PCR-DGGE法评价连续培养模型中肠道菌群的多样性

目的建立人体肠道菌群连续培养模型,验证连续培养模型培养肠道菌群的可行性和稳定性。方法建立连续培养系统,把正常人粪便接种于发酵罐中培养,通过活菌计数和PCR—DGGE法分析连续培养系统中菌群的多样性变化。结果连续培养系统中菌群数量由接种前的10^10～10^11CFU／ml降至10^8-10^9CFU／ml并最终达到稳态;PCR—DGGE法分析结果表明,菌群的多样性指数稳定,各条带均匀度趋于一致。结论连续培养模型能较好模拟人体肠道微生态环境,再现了肠道菌群组成的多样性,可作为肠道菌群培养及菌群相关性研究的离体模型。     

固定化植物乳杆菌的制备及其发酵条件优化

采用海藻酸钠包埋植物乳杆菌并通过测定固定化细胞发酵清液的抑菌效果,优化得到的固定化最佳工艺条件为:海藻酸钠浓度为3%,CaCl2浓度为1.5%,菌悬液体积为3.5 mL(4.0×108 cfu/mL).固定化细胞重复发酵多批次效果良好.固定化细胞发酵条件优化结果表明:最适pH为7.0,最适温度为36℃,培养基中添加0....     

口服肝素与小鼠肠道菌群的相互作用

口服肝素药物的开发需要系统地理解口服肝素与肠道菌群之间的互作过程。通过荧光体视镜观察荧光素标记的肝素经小鼠口服后在体内的分布情况,利用高效液相色谱法检测肝素在模拟胃肠液中的稳定性和体外培养肠道菌群模拟肠道菌对肝素的降解作用,发现口服肝素主要分布在小鼠胃肠道内,在体外模拟胃肠液条件下肝素结构稳定,但能够被添加肝素的厌氧培养基培养后的肠道菌群降解。为了进一步揭示口服肝素对健康小鼠肠道菌群的影响,利用Illumina MiSeq高通量测序技术测定口服肝素后C57BL/6J小鼠粪便菌群的16S rRNA序列,与口服生理盐水的小鼠粪便菌群进行对比,发现口服肝素的小鼠粪便菌群的生物多样性降低;在门水平上,菌群结构差异不显著;而在属水平上,别样杆菌属Alistipes、副萨特氏菌属Parasutterella和艾克曼菌属Akkermansia相对丰度增高,而嗜胆菌属Bilophila、肠杆菌属Enterorhabdus、瘤胃梭菌属Ruminiclostridium、普雷沃氏菌科Prevotellaceae_UCG_001、瘤胃梭菌属Ruminiclostridium-9、拟杆菌属Bacteroides、Lachnoclostridium、Candidatus_Saccharimonas、Intestinimonas和Dubosiella的相对丰度减少,表明口服肝素能够影响小鼠肠道菌群结构。此外,实验发现口服肝素对小鼠无明显毒副作用,具有较高安全性。研究结果将为开发肝素口服递送策略提供新的思路,为口服肝素类药物的开发提供参考。     

粪菌移植治疗儿童难治性功能性便秘4例

目的观察粪菌移植对儿童难治性功能性便秘的临床疗效并探讨其机制。方法对4例临床确诊为难治性功能性便秘患儿给予粪菌移植治疗,观察和记录患儿临床症状改善情况并收集供体和粪菌移植治疗前后患儿粪便标本,利用Illumina MiSeq测序平台进行16SrRNA测序,并对测序结果进行生物信息学分析。结果 4例患儿接受粪菌移植治疗后排便状况明显改善,大便次数增加、粪便硬度变软、腹部胀痛明显缓解。粪菌移植后,患儿肠道菌群多样性下降,患儿与供体的肠道菌群差异先增大后逐渐缩小。菌群分析显示患儿肠道有害菌受到抑制、有益菌增加。结论粪菌移植可有效改善儿童难治性功能性便秘的临床症状,具有疗程短、治疗方便、无明显不良反应等优点。     

用固定化黑曲霉完整细胞连续生产柠檬酸

本研究比较了两种固定化黑曲霉完整细胞的方法:黑曲霉KCU520在30℃培养5天,用无菌水制成分生孢子悬液(10~7—10~8孢子/ml)。①在400ml80％海藻酸钠溶液中加入孢子悬液600ml,然后逐滴加到1％CaCl_2溶液中,形成的颗粒在10℃固定1小时备用。②聚丙烯酰胺凝胶(PAG)固定化,在64ml孢子悬液(4℃)中加丙烯酰胺12克,双丙烯酰胺     

T-RFLP分析厌氧真菌传代频率对共存产甲烷菌菌群的影响

【目的】建立瘤胃产甲烷菌T-RFLP多样性分析方法,并研究厌氧真菌与产甲烷菌共培养液在不同时间传代对共存产甲烷菌菌群的影响。【方法】利用产甲烷菌mcrA基因特异性引物PCR扩增后,选择合适内切酶对扩增产物进行内切,分析内切后末端片段长度多态性,测定共培养液在不同传代频率时共存产甲烷菌多样性的变化。【结果】利用Msp I内切酶分析发现,末端片段长度约为470 bp的产甲烷菌为共培养液中的优势甲烷菌,共培养液传代至第15代时,片段长度约为130 bp和200 bp的产甲烷菌也成为共培养中的优势菌株;比较发现,Taq I能更好地内切共培养液中甲烷菌mcrA基因序列,瘤胃内容物及3 d传代共培养液中产甲烷菌主要为末端片段长度约为70、100、200、270、300、330和470 bp的菌株,共培养液在体外传代培养过程中,末端片段长度约为70、100、270和470 bp的产甲烷菌变化更为显著。Taq I比较分析不同传代频率(3、5和7 d)对共培养液中产甲烷菌菌群结构的影响表明,3 d传代的共培养液中产甲烷菌菌群与瘤胃内容物较为相似,而5 d和7 d传代的共培养液中产甲烷菌菌群间差异较小,但与瘤胃内容物差异较大,导致不同传代频率的共培养液中产甲烷菌菌群间显著差异的最主要菌株为末端片段长度约为100 bp的产甲烷菌,其次为末端片段长度约为70 bp和270 bp的产甲烷菌。【结论】利用建立的快速可行的瘤胃产甲烷菌T-RFLP方法分析表明,传代频率显著影响厌氧真菌与产甲烷菌共培养液中产甲烷菌的菌群结构,3 d传代共培养液内产甲烷菌菌群与瘤胃内容物更相似。     

32例消化道癌症患者的粪便菌群检查

本文报告10例食管癌、12例胃癌贲门癌、10例大肠癌患者和12例正常人的粪菌群检查结果。这些粪菌群包括厌氧菌中的双歧杆菌属、拟杆菌属和梭菌属、兼性厌氧菌中的乳酸杆菌属,需氧菌中的大肠杆菌属和肠球菌。用每克粪便中菌落形成单位(CFU/克粪)的对数值来表示细菌的数量。结果发现:癌症患者粪便菌群中,双歧杆菌的数量在食     

五种益生菌在纤维固定化连续培养系统的共存定殖

模拟肠道的半固态生境,建立以玉米纤维为载体的固定化连续搅拌培养系统、并以非固定化连续搅拌培养系统为对照,稀释率为0.0417,分别连续培养12 d,双歧杆菌、酪酸菌、嗜酸乳杆菌、肠膜芽孢杆菌、粪肠球菌五种菌在两种系统中均可稳定共存,固定化系统固相五种菌数均高于非固定化系统,以双歧杆菌增幅最大,半固态的固定化连续培养较液态连续培养的菌相与肠道菌相较一致,能更好地模拟肠道微生态.扫描电镜观察五种菌在玉米纤维上固定形成了生物膜.     

五种益生菌在纤维固定化连续培养系统的共存定殖

模拟肠道的半固态生境, 建立以玉米纤维为载体的固定化连续搅拌培养系统、并以非固定化连续搅拌培养系统为对照, 稀释率为0.0417, 分别连续培养12 d, 双歧杆菌、酪酸菌、嗜酸乳杆菌、肠膜芽孢杆菌、粪肠球菌五种菌在两种系统中均可稳定共存, 固定化系统固相五种菌数均高于非固定化系统, 以双歧杆菌增幅最大, 半固态的固定化连续培养较液态连续培养的菌相与肠道菌相较一致, 能更好地模拟肠道微生态。扫描电镜观察五种菌在玉米纤维上固定形成了生物膜。     

早期灌喂母源粪菌对新生仔猪肠道菌群发育的影响

【目的】粪菌移植(fecal microbiota transplantation,FMT)作为一种治疗手段,已在人类肠道疾病治疗中有较多应用,但在干预新生仔猪肠道菌群上的研究未见报道。本文旨在研究早期母源粪菌移植对新生仔猪肠道菌群发育的影响。【方法】选取一窝12头杜长大新生仔猪,随机分为粪菌处理组(feces treatment,FT)和对照组(control,CO)。FT组仔猪出生后1–5 d每日灌注母源粪菌接种液,CO组灌注等量生理盐水。于1、3、5、7、10、14、18和22日龄采集仔猪粪样,Miseq高通量测序分析仔猪粪便菌群。【结果】灌喂母源粪菌有增加仔猪肠道菌群丰富度的趋势;主坐标分析显示,两组仔猪粪样菌群结构簇并未分开,并在18和22日龄时靠近母猪粪样菌群结构簇;随日龄增加,两组仔猪肠道中的变形菌门丰度均显著降低,而厚壁菌门的丰度显著增加,且从10日龄起拟杆菌门和厚壁菌门之和约为90%;与对照组相比,灌喂母源粪菌增加了10日龄时Escherichia-Shigella的丰度,而降低了18日龄时该菌属的丰富度,18日龄时肠球菌属和普氏菌属的丰度则显著增加。【结论】1–3日龄口服灌喂母源粪菌液并不能影响仔猪肠道菌群的定殖,这一阶段主要受母体微生物结构的影响;灌喂粪菌液对仔猪肠道菌群定殖的影响最多持续10–14 d;而且仔猪在22 d左右,肠道菌群结构逐渐趋同于母猪肠道菌群。     

In Vitro Continuous Fermentation Model (PolyFermS) of the Swine Proximal Colon for Simultaneous Testing on the Same Gut Microbiota

In vitro gut modeling provides a useful platform for a fast and reproducible assessment of treatment-related changes. Currently, pig intestinal fermentation models are mainly batch models with important inherent limitations. In this study we developed a novel in vitro continuous fermentation model, mimicking the porcine proximal colon, which we validated during 54 days of fermentation. This model, based on our recent PolyFermS design, allows comparing different treatment effects on the same microbiota. It is composed of a first-stage inoculum reactor seeded with immobilized fecal swine microbiota and used to constantly inoculate (10% v/v) five second-stage reactors, with all reactors fed with fresh nutritive chyme medium and set to mimic the swine proximal colon. Reactor effluents were analyzed for metabolite concentrations and bacterial composition by HPLC and quantitative PCR, and microbial diversity was assessed by 454 pyrosequencing. The novel PolyFermS featured stable microbial composition, diversity and metabolite production, consistent with bacterial activity reported for swine proximal colon in vivo. The constant inoculation provided by the inoculum reactor generated reproducible microbial ecosystems in all second-stage reactors, allowing the simultaneous investigation and direct comparison of different treatments on the same porcine gut microbiota. Our data demonstrate the unique features of this novel PolyFermS design for the swine proximal colon. The model provides a tool for efficient, reproducible and cost-effective screening of environmental factors, such as dietary additives, on pig colonic fermentation.     

Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.     

Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.     

Increased amount of Bifidobacterium thermacidophilum and Megasphaera elsdenii in the colonic microbiota of pigs fed a swine dysentery preventive diet containing chicory roots and sweet lupine

AIMS: To investigate which specific bacterial species that were stimulated or inhibited in the proximal colon of pigs when a fructan-rich diet was compared with a diet that contained resistant carbohydrates. The study focussed especially on Bifidobacterial species by using a noncultureable approach. METHODS AND RESULTS: Terminal restriction fragment length polymorphism (T-RFLP) was used to describe differences in the total colonic microbiota as well as in the populations of Bifidobacterium spp. in pigs fed with a fructan-rich diet and a diet containing resistant carbohydrates. The fructan-rich diet has previously been shown to prevent swine dysentery caused by Brachyspira hyodysenteriae. The T-RFLP profiling, 16S rRNA gene cloning and in situ hybridization showed that the pigs fed with the fructan-rich diet had a higher proportion of Bifidobacterium thermacidophilum subsp. porcinum and Megasphaera elsdenii. CONCLUSIONS: These findings suggested that the bacterial fructan fermentation occurring in the porcine colon might be cross-feeding of lactate produced by B. thermacidophilum and used by M. elsdenii. SIGNIFICANCE AND IMPACT OF THE STUDY: B. thermacidophilum and M. elsdenii may be the course of the inhibition of the pathogenic bacteria Brach. hyodysenteriae in colon of pigs when they are fed fructan-rich diets.     

Bacterial community dynamics during the ensilage of wilted grass

Aims:  Grass silage is the product formed by a natural lactic acid bacterial fermentation when grass is stored under anaerobic conditions, and represents an important ruminant feedstuff on farms during winter. Of the two commonly employed methods of ensiling forage, baled silage composition frequently differs from that of comparable precision-chop silage reflecting a different ensiling environment. The aim of this study was to investigate the dynamics of the silage fermentation in wilted grass and between ensiling systems.
Methods and Results:  Fermentation dynamics were examined using traditional methods of silage analyses, including microbial enumeration and analysis of fermentation products, and culture-independent terminal restriction fragment length polymorphism (T-RFLP). A successful fermentation was achieved in both systems, with the fermentation (increase in lactic acid bacteria and lactic acid concentration, decrease in pH) proceeding rapidly once the herbage was ensiled.
Conclusions:  Under controlled conditions, little difference in silage quality and microbial composition were observed between ensiling systems and this was further reflected in the T-RFLP community analysis.
Significance and Impact of the Study:  T-RFLP proved a potentially useful tool to study the ensilage process and could provide valid support to traditional methods, or a viable alternative to these methods, for investigating the dynamics of the bacterial community over the course of the fermentation.     

Inulin-type fructans of longer degree of polymerization exert more pronounced in vitro prebiotic effects

AIMS: We assessed to what extent fructans of different degrees of polymerization (DP) differ in their prebiotic effectiveness towards in vitro microbial communities from the proximal and distal colon. METHODS AND RESULTS: Two short chain fructans - oligofructose (DP 2-20) and inulin (DP 3-60) - were administered to the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) at 2.5 g day(-1). The influence of fructan addition towards fermentation activity and microbial community composition from the different SHIME colon compartments were evaluated. Both fructans exerted prebiotic effects with significantly higher butyrate and propionate production and stimulation of lactic acid-producing bacteria. Compared with oligofructose, it was noted that it took more time before significant effects from inulin addition were observed. Yet, the higher short-chain fatty acid production and lower proteolytic activity showed that the prebiotic effects from inulin were more pronounced than oligofructose. Also, the bifidogenic effects from inulin vs oligofructose were higher in the distal colon compartments and this effect was prolonged in the distal colon once the addition was stopped. CONCLUSIONS: Inulin has more pronounced prebiotic effects than oligofructose towards both fermentation activity and bacterial community composition in the SHIME model. SIGNIFICANCE AND IMPACT OF THE STUDY: Its slower fermentation rate and higher prebiotic potency makes inulin a more interesting compound than oligofructose to beneficially influence the microbial community from both the proximal and distal colon regions.     

Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon

In vitro gut modeling is a useful approach to investigate some factors and mechanisms of the gut microbiota independent of the effects of the host. This study tested the use of immobilized fecal microbiota to develop different designs of continuous colonic fermentation models mimicking elderly gut fermentation. Model 1 was a three-stage fermentation mimicking the proximal, transverse and distal colon. Models 2 and 3 were based on the new PolyFermS platform composed of an inoculum reactor seeded with immobilized fecal microbiota and used to continuously inoculate with the same microbiota different second-stage reactors mounted in parallel. The main gut bacterial groups, microbial diversity and metabolite production were monitored in effluents of all reactors using quantitative PCR, 16S rRNA gene 454-pyrosequencing, and HPLC, respectively. In all models, a diverse microbiota resembling the one tested in donor’s fecal sample was established. Metabolic stability in inoculum reactors seeded with immobilized fecal microbiota was shown for operation times of up to 80 days. A high microbial and metabolic reproducibility was demonstrated for downstream control and experimental reactors of a PolyFermS model. The PolyFermS models tested here are particularly suited to investigate the effects of environmental factors, such as diet and drugs, in a controlled setting with the same microbiota source.     

Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices

Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.     

Comparison of Bacterial Communities in New England Sphagnum Bogs Using Terminal Restriction Fragment Length Polymorphism (T-RFLP)

Wetlands are major sources of carbon dioxide, methane, and other greenhouse gases released during microbial degradation. Despite the fact that decomposition is mainly driven by bacteria and fungi, little is known about the taxonomic diversity of bacterial communities in wetlands, particularly Sphagnum bogs. To explore bacterial community composition, 24 bogs in Vermont and Massachusetts were censused for bacterial diversity at the surface (oxic) and 1 m (anoxic) regions. Bacterial diversity was characterized by a terminal restriction fragment length (T-RFLP) fingerprinting technique and a cloning strategy that targeted the 16S rRNA gene. T-RFLP analysis revealed a high level of diversity, and a canonical correspondence analysis demonstrated marked similarity among bogs, but consistent differences between surface and subsurface assemblages. 16S rDNA sequences derived from one of the sites showed high numbers of clones belonging to the Deltaproteobacteria group. Several other phyla were represented, as well as two Candidate Division-level taxonomic groups. These data suggest that bog microbial communities are complex, possibly stratified, and similar among multiple sites.     

Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices

Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.