic microbiota.     

Gastrointestinal and microbial responses to sulfate-supplemented drinking water in mice

There is increasing evidence that hydrogen sulfide (H2S), produced by intestinal sulfate-reducing bacteria (SRB), may be involved in the etiopathogenesis of chronic diseases such as ulcerative colitis and colorectal cancer. The activity of SRB, and thus H2S production, is likely determined by the availability of sulfur-containing compounds in the intestine. However, little is known about the impact of dietary or inorganic sulfate on intestinal sulfate and SRB-derived H2S concentrations. In this study, the effects of short-term (7 day) and long-term (1 year) inorganic sulfate supplementation of the drinking water on gastrointestinal (GI) sulfate and H2S concentrations (and thus activity of resident SRBs), and the density of large intestinal sulfomucin-containing goblet cells, were examined in C3H/HeJBir mice. Additionally, a PCR-denaturing gradient gel electrophoresis (DGGE)-based molecular ecology technique was used to examine the impact of sulfate-amended drinking water on microbial community structure throughout the GI tract. Average H2S concentrations ranged from 0.1 mM (stomach) to 1 mM (cecum). A sulfate reduction assay demonstrated in situ production of H2S throughout the GI tract, confirming the presence of SRB. However, H2S generation and concentrations were greatest in the cecum and colon. Sulfate supplementation of drinking water did not significantly increase intestinal sulfate or H2S concentrations, suggesting that inorganic sulfate is not an important modulator of intestinal H2S concentrations, although it altered the bacterial profiles of the stomach and distal colon of 1-year-old mice. This change in colonic bacterial profiles may reflect a corresponding increase in the density of sulfomucin-containing goblet cells in sulfate-supplemented compared with control mice.     

Functional analysis of colonic bacterial metabolism: relevant to health?

With the use of molecular techniques, numerous studies have evaluated the composition of the intestinal microbiota in health and disease. However, it is of major interest to supplement this with a functional analysis of the microbiota. In this review, the different approaches that have been used to characterize microbial metabolites, yielding information on the functional end products of microbial metabolism, have been summarized. To analyze colonic microbial metabolites, the most conventional way is by application of a hypothesis-driven targeted approach, through quantification of selected metabolites from carbohydrate (e.g., short-chain fatty acids) and protein fermentation (e.g., p-cresol, phenol, ammonia, or H(2)S), secondary bile acids, or colonic enzymes. The application of stable isotope-labeled substrates can provide an elegant solution to study these metabolic pathways in vivo. On the other hand, a top-down approach can be followed by applying metabolite fingerprinting techniques based on (1)H-NMR or mass spectrometric analysis. Quantification of known metabolites and characterization of metabolite patterns in urine, breath, plasma, and fecal samples can reveal new pathways and give insight into physiological regulatory processes of the colonic microbiota. In addition, specific metabolic profiles can function as a diagnostic tool for the identification of several gastrointestinal diseases, such as ulcerative colitis and Crohn's disease. Nevertheless, future research will have to evaluate the relevance of associations between metabolites and different disease states.     

The composition and metabolic activity of child gut microbiota demonstrate differential adaptation to varied nutrient loads in an in vitro model of colonic fermentation

The extent to which the dietary loads of simple sugars, carbohydrates, protein, and fiber impact colonic fermentation in children is unknown. This study assessed the impact of dietary energy on gut microbial communities and metabolism using a three-stage in vitro continuous fermentation model. Two separate models, replicating the proximal, transverse, and distal colon regions, were inoculated with immobilized fecal microbiota from one of two female children. Three different fermentation media were designed to examine the effects of prevalent Western dietary trends on gut microbiota. Media compositions reflected obese (high energy), normal weight (normal energy), and anorectic (low energy) child dietary intakes and were alternately supplied to each microbiota during separate fermentation periods. Gut microbiota demonstrated differential metabolic and compositional adaptation to varied substrate availability. High energy medium was strongly butyrogenic, resulting in significant stimulation of butyrate-producing members of clostridia cluster XIVa, whereas members of cluster IV demonstrated greater adaptive variability. Normal and low energy nutrient loads induced significantly less metabolic activity in both microbiota, with low energy medium inducing a broad reorganization of the commensal community structure. These results suggest a concerted metabolic adaptation in response to nutrient load, exercised by different microbial populations, indicating substantial redundancy in gastrointestinal metabolic pathways.     

The association of diet,gut microbiota and colorectal cancer: what we eat may imply what we get

Despite the success of colonoscopy screening and recent advances in cancer treatment, colorectal cancer (CRC) still remains one of the most commonly diagnosed and deadly cancers, with a significantly increased incidence in developing countries where people are adapting to Western lifestyle. Diet has an important impact on risk of CRC. Multiple epidemiological studies have suggested that excessive animal protein and fat intake, especially red meat and processed meat, could increase the risk of developing CRC while fiber could protect against colorectal tumorigenesis. Mechanisms have been investigated by animal studies.Diet could re-shape the community structure of gut microbiota and influence its function by modulating the production of metabolites. Butyrate, one of the short-chain fatty acids (SCFAs), which act as a favorable source for colonocytes, could protect colonic epithelial cells from tumorigenesis via anti-inflammatory and antineoplastic properties through cell metabolism, microbiota homeostasis, antiproliferative, immunomodulatory and genetic/epigenetic regulation ways. In contrast, protein fermentation and bile acid deconjugation, which cause damage to colonic cells through proinflammatory and proneoplastic ways, lead to increasedriskofdevelopingCRC.In conclusion, abalanced diet with an increased abundance of fiber should be adopted to reduce the risk and prevent CRC.     

The development of human gut microbiota fermentation capacity during the first year of life

Fermentation capacity of microbial ecosystems intrinsically depends on substrate supply and the ability of a microbial community to deliver monomers for fermentation. In established microbial ecosystems, the microbial community is adapted to efficiently degrade and ferment available biopolymers which is often concurrently reflected in the richness of the microbial community and its functional potential. During the first year of life, the human gut microbial environment is a rather dynamic system that is characterized by a change in physiological conditions (e.g. from aerobic to anaerobic conditions, physical growth of the gastrointestinal tract, development of the intestinal immune system) but also by a change in nutrient supply from a compositionally limited liquid to a diverse solid diet, which demands major compositional and functional changes of the intestinal microbiota. How these transitions link to intestinal microbial fermentation capacity has gained comparatively little interest so far. This mini-review aims to collect evidence that already after birth, there is seeding of a hidden population of various fermentation organisms which remain present at low abundance until the cessation of breastfeeding removes nutritional restrictions of a liquid milk-based diet. The introduction of solid food containing plant and animal material is accompanied by an altering microbiota. The concurrent increases in the abundance of degraders and fermenters lead to higher intestinal fermentation capacity indicated by increased faecal levels of the final fermentation metabolites propionate and butyrate. Recent reports indicate that the development of fermentation capacity is an important step during gut microbiota development, as chronic disorders such as allergy and atopic dermatitis have been linked to lower degradation and fermentation capacity indicated by reduced levels of final fermentation metabolites at 1 year of age.     

Inclusion of chicory (Cichorium intybus L.) in pigs' diets affects the intestinal microenvironment and the gut microbiota

The content and composition of prebiotic plant fiber in the diet is important in promoting gut-related health. This study investigated the effects of the dietary inclusion of chicory forage and roots on the intestinal microenvironment of pigs. Thirty-seven-week-old pigs were fed 1 of 5 diets for 18 days, including a cereal-based control diet and 4 diets with the inclusion of 80 and 160 g kg(-1) of body weight chicory forage (CF80 and CF160), 80 g kg(-1) chicory root (CR80), and a mix of 80 g kg(-1) forage and 80 g kg(-1) chicory root (CFR). The animals maintained good performance and health irrespective of diet. Bacterial community structure and diversity in ileal and colonic samples was assessed using terminal restriction fragment length polymorphism (T-RFLP), combined with cloning and sequencing. Samples clustered perfectly according to gut segment with a higher bacterial diversity in colon than ileum. Distal ileum was dominated by lactic acid bacteria (LAB), and the relative amount of this group was increased by the CF160 and CFR diets. The colonic bacterial community was dominated by butyrate-producing bacteria and Prevotella. The increased relative abundance of butyrate-producing bacteria in the colon was positively correlated with the molar proportion of acetic acid and furthermore linked to the chicory forage diets (CF80 and CF160). Diets including chicory roots (CR80 and CFR) were correlated with a higher colonic abundance of Megasphaera elsdenii. The fermentation products and pH in digesta responded to diet type and were correlated with shifts in the microbiota, showing that chicory influences the intestinal microenvironment of pigs.     

Dietary calcium phosphate content and oat β-glucan influence gastrointestinal microbiota, butyrate-producing bacteria and butyrate fermentation in weaned pigs

This study aimed to evaluate the effects of oat β-glucan in combination with low- and high-dietary calcium phosphate (CaP) content on gastrointestinal bacterial microbiota, prevalence of butyrate-production pathway genes and fermentation end-products in 32 weaned pigs allocated to four diets: a cornstarch-casein-based diet with low [65% of the calcium (Ca) and phosphorous (P) requirement] and high CaP content (125% and 115% of the Ca and P requirement, respectively); and low and high CaP diets supplemented with 8.95% of oat β-glucan concentrate. Pigs were slaughtered after 14 days, and digesta were collected for quantitative PCR analysis, and quantification of short-chain fatty acids and lactate. The high CaP content reduced gastric lactate and streptococci and propionate in the large intestine. Oat β-glucan distinctly raised gastric bacterial numbers, and colonic lactobacilli and bifidobacteria. Although not reflected by gene copies of butyrate-production pathway genes, oat β-glucan also increased gastric, caecal and colonic butyrate concentrations, which may be favourable for intestinal development in weaned pigs. Thus, a high CaP content negatively affected the intestinal abundance of certain fermentation end-products, whereas oat β-glucan generally enhanced bacterial numbers and activity. The results emphasize the importance of the stomach for bacterial metabolism of oat β-glucan in weaned pigs.     

铁皮石斛多糖对高脂饮食小鼠肠黏膜结构及菌群的影响

为考察铁皮石斛多糖对高脂饮食小鼠肠黏膜屏障的影响,采用水提醇沉法提取铁皮石斛多糖,联合高脂饲料给予小鼠8周后观察肠黏膜结构及肠黏膜菌群的变化。结果显示高脂饮食显著破坏了肠黏膜结构,表现为肠黏膜萎缩,上皮细胞脱落并伴有炎性渗出,Corynebacterium_1及Staphylococcus等与感染及炎症相关的菌属大量增殖。铁皮石斛多糖对肠黏膜结构有较好的保护作用,并可减少Corynebacterium_1的丰度,同时提高肠黏膜共生菌Candidatus_Arthromitus的丰度,促进了Muribaculaceae、Bacteroides、Lachnospiraceae_NK4A136_group等碳水化合物代谢、短链脂肪酸产生相关菌的增殖。研究表明铁皮石斛多糖对肠黏膜屏障的保护作用或与其维持肠黏膜结构完整,调节肠黏膜菌群组成及促进碳水化合物代谢,生成短链脂肪酸有关。     

Alterations in the Colonic Microbiota of Pigs Associated with Feeding Distillers Dried Grains with Solubles

In an effort to reduce feed costs, many pork producers have increased their use of coproducts of biofuel production in commercial pig diets, including increased feeding of distiller’s dried grains with solubles (DDGS). The inclusion of DDGS increases the insoluble fiber content in the ration, which has the potential to impact the colonic microbiota considerably as the large intestine contains a dynamic microenvironment with tremendous interplay between microorganisms. Any alteration to the physical or chemical properties of the colonic contents has the potential to impact the resident bacterial population and potentially favor or inhibit the establishment of pathogenic species. In the present study, colonic contents collected at necropsy from pigs fed either 30% or no DDGS were analyzed to examine the relative abundance of bacterial taxa associated with feeding this ingredient. No difference in alpha diversity (richness) was detected between diet groups. However, the beta diversity was significantly different between groups with feeding of DDGS being associated with a decreased Firmicutes:Bacteriodetes ratio (P = .004) and a significantly lower abundance of Lactobacillus spp. (P = .016). Predictive functional profiling of the microbiota revealed more predicted genes associated with carbohydrate metabolism, protein digestion, and degradation of glycans in the microbiota of pigs fed DDGS. Taken together, these findings confirm that alterations in dietary insoluble fiber significantly alter the colonic microbial profile of pigs and suggest the resultant microbiome may predispose to the development of colitis.     

高通量测序方法分析两种草食性淡水螺肠道菌群多样性

淡水螺是水生态系统中重要的生物类群，也是多种寄生虫的中间宿主。肠道菌群在动物能量代谢和抵抗病原体方面起着重要作用。本文分析了耳萝卜螺Radix auricularia和三旋卷丽螺Planorbella trivolvis肠道菌群的多样性。结果表明：在门水平上，耳萝卜螺有23个菌门，以变形菌门 (Proteobacteria，33.63%)、蓝细菌门(Cyanobateria，15.33%)、绿弯菌门 (Chloroflexi，13.95%) 和放线菌门 (Actinobacteria，12.99%)为主；三旋卷丽螺有13个菌门，以变形菌门 (54.88%)、拟杆菌门 (Bacteroidetes，28.49%) 和放线菌门 (7.65％) 为主。属水平上，耳萝卜螺有厚皮藻属Pleurocapsa、硫网菌属Thiodictyon、纤毛菌属Leptotrichia及类诺卡氏菌属Nocardioides等445个属；三旋卷丽螺有Cloacibacterium、OM60NOR5_clade、假单胞菌属Pseudomonas及红杆菌属Rhodobacter等238个属。有93个菌属为两种螺的共有核心菌群 (所有样本中都存在)，其中27个菌属丰度大于0.5%。两种螺肠道菌群结构差异显著 (P=0.027)。PICRUSt功能预测分析表明，两种螺肠道菌群KEGG功能组成相似，氨基酸代谢、碳水化合物代谢及膜转运丰度较大。综上，两种草食性淡水螺肠道菌群多样性较高且差异显著，但有数量较多的共有核心菌群。     

铁皮石斛多糖对高脂饮食小鼠肠黏膜结构及菌群的影响

为考察铁皮石斛多糖对高脂饮食小鼠肠黏膜屏障的影响,采用水提醇沉法提取铁皮石斛多糖,联合高脂饲料给予小鼠8周后观察肠黏膜结构及肠黏膜菌群的变化。结果显示高脂饮食显著破坏了肠黏膜结构,表现为肠黏膜萎缩,上皮细胞脱落并伴有炎性渗出,Corynebacterium_1及Staphylococcus等与感染及炎症相关的菌属大量增殖。铁皮石斛多糖对肠黏膜结构有较好的保护作用,并可减少Corynebacterium_1的丰度,同时提高肠黏膜共生菌Candidatus_Arthromitus的丰度,促进了Muribaculaceae、Bacteroides、Lachnospiraceae_NK4A136_group等碳水化合物代谢、短链脂肪酸产生相关菌的增殖。研究表明铁皮石斛多糖对肠黏膜屏障的保护作用或与其维持肠黏膜结构完整,调节肠黏膜菌群组成及促进碳水化合物代谢,生成短链脂肪酸有关。     

Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon

Hydrogenotrophic microbiota have a significant impact on colonic health; however, little is known about their diversity and ecology in situ. Here, molecular-based methods and multivariate analyses were used to examine the abundance and diversity of mucosa-associated hydrogenotrophic microbes in 90 biopsies collected from right colon, left colon and rectum of 25 healthy subjects. Functional genes of all three hydrogenotrophic groups were detected in at least one colonic region of all subjects. Methanogenic archaea (MA) constituted approximately one half of the hydrogenotrophic microbiota in each colonic region. Sulfate-reducing bacteria (SRB) were more abundant than acetogens in right colon, while acetogens were more abundant than SRB in left colon and rectum. MA genotypes exhibited low diversity, whereas SRB genotypes were diverse and generally similar across the three regions within subject but significantly variable among subjects. Multivariate cluster analysis defined subject-specific patterns for the diversity of SRB genotypes; however, neither subject- nor region-specific clusters were observed for the abundance of hydrogenotrophic functional genes. Sequence analyses of functional gene clones revealed that mucosa-associated SRB were phylogenetically related to Desulfovibrio piger, Desulfovibrio desulfuricans and Bilophila wadsworthia; whereas MA were related to Methanobrevibacter spp., Mb. smithii and the order Methanomicrobiales. Together these data demonstrate for the first time that the human colonic mucosa is persistently colonized by all three groups of hydrogenotrophic microbes, which exhibit segmental and interindividual variation in abundance and diversity.     

Curdlan intake changes gut microbial composition,short-chain fatty acid production,and bile acid transformation in mice

Indigestible polysaccharides, such as dietary fibers, benefit the host by improving the intestinal environment. Short-chain fatty acids (SCFAs) produced by gut microbial fermentation from dietary fibers exert various physiological effects. The bacterial polysaccharide curdlan benefits the host intestinal environment, although its effect on energy metabolism and SCFA production remains unclear. Hence, this study aimed to elucidate the effect of curdlan intake on gut microbial profiles, SCFA production, and energy metabolism in a high-fat diet (HFD)-induced obese mouse model. Gut microbial composition of fecal samples from curdlan-supplemented HFD-fed mice indicated an elevated abundance of Bacteroidetes, whereas a reduced abundance of Firmicutes was noted at the phylum level compared with that in cellulose-supplemented HFD-fed mice. Moreover, curdlan supplementation resulted in an abundance of the family Bacteroidales S24-7 and Erysipelotrichaceae, and a reduction in Deferribacteres in the feces. Furthermore, curdlan supplementation elevated fecal SCFA levels, particularly butyrate. Although body weight and fat mass were not affected by curdlan supplementation in HFD-induced obese mice, HFD-induced hyperglycemia was significantly suppressed with an increase in plasma insulin and incretin GLP-1 levels. Curdlan supplementation elevated fecal bile acid and SCFA production, improved host metabolic functions by altering the gut microbial composition in mice.     

江山乌猪肠道黏膜菌群组成及其功能的性别差异

肠道黏膜微生物在调控宿主生理功能方面发挥重要作用,其结构组成受到多种因素影响。性别被认为是塑造肠道微生物的因素之一。然而,性别对肠道黏膜菌群的差异影响还不清楚。【目的】以江山乌猪为研究对象,探究性别差异对其肠道黏膜微生物组成及功能的影响。【方法】选取性成熟的雌性和雄性江山乌猪各8头,利用16S rRNA基因高通量测序技术分析回肠和结肠黏膜菌群。【结果】在回肠黏膜中,雄性江山乌猪菌群的Chao1指数和Shannon指数显著高于雌性(P<0.05),在结肠黏膜中,不同性别江山乌猪菌群Chao1指数和Shannon指数无显著差异(P>0.05)。菌群差异分析显示,回肠黏膜中,沙雷氏菌属(Serratia)和埃希氏志贺菌属(Escherichia_Shigella)在雌性组中的相对丰度显著高于雄性组(P<0.05),雄性组中Oscillospiraceae UCG-005、拟普雷沃氏菌属(Alloprevotella)、布劳特氏菌属(Blautia)和Prevotellaceae_NK3B31_group相对丰度显著高于雌性组(P<0.05);结肠黏膜中,雌性组中unclassified_Muribaculaceae、Rikenellaceae_RC9_gut_group和Prevotellaceae UCG-003相对丰度显著高于雄性组(P<0.05),Oscillospiraceae UCG-005、Lachnospiraceae_NK4A136_group和unclassified_Lachnospiraceae在雄性组中相对丰度更高(P<0.05)。功能预测发现,雄性乌猪回肠黏膜菌群显著富集了氨基酸代谢、碳水化合物代谢和能量代谢等功能途径(P<0.05);结肠黏膜菌群主要富集了膜转运相关的ABC转运蛋白和信号转导相关的双组分系统等功能途径(P<0.05)。【结论】不同性别江山乌猪肠黏膜菌群结构及功能具有明显差异。这些结果揭示了不同性别江山乌猪肠道黏膜菌群的差异特征,为了解和挖掘我国地方畜禽品种肠道微生物资源提供部分参考。     

Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression

Background

Inappropriate cross talk between mammals and their gut microbiota may trigger intestinal inflammation and drive extra-intestinal immune-mediated diseases. Epithelial cells constitute the interface between gut microbiota and host tissue, and may regulate host responses to commensal enteric bacteria. Gnotobiotic animals represent a powerful approach to study bacterial-host interaction but are not readily accessible to the wide scientific community. We aimed at refining a protocol that in a robust manner would deplete the cultivable intestinal microbiota of conventionally raised mice and that would prove to have significant biologic validity.

Methodology/Principal Findings

Previously published protocols for depleting mice of their intestinal microbiota by administering broad-spectrum antibiotics in drinking water were difficult to reproduce. We show that twice daily delivery of antibiotics by gavage depleted mice of their cultivable fecal microbiota and reduced the fecal bacterial DNA load by 400 fold while ensuring the animals'' health. Mice subjected to the protocol for 17 days displayed enlarged ceca, reduced Peyer''s patches and small spleens. Antibiotic treatment significantly reduced the expression of antimicrobial factors to a level similar to that of germ-free mice and altered the expression of 517 genes in total in the colonic epithelium. Genes involved in cell cycle were significantly altered concomitant with reduced epithelial proliferative activity in situ assessed by Ki-67 expression, suggesting that commensal microbiota drives cellular proliferation in colonic epithelium.

Conclusion

We present a robust protocol for depleting conventionally raised mice of their cultivatable intestinal microbiota with antibiotics by gavage and show that the biological effect of this depletion phenocopies physiological characteristics of germ-free mice.     

The bacterial community and metabolome dynamics and their interactions modulate fermentation process of whole crop corn silage prepared with or without inoculants

Multi-omics approach was adopted to investigate the modulation of bacterial microbiota and metabolome as well as their interactions in whole crop corn ensiling systems by inoculating homofermentative Lactobacillus plantarum or heterofermentative Lactobacillus buchneri. Inoculations of the two different inoculants resulted in substantial differences in microbial community and metabolic composition as well as their dynamics in ensiled corn. Inoculants also altered the correlations of microbiota in different manners, and various keystone species were identified in corn silages with different treatments. Many metabolites with biofunctional activities like bacteriostatic, antioxidant, central nervous system inhibitory and anti-inflammatory were found in the present silage. A constitutive difference in microbiota dynamics was found for several pathways, which were upregulated by specific taxa in middle stage of fermentation, and widespread associations between metabolites with biofunctions and the species of lactic acid bacteria dominated in silage were observed. Multiple microbial and metabolic structures and dynamics were correlated and affected the fermentation process of the corn ensiling systems. Results of the current study improve our understanding of the complicated biological process underlying silage fermentation and provide a framework to re-evaluate silages with biofunctions, which may contribute to target-based regulation methods to produce functional silage for animal production.