Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing

Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under human colon-like conditions. To the microbiota of the TIM-2 in vitro model of the human colon 7.4 g l⁻¹ of [U-¹³C]-starch was added. RNA extracted from lumen samples after 0 (control), 2, 4 and 8 h was subjected to density-gradient ultracentrifugation. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting and phylogenetic analyses of the labelled and unlabelled 16S rRNA suggested populations related to Ruminococcus bromii, Prevotella spp. and Eubacterium rectale to be involved in starch metabolism. Additionally, 16S rRNA related to that of Bifidobacterium adolescentis was abundant in all analysed fractions. While this might be due to the enrichment of high-GC RNA in high-density fractions, it could also indicate an active role in starch fermentation. Comparison of the T-RFLP fingerprints of experiments performed with labelled and unlabelled starch revealed Ruminococcus bromii as the primary degrader in starch fermentation in the studied model, as it was found to solely predominate in the labelled fractions. LC-MS analyses of the lumen and dialysate samples showed that, for both experiments, starch fermentation primarily yielded acetate, butyrate and propionate. Integration of molecular and metabolite data suggests metabolic cross-feeding in the system, where populations related to Ruminococcus bromii are the primary starch degrader, while those related to Prevotella spp., Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain.     

传统分离培养结合DGGE法检测榨菜腌制过程的细菌多样性

采用传统分离培养和基于16S rRNA 作为分子标记的变性梯度凝胶电泳(Denaturing gradient gel electrophoresis, DGGE)的方法, 分析榨菜腌制过程中不同时期的可培养细菌数量、多样性及其群落结构。结果表明, 用传统分离与分子鉴定方法获得7个属的细菌类群, 其中乳杆菌属(Acidobacterium)是优势菌群, 明串珠菌属(Leuconostoc)是次优势菌群。对通过DGGE方法得到的11条16S rRNA优势条带序列进行了比对, 结果表明明串珠菌属(Leucon     

一株人消化道中韦荣氏球菌的分离、鉴定及其代谢特性研究

【目的】分离与鉴定人肠道乳酸利用菌,研究其乳酸利用的代谢特性。【方法】利用Hungate滚管技术从人粪便中分离厌氧细菌,通过形态、生化和16S r RNA基因鉴定;通过体外发酵技术研究乳酸代谢,并且与乳酸产生菌共培养,研究二者之间交互饲喂。【结果】验证了乳酸可作为代谢中间产物被人肠道混合菌群利用;分离到一株乳酸利用菌,在24 h内消耗乳酸超过50 mmol/L,经鉴定为韦荣氏球菌,并将其形成乙酸和丙酸。当和肠球菌共培养时,可以有效地减缓乳酸的积累。【结论】本株乳酸利用菌可以作为潜在的益生菌,和乳酸菌一起调节人肠道的乳酸动态平衡。     

Stable isotope probing reveals the dominant role of Burkholderia species in aerobic degradation of PCBs

The active bacteria of a biofilm community grown directly on polychlorinated biphenyl (PCB) droplets were analyzed by 16S rRNA fingerprinting, identified by their 16S rRNA gene sequences and fatty acid profiling, and compared with isolates from the biofilm. Although, the multi-species biofilm degraded di- and trichlorinated PCB-congeners these substrates were not attacked by its individual isolated members, which suggests that a metabolic network is responsible for PCB degradation in the biofilm. The community metabolized [U-13C]-2,2'-dichlorobiphenyl incorporating the label into certain phospholipid fatty acids matching those found in Burkholderia species. In contrast, abundant biofilm community members, like Methylobacterium species, did not incorporate the label. These results provide prima faciae evidence for Burkholderia species as the main degraders of PCBs in this type of aerobic soils.     

Chicken intestine microbiota following the administration of lupulone, a hop-based antimicrobial

The use of antibiotic growth promotants in poultry rearing is a public health concern due to antibiotic resistance in bacteria and the harborage of resistance genes. Lupulone, a hop β-acid from Humulus lupulus, has been considered as a potential feed additive growth promotant. Here, the effect of lupulone was evaluated for its effect on the microbiota of the chicken intestine. The intestinal microbiota of broilers was quantified after the addition of 125 mg L(-1) lupulone to water and challenge with Clostridium perfringens. Microbial DNA was extracted from the broiler midgut and cecal sections and bacterial groups were quantified using real-time PCR. The predominant cecal bacterial groups were Clostridium leptum subgroup 16S rRNA gene Cluster IV, Clostridium coccoides subgroup 16S rRNA gene Clusters XIVa and XIVb and Bacteroides, whereas Lactobacillus, the Enterobacteriaceae family and Enterococcus dominated the midgut. Lupulone at 125 mg L(-1) significantly decreased the C. perfringens subgroup 16S rRNA gene Cluster I, which contains several pathogenic species, in both the midgut and the cecum and Lactobacillus in the midgut. No significant changes were noted in the overall microbiota for the cecum or the midgut. Lupulone warrants further evaluation as a botanical agent to mitigate C. perfringens overgrowth in antibiotic-free reared poultry.     

Detection and identification of Escherichia coli,Shigella, and Salmonella by microarrays using the gyrB gene

Commonly, 16S ribosome RNA (16S rRNA) sequence analysis has been used for identifying enteric bacteria. However, it may not always be applicable for distinguishing closely related bacteria. Therefore, we selected gyrB genes that encode the subunit B protein of DNA gyrase (a topoisomerase type II protein) as target genes. The molecular evolution rate of gyrB genes is higher than that of 16S rRNA, and gyrB genes are distributed universally among bacterial species. Microarray technology includes the methods of arraying cDNA or oligonucleotides on substrates such as glass slides while acquiring a lot of information simultaneously. Thus, it is possible to identify the enteric bacteria easily using microarray technology. We devised a simple method of rapidly identifying bacterial species through the combined use of gyrB genes and microarrays. Closely related bacteria were not identified at the species level using 16S rRNA sequence analysis, whereas they were identified at the species level based on the reaction patterns of oligonucleotides on our microarrays using gyrB genes.     

Glucose and lactate catabolism by bacteria of the pig large intestine and sheep rumen as assessed by 13C nuclear magnetic resonance.

The fermentation of [1-13C] glucose and [3-13C]lactate by bacteria isolated from sheep rumen and pig large intestine was compared by the nuclear magnetic resonance (NMR) technique. Washed cell suspensions were incubated directly in the NMR spectrometer and spectra were recorded every 10 min after injection of the labelled substrates. The results showed large differences in the fermentation patterns between rumen and hindgut bacteria. The latter pattern indicated a greater ability for formation and fermentation of lactate than that of the rumen. Moreover, with both substrates the amount of propionate formed via the acrylate pathway was always greater with hindgut than with rumen bacteria, 50% and 20% of the total, respectively.     

蟋蟀后肠纤维素降解细菌的分离与鉴定

近年来,具有农业、能源和环保价值的昆虫微生物种类和基因得到了开发,昆虫肠道微生物展示了其巨大的应用潜力,本研究旨在从蟋蟀后肠分离和鉴定纤维素降解细菌。首先采用羧甲基纤维素钠液体培养基对蟋蟀后肠中的微生物进行富集培养,然后使用羧甲基纤维素钠固体培养基分离和筛选单菌落,再通过16S rRNA测序对纤维素降解细菌进行分子鉴定,最后通过刚果红染色来进一步分析细菌降解纤维素的能力。从蟋蟀后肠中共分离出20株纤维素降解细菌,16S rRNA基因测序结果显示来自肠杆菌属(Enterobacter)9株,不动杆菌属(Acinetobacter)7株,克雷伯氏菌属(Klebsiella)2株,鞘氨醇杆菌属(Sphingobacterium)1株和葡萄球菌属(Staphylococcus)1株。刚果红染色试验结果显示,克雷伯氏菌属两株PDSCDXS_2B和8B,鞘氨醇杆菌属PDSCDXS_7C和不动杆菌属PDSCDXS_12C具有较高的纤维素降解能力。这是首次从蟋蟀后肠分离和筛选出来具有纤维素降解能力的细菌,为昆虫源纤维素降解细菌的研究提供了微生物资源。     

Quantitative determination of bile salt hydrolase activity in bacteria isolated from the small intestine of chickens

A quantitative assay based on high-performance liquid chromatography analysis of bile salts and bacterial protein determination was established for investigating bile salt hydrolase (BSH) activity in bacteria isolated from the small intestine of chickens. Bacteria were isolated using various media and were subsequently grouped according to cell morphology, fermentation profile, and 16S ribosomal DNA sequence. Representative isolates from each bacterial group were assayed for BSH activity. The isolates differed in BSH activity with respect to the state of growth and preculturing with and without taurochenodeoxycholate. The highest levels of BSH activity were found with Enterococcus faecium and Clostridium perfringens.     

Enterobacteriaceae facilitate the anaerobic degradation of glucose by a forest soil

Anoxic micro zones that occur in soil aggregates of oxic soils may be temporarily extended after rainfall and thus facilitate the anaerobic degradation of organic compounds in soils. The microbial degradation of glucose by anoxic slurries of a forest soil yielded acetate, CO₂, H₂, succinate, and ethanol, products indicative of mixed acid fermentation. Prokaryotes involved in this process were identified by time-resolved 16S rRNA gene-targeted stable isotope probing with [¹³C-U]-glucose. All labeled phylotypes from the ¹³C-enriched 16S rRNA gene were most closely related to Rahnella and Ewingella , enterobacterial genera known to catalyze mixed acid fermentation. These results indicate that facultative aerobes, in particular Enterobacteriaceae , (1) can outcompete obligate anaerobes when conditions become anoxic in forest soils and (2) may be involved in the initial decomposition of monosaccharides in anoxic micro zones of aerated forest soils.     

污损生物膜细菌Pseudoalteromonas issachenkonii YT1305-1的鉴定及其代谢物化学成分分析

【目的】对污损生物膜细菌YT1305-1进行菌种鉴定;研究其作为污损生物膜优势菌之一的代谢产物。【方法】通过16S rRNA基因序列分析,结合系统进化树和细菌生理生化实验对菌种进行鉴定,通过硅胶柱层析分离方法和核磁共振检测技术分析其代谢物的化学成分。【结果】发现生物膜中存在明显的优势菌株,假交替单胞菌属为优势菌属之一。16S rRNA序列比对分析表明Pseudoalteromonas issachenkonii为优势菌种之一,将目标菌种命名为Pseudoalteromonas issachenkonii YT1305-1,对其代谢物化学成分进行分析,共得到10个化合物,其中包括5个二酮哌嗪(DKPs)类信号分子,环(甘氨酸-丙氨酸)(1)、环(脯氨酸-甘氨酸)(2)、环(脯氨酸-酪氨酸)(3)、环(4-羟基-脯氨酸-亮氨酸)(4)和环(4-羟基-脯氨酸-丙氨酸)(5),以及尿嘧啶(6)、胸腺嘧啶(7)、胸腺嘧啶脱氧核苷(8)、己二酸二(2-乙基己)酯(9)和邻苯二甲酸二(2-乙基己)酯(10)。【结论】污损生物膜中存在明显的优势菌,其中之一为P.issachenkonii YT1305-1,在其代谢产物中发现了疑似信号分子的物质DKPs,有研究表明该物质能调控生物膜的形成,进而影响生物污损的形成,为探究生物污损现象奠定了物质基础。     

The role of pH in determining the species composition of the human colonic microbiota

The pH of the colonic lumen varies with anatomical site and microbial fermentation of dietary residue. We have investigated the impact of mildly acidic pH, which occurs in the proximal colon, on the growth of different species of human colonic bacteria in pure culture and in the complete microbial community. Growth was determined for 33 representative human colonic bacteria at three initial pH values (approximately 5.5, 6.2 and 6.7) in anaerobic YCFA medium, which includes a mixture of short-chain fatty acids (SCFA) with 0.2% glucose as energy source. Representatives of all eight Bacteroides species tested grew poorly at pH 5.5, as did Escherichia coli , whereas 19 of the 23 Gram-positive anaerobes tested gave growth rates at pH 5.5 that were at least 50% of those at pH 6.7. Growth inhibition of B. thetaiotaomicron at pH 5.5 was increased by the presence of the SCFA mix (33 mM acetate, 9 mM propionate and 1 mM each of iso-valerate, valerate and iso-butyrate). Analysis of amplified 16S rRNA sequences demonstrated a major pH-driven shift within a human faecal bacterial community in a continuous flow fermentor. Bacteroides spp. accounted for 27% of 16S rRNA sequences detected at pH 5.5, but 86% of sequences at pH 6.7. Conversely, butyrate-producing Gram-positive bacteria related to Eubacterium rectale represented 50% of all 16S rRNA sequences at pH 5.5, but were not detected at pH 6.7. Inhibition of the growth of a major group of Gram-negative bacteria at mildly acidic pH apparently creates niches that can be exploited by more low pH-tolerant microorganisms.     

Identification of lactic acid bacteria from spoilage associations of cooked and brined shrimps stored under modified atmosphere between 0 degrees C and 25 degrees C

AIMS: To evaluate spoilage and identify lactic acid bacteria (LAB) from spoilage associations of cooked and brined shrimps stored under modified atmosphere packaging (MAP) at 0, 5, 8, 15 and 25 degrees C. METHODS AND RESULTS: Bacterial isolates (102) from spoilage associations of cooked and brined MAP shrimps were characterized by phenotypic tests and identified as lactic acid bacteria (78 isolates), other Gram-positive bacteria (13 isolates) and Gram-negative bacteria (11 isolates). A selection of 48 LAB isolates were further characterized and identified by phenotypic tests and SDS-PAGE electrophoresis of whole cell proteins. Selected clusters of LAB isolates were analysed by plasmid profiling, pulsed field gel electrophoresis and 16S rRNA gene sequencing. Enterococcus faecalis was identified in spoilage associations at 15 degrees C and 25 degrees C, and its metabolic activity corresponded to chemical changes in spoiled products. Carnobacterium divergens, a non-motile Carnobacterium sp. nov. and Lactobacillus curvatus were the LAB species observed in spoilage associations of products stored at 0 degrees C, 5 degrees C and 8 degrees C. CONCLUSIONS: Enterococcus spp. and Carnobacterium spp. were the dominant parts of spoilage associations of cooked and brined MAP shrimps stored at high and low temperatures, respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: The SDS-PAGE technique and simple biochemical keys allowed the majority of LAB isolates from spoilage associations of cooked and brined MAP shrimps to be identified at the species level.     

rRNA-based profiling of bacteria in the axilla of healthy males suggests right-left asymmetry in bacterial activity

The activity of the human armpit microbiota triggers the formation of body odor. We used differential 16S rRNA gene (rDNA)- and rRNA-based terminal-restriction fragment length polymorphism fingerprinting in combination with cloning and sequencing to identify active members of the human armpit microbiota. DNA and RNA were isolated from skin scrub samples taken from both armpits of 10 preconditioned, healthy males. The fingerprint profiles indicated pronounced similarities between the armpit microbiota in the right and the left axillae of an individual test person, but larger differences between the axilla microbiota of different individuals. Using 16S rDNA and rRNA sequence data, the majority of peaks in the armpit profiles were assigned to bacteria affiliated with well-known genera of skin bacteria. The relative abundances of all groups were similar among the rDNA and rRNA samples, suggesting that all groups of armpit bacteria were active. Surprisingly, the relative abundance of sequences affiliated with Peptoniphilus sp. was by far and with statistical significance the highest in the rRNA samples of the right armpits. Thus, bacteria affiliated with Peptoniphilus sp. might have been particularly active in the right axillae of the test persons, possibly owing to the handedness of the test persons, which might cause different environmental conditions in the right axillae.     

Clostridium asparagiforme sp. nov., isolated from a human faecal sample

An obligatory anaerobic, Gram-positive, rod-shaped organism was isolated from faeces of a healthy human donor. It was characterized using biochemical, phenotypic and molecular taxonomic methods. The organism produced acetate, lactate, and ethanol as the major products of glucose fermentation. The G + C content was 53 mol%. Based on comparative 16S rRNA gene sequencing, the unidentified bacterium is a member of the Clostridium subphylum of the Gram-positive bacteria, and most closely related to species of the Clostridium coccoides cluster (rRNA cluster XIVa) [M.D. Collins et al., The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations, Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Clostridium bolteae and Clostridium clostridioforme were identified as the most closely related described species. A 16S rRNA sequence divergence value of > 3% suggested that the isolate represents a new species. This was also supported by the gyrase-encoding gyrB gene sequences. Based on these findings, we propose the novel bacterium from human faeces to be classified as a new species, Clostridium asparagiforme. The type strain of C. asparagiforme is N6 (DSM 15981 and CCUG 48471).     

耐乙酸乳杆菌的筛选及其产乳酸特性

【背景】耐受乙酸的乳酸菌是传统谷物醋醋酸发酵过程中产生乳酸及其风味衍生物的重要功能微生物。【目的】从镇江香醋醋醅中分离鉴定具有耐乙酸特性的乳酸菌,并评价不同条件下该菌株的产乳酸能力。【方法】利用4%(体积比)乙酸含量的MRS培养基分离耐乙酸乳酸菌;对其进行16S rRNA基因鉴定、基因组测序、形态观察以及生理生化特性研究;考察不同乙酸浓度、葡萄糖浓度、发酵温度和时间对菌株产乳酸能力的影响。【结果】分离得到一株可耐受6%乙酸的乳杆菌Lactobacillus sp. JN500903;在厌氧静置、接种量5%、乙酸浓度5%、葡萄糖浓度40 g/L、发酵温度37°C、发酵时间10 d条件下,该菌株乳酸产量为16.1 g/L。【结论】乳杆菌JN500903能够耐受6%乙酸浓度,具有在酸性环境下合成乳酸的能力,有一定的应用潜力。     

Isolation and identification of equol-producing bacterial strains from cultures of pig faeces.

Transformation of daidzein to equol was compared during fermentation of three growth media inoculated with faeces from Erhualian piglets, but equol was produced from only one medium, M1. Two equol-producing strains (D1 and D2) were subsequently isolated using medium M1. Both strains were identified as Eubacterium sp., on the basis of morphological and physiological characteristics, and 16S rRNA gene sequence analysis showed that strains D1 and D2 were most closely related to previously characterized daidzein-metabolizing bacteria isolated from human faecal and rumen samples, respectively. This suggests that the ability to metabolize daidzein can be found among bacteria present within the mammalian intestine. The results provided the first account of conversion of daidzein directly to equol by bacterial species from farm animals. These strains may be of importance to the improvement of animal performance, and the use of medium M1 could provide a simple way to isolate bacterial strains capable of transforming daidzein into equol.     

贡嘎蝠蛾幼虫肠道细菌多样性分析

[目的]对实验室养殖条件下的重要经济昆虫冬虫夏草寄主-贡嘎蝠蛾(Hepialus gonggaensis,Hg)幼虫肠道微生物群落的多样性进行了研究.[方法]采用常规分离培养与分子鉴定的方法和基于16S rRNA作为分子标记的变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)的方法.[结果]用常规分离与分子鉴定方法获得8个属的细菌类群,其中肠杆菌属(Enterobacter)是优势菌群,肉食杆菌属(Carnobacterium)是次优势菌群.对通过DGGE方法得到的11条16S rRNA优势条带序列进行了比对和系统进化树分析,结果表明肉食杆菌属(Carnobacterium)的丰度最高,是肠道细菌中主要的优势菌群,芽孢杆菌属(Bacillus)是次优势菌群.DGGE图谱还显示Hg幼虫不同虫龄肠道细菌菌群的结构存在差异,推测可能与其发育生理状态的差异有关系.[结论]结合常规分离法与DGGE法能够更有效的分析肠道微生物的多样性,获得更多更全面的微生物多样性信息.     

The use of PCR to monitor the population abundance of six human intestinal bacterial species in an in vitro semicontinuous culture system

Abstract Six PCR primer sets complementary to the 16S rDNAs (rRNA genes) were developed and shown to be specific for the following anaerobic bacteria: Clostridium clostridiiforme, C. perfringens, C. leptum, Bacteroides vulgatus, B. distasonis , and B. thetaiotaomicron , respectively. These primers were used for PCR to detect and monitor the bacteria in a semicontinuous culture system designed to mimic intestinal microflora in the human gastrointestinal tract. Except for C. perfringens , the five species of Bacteroides and Clostridia present in the in vitro culture system were detected by the PCR, and the titers varied from 10⁻² to 10⁻⁶ dilutions. The role of azo dye reduction by these bacterial species in the system was examined and discussed.