普氏蹄蝠胃肠道菌群的多样性

【目的】研究普氏蹄蝠(Hipposideros pratti)胃肠道菌群多样性及致病菌的种类。【方法】采用Mi Seq高通量测序技术,通过对16S r RNA基因V1-V2区基因进行测序,研究普氏蹄蝠胃肠道细菌的群落组成。应用MG-RAST V3.3.6分析和统计样品序列和操作分类单元(OTU)数目,分析胃肠道菌群物种丰度,并进行聚类分析。【结果】从普氏蹄蝠胃和肠道中分别获得144 998条和275 274条原始序列以及48 332条和91 758条有效序列,分属于894个和756个操作分类单元。胃中菌群丰度指数Chao指数(1 490)和ACE指数(2 221)分别低于肠道菌群的Chao指数(2 051)和ACE指数(3 556);Shannon多样性指数(2.405)低于肠道(2.407);Simpson多样性指数(0.168)高于肠道(0.151)。系统进化分析表明胃肠中的细菌主要分布在6个门,均以变形菌门(Proteobacteria)(胃中占56.4%,肠中占46.0%)和厚壁菌门(Firmicutes)(胃中占40.7%,肠中占49.2%)为优势菌门。胃肠道中丰度在0.1%以上的属有24个,胃中优势类群为乳球菌属(Lactococcus)和哈夫尼菌属(Hafnia),分别占整个菌群的26.1%和21.0%;肠道中优势类群为肠球菌属(Enterococcus)和沙门氏菌属(Salmonella),分别占整个菌群的15.2%和12.7%。普氏蹄蝠胃肠道中的优势菌群均为人类的致病菌或者条件致病菌。【结论】普氏蹄蝠携带有大量人类致病菌。因此,应注意防止向人类传播。     

Cold stress-induced changes in the aerobic heterotrophic gastrointestinal tract bacterial flora of red hybrid tilapia

Fifteen juvenile red hybrid tilapia Oreochromis mossambicus × O. macrochir averaging 50 g body weight were cold-stressed by immersion in 18° C sea water; control fish ( n = 15) were kept at the acclimation temperature of 26° C. Three fish from each group were killed 0, 24, 48 and 72 h after the start of the experiment. Gastrointestinal tracts were removed and dissected into the stomach, anterior gut and posterior gut regions. Aerobic heterotrophic bacteria were identified and enumerated relative to temperature, exposure time and gastrointestinal tract region. Gram negative genera included Alcaligenes, Flavobacterium, Photobacterium, Pseudomonas and Vibrio ; the latter three were predominant. Mean bacterial numbers and taxonomic composition of the microflora varied significantly ( P <0·05) in response to the three test variables. There were greater mean total bacterial numbers at 18 than at 26° C, due primarily to proliferation of Vibrio spp. Mean bacterial numbers after 24 h were greater than those at both the earlier and later sampling periods. Mean bacterial numbers in the stomach were less than those in the anterior and posterior gut, which were not significantly different. The relative abundance of Vibrio spp. was negatively correlated with that of Flavobacterium , which may have reflected competition between pathogenic and nonpathogenic species. Such stress-induced changes in the bacterial microflora may contribute to the onset of disease because several species of Vibrio are known primary or opportunistic fish pathogens.     

Laser microdissection: exploring host-bacterial encounters at the front lines

The mucosal surfaces of tissues such as the stomach and intestines are in constant contact with indigenous bacterial populations and are major portals of entry for bacterial pathogens. Host responses to bacterial encounters at these surfaces frequently involve complex interactions between epithelial cells and immune cells, and are thus difficult to model in vitro. Laser microdissection is a technique in which pure populations of host cells are acquired from sections of complex tissue. When coupled with an expanding repertoire of techniques for molecular analysis of microdissected cells, laser microdissection allows host cellular responses to bacteria to be studied in their native tissue context. This approach has already yielded key insights into the nature of mucosal responses to commensal, as well as pathogenic bacteria, and promises to be an important addition to the cellular microbiologist's toolkit.     

Characterization of bacterial community in the stomach of yellow catfish (<Emphasis Type="Italic">Pelteobagrus fulvidraco</Emphasis>)

In this study, the traditional culture-based technique and the 16S rDNA sequencing method were used to investigate the characterization of bacterial community in the stomach contents and mucus of yellow catfish (Pelteobagrus fulvidraco). The culture-based technique disclosed that the average bacterial numbers in the gastric contents and mucus were 5.79 × 10⁷ cfu/g (cfu: colony forming unit) and 1.89 × 10⁵ cfu/g, respectively. Several different bacteria were obtained from gastric contents, including species from genera Bradyrhizobium, Phyllobacterium, Plesiomonas, Hafnia, Edwardsiella, Pseudomonas, and Bacillus. However, only two species were isolated from the gastric mucus, including species from genera Plesiomonas and Aeromonas. Forty-five phylotypes were observed from the 65 positive clones from the stomach contents (library SC); nineteen phylotypes were detected from the 45 clones from the stomach mucus (library SM). Further analyses revealed that the fish stomach harbored characteristic microbiota, where Firmicutes was dominant, followed by Proteobacteria and Bacteroidetes and Fusobacteria. This characterization of bacterial community is markedly different from that of the fish intestine, where Proteobacteria is predominant, followed by Fusobacteria and Firmicutes. Chloroflexi (1.5%) was only found in the library SC, while Actinobacteria (4.4%) was only found in the library SM, suggesting that microbiota of GI contents was quite different from that of GI mucus. In addition, several species of bacteria found in the stomach may be potentially opportunistic pathogens, indicating that fish digestive tract is a reservoir for many nosocomial pathogens.     

Tracking human sewage microbiome in a municipal wastewater treatment plant

Human sewage pollution is a major threat to public health because sewage always comes with pathogens. Human sewage is usually received and treated by wastewater treatment plants (WWTPs) to control pathogenic risks and ameliorate environmental health. However, untreated sewage that flows into water environments may cause serious waterborne diseases, as reported in India and Bangladesh. To examine the fate of the human sewage microbiome in a local municipal WWTP of Hong Kong, we used massively parallel sequencing of 16S rRNA gene to systematically profile microbial communities in samples from three sections (i.e., influent, activated sludge, and effluent) obtained monthly throughout 1 year. The results indicated that: (1) influent sewage bacterial profile reflected the human microbiome; (2) human gut bacterial community was the dominant force shaping influent sewage bacterial profile; (3) most human sewage bacteria could be effectively removed by the WWTP; (4) a total of 75 genera were profiled as potentially pathogenic bacteria, most of which were still present in the effluent although at a very low level; (5) a grouped pattern of bacterial community was observed among the same section samples but a dispersed pattern was found among the different section samples; and (6) activated sludge was less affected by the influent sewage bacteria, but it showed a significant impact on the effluent bacteria. All of these findings provide novel insights toward a mechanistic understanding of the fate of human sewage microbiome in the WWTP.     

贵州苗岭地区野猪肠道菌群结构与功能分析

野猪是当前南方山地森林生态系统中数量激增的主要有蹄类。为揭示贵州苗岭地区野猪肠道细菌的群落结构、多样性及菌群功能,本研究采用16S rRNA高通量测序技术检测了4头野猪胃肠道(胃、回肠、结肠和直肠)的细菌群落,共获得1 268 577条有效序列。经质控过滤,所有序列归类于1 019个OTU,包含19门292属。在门分类水平上,野猪肠道内核心菌群主要为厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)、变形菌门(Proteobacteria)和放线菌门(Actinobacteria),优势菌属包括普雷沃氏菌属(Prevotella)、乳酸杆菌属(Lactobacillus)、大肠—志贺氏菌属(Escherichia-Shigella)和双歧杆菌属(Bifidobacterium)等15个菌属。稀疏曲线表明测序深度已基本覆盖样品中所有细菌,测序充分。alpha多样性指数中,结肠和直肠的Chao1和Shannon指数显著高于胃和回肠(P<0.05),证明结肠和直肠比胃和回肠具有更高的菌群丰富度和多样性。主坐标分析(PCoA)和相似性分析(Anosim)结果也同样表...     

16S rRNA基因高通量测序方法检测奶牛场常用干草表面微生物群落结构及多样性

【目的】随着中国奶牛业的发展,干草需求量与日俱增。作为天然牧草,干草可以成为家畜传播病原体的载体。以干草表面附着物为研究对象,了解干草中细菌群落结构以及致病菌属特征。【方法】对来自6个不同奶牛场饲草舍的干草样本,应用Illumina Mi Seq高通量测序技术测定干草表面附着物细菌的16S r RNA基因V3-V4变异区序列,分析不同干草样本细菌群落组成。【结果】干草样本中的细菌在97%的相似水平下共得到OTU个数为15 416,涵盖了29门87纲144目219科323属的细菌。微生物多样性分析表明,干草样本具有很高的细菌多样性,不同样本多样性存在差异。对干草样本菌群中丰度较高的14种病原菌属进行分析,发现相较于人工种植牧草制备的干草,天然牧草制备的干草中病原菌属丰度较高。【结论】研究解析了干草样本中微生物的多样性、丰度及主要病原菌属的特征,对奶牛场疾病防控有一定指导意义。     

Otolith size and location in digestive tracts of northern fur seals (Callorhinus ursinus): Implications for dietary interpretations

Walleye pollock (Theragra chalcogramma) otoliths (n= 2,706) recovered from stomachs, small intestines, and colons of 43 northern fur seals (Callorhinus ursinus) were evaluated for size and wear by location in the digestive tract. Pollock fork length was regressed on otolith length after correction for erosion, and age was estimated from the calculated body size. Age‐1+ pollock otoliths (≥6.3‐mm length) were concentrated in stomachs while age‐0 otoliths (≤6.2‐mm length) were concentrated in colons. Less than 10% of otoliths were found in the small intestines. Pollock age decreased with progression along seal gastrointestinal tracts. Otolith quality increased along gastrointestinal tracts in numbers ≥20, which was typical of age‐0 otoliths recovered from colons. Otolith distribution by age and quality along gastrointestinal tracts suggests that small (≤12 cm) schooling prey are consumed in large volume and passed as a bolus rapidly through the digestive tract before significant erosion of bony remains occurs; while larger prey are eaten in smaller volume and subjected to otolith erosion due to longer retention in the stomach. Our results illustrate the importance of multiple sampling strategies to comprehensively represent prey size in pinniped diet.     

The production and detoxification of a potent cytotoxin, nitric oxide, by pathogenic enteric bacteria

The nitrogen cycle is based on several redox reactions that are mainly accomplished by prokaryotic organisms, some archaea and a few eukaryotes, which use these reactions for assimilatory, dissimilatory or respiratory purposes. One group is the Enterobacteriaceae family of Gammaproteobacteria, which have their natural habitats in soil, marine environments or the intestines of humans and other warm-blooded animals. Some of the genera are pathogenic and usually associated with intestinal infections. Our body possesses several physical and chemical defence mechanisms to prevent pathogenic enteric bacteria from invading the gastrointestinal tract. One response of the innate immune system is to activate macrophages, which produce the potent cytotoxin nitric oxide (NO). However, some pathogens have evolved the ability to detoxify NO to less toxic compounds, such as the neuropharmacological agent and greenhouse gas nitrous oxide (N?O), which enables them to overcome the host's attack. The same mechanisms may be used by bacteria producing NO endogenously as a by-product of anaerobic nitrate respiration. In the present review, we provide a brief introduction into the NO detoxification mechanisms of two members of the Enterobacteriaceae family: Escherichia coli and Salmonella enterica serovar Typhimurium. These are discussed as comparative non-pathogenic and pathogenic model systems in order to investigate the importance of detoxifying NO and producing N?O for the pathogenicity of enteric bacteria.     

Ecological and evolutionary drivers of haemoplasma infection and bacterial genotype sharing in a Neotropical bat community

Most emerging pathogens can infect multiple species, underlining the importance of understanding the ecological and evolutionary factors that allow some hosts to harbour greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is based primarily around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (order Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of bacterial prevalence and barriers to pathogen sharing are crucially needed. Here were studied haemotropic Mycoplasma spp. (i.e., haemoplasmas) across a species‐rich bat community in Belize over two years. Across 469 bats spanning 33 species, half of individuals and two‐thirds of species were haemoplasma positive. Infection prevalence was higher for males and for species with larger body mass and colony sizes. Haemoplasmas displayed high genetic diversity (21 novel genotypes) and strong host specificity. Evolutionary patterns supported codivergence of bats and bacterial genotypes alongside phylogenetically constrained host shifts. Bat species centrality to the network of shared haemoplasma genotypes was phylogenetically clustered and unrelated to prevalence, further suggesting rare—but detectable—bacterial sharing between species. Our study highlights the importance of using fine phylogenetic scales when assessing host specificity and suggests phylogenetic similarity may play a key role in host shifts not only for viruses but also for bacteria. Such work more broadly contributes to increasing efforts to understand cross‐species transmission and the epidemiological consequences of bacterial pathogens.     

甘南高寒地区不同海拔西藏沙棘根瘤内生菌多样性

为了研究甘南高寒地区3个不同海拔西藏沙棘根瘤中内生菌的多样性,采用Illumina MiSeq高通量测序技术对3种不同海拔的西藏沙棘根瘤内生菌的菌群组成和多样性进行了分析。实验结果表明,3个不同海拔西藏沙棘根瘤中的内生菌主要包括6大门,分别为蓝藻门(Cyanobacteria),放线菌门(Actinobacteria),变形菌门(Proteobacteria),拟杆菌门(Bacteroidetes),梭杆菌门(Fusobacteria)和厚壁菌门(Firmicutes)。其中占主导地位的微生物是蓝藻门和放线菌门,蓝藻门在3个海拔的西藏沙棘根瘤中的丰度分别为68.1%,64.7%和66.0%,放线菌门在3个海拔的西藏沙棘根瘤中的丰度分别为28.6%,30.2%和29.5%。放线菌门弗兰克氏菌属(Frankia)为共同的优势菌属之一,在3个海拔的丰度分别为28.2%,29.8%和29.1%。3个不同海拔西藏沙棘根瘤中的内生菌除了能与沙棘共生固氮的弗兰克氏菌外,还存在其他的微生物群落,可能存在一些潜在的有价值的内生菌种资源。     

贵州6种蝙蝠的核型

采用常规骨髓细胞空气干燥法,研究了贵州6种蝙蝠的核型。白腹管鼻蝠(Murina leucogaster)2n=44,染色体臂数(FN)为58;普通长翼蝠(Miniopterus schreibersi)染色体数是2n=46,FN为50,黄大蹄蝠(Hipposideros pratti)2n=32,FN为60;角菊头蝠(Rhinolophus cornutus)2n=62,FN为60;云南菊头蝠(R.yunnanensis)2n=44,FN是60;犬蝠(Cynopterus sphinx)2n=34,FN=58。其中白腹管鼻蝠、云南菊头蝠和犬蝠为国内首次报道。     

Influence of dietary zinc oxide and copper sulfate on the gastrointestinal ecosystem in newly weaned piglets

Dietary doses of 2,500 ppm ZnO-Zn reduced bacterial activity (ATP accumulation) in digesta from the gastrointestinal tracts of newly weaned piglets compared to that in animals receiving 100 ppm ZnO-Zn. The amounts of lactic acid bacteria (MRS counts) and lactobacilli (Rogosa counts) were reduced, whereas coliforms (MacConkey counts) and enterococci (Slanetz counts, red colonies) were more numerous in animals receiving the high ZnO dose. Based on 16S rRNA gene sequencing, the colonies on MRS were dominated by three phylotypes, tentatively identified as Lactobacillus amylovorus (OTU171), Lactobacillus reuteri (OTU173), and Streptococcus alactolyticus (OTU180). The colonies on Rogosa plates were dominated by the two Lactobacillus phylotypes only. Terminal restriction fragment length polymorphism analysis supported the observations of three phylotypes of lactic acid bacteria dominating in piglets receiving the low ZnO dose and of coliforms and enterococci dominating in piglets receiving the high ZnO dose. Dietary doses of 175 ppm CuSO(4)-Cu also reduced MRS and Rogosa counts of stomach contents, but for these animals, the numbers of coliforms were reduced in the cecum and the colon. The influence of ZnO on the gastrointestinal microbiota resembles the working mechanism suggested for some growth-promoting antibiotics, namely, the suppression of gram-positive commensals rather than potentially pathogenic gram-negative organisms. Reduced fermentation of digestible nutrients in the proximal part of the gastrointestinal tract may render more energy available for the host animal and contribute to the growth-promoting effect of high dietary ZnO doses. Dietary CuSO(4) inhibited the coliforms and thus potential pathogens as well, but overall the observed effect of CuSO(4) was limited compared to that of ZnO.     

青紫蓝兔体内Ghrelin的免疫组化定位

采用免疫组织化学方法研究了Ghrelin在青紫蓝兔(Oryctolagus cuniculus)体内的分布定位。结果显示,Ghrelin免疫阳性细胞分布于下丘脑、大脑皮质、延髓、脊髓、胃、小肠和大肠。下丘脑内的阳性神经元胞体主要分布于弓状核、室旁核、腹内侧核、背内侧核和下丘脑外侧区。胃肠道内的Ghrelin免疫阳性细胞存在两种类型,即"闭合型"细胞和"开放型"细胞。实验结果表明,兔体内Ghrelin的分布与人和其他动物的分布基本相似,但也存在一些差异。     

大菊头蝠在湖南省分布新纪录

2007年1月11日,在湘西土家族苗族自治州吉首市寨阳乡堂乐洞采到菊头蝠雌性标本1只,经鉴定为湖南省翼手目新纪录,属大菊头蝠华南亚种(Rhinolophus luctus lanosus)。     

Phytate hydrolysis in rat gastrointestinal tracts, as observed by 31P Fourier transform nuclear magnetic resonance spectroscopy

Phytate hydrolysis was followed through rat gastrointestinal tracts by (31)P nuclear magnetic resonance spectroscopy. No phytate hydrolysis products were detected in the diet, stomach, or small intestine. It was concluded that cecal bacteria were responsible for phytate hydrolysis, which continued in the colon and fecal pellet.     

Long W tracts are over-represented in the Escherichia coli and Haemophilus influenzae genomes.

The occurrence of DNA tracts of the three binary base combinations: R.Y, K.M and W;S has been mapped in the complete genomes of Haemophilus influenzae and Escherichia coli. A highly significant over-representation of W tracts is observed in both bacteria. The excess of W tracts is particularly striking in the 10% intercoding regions. Subdivision of intercoding regions into divergent (promoting), convergent (terminating) and sequential subregions shows that the excess of W tracts is most concentrated in the promoter regions. A particularly high excess of W tracts is observed in the first 200 bases 5' upstream of coding start sites. The data suggest that W tracts have a role in promoter function. A function as unwinding centers, analogous to the role of R.Y tracts in eukaryotes, is proposed. R.Y and K.M tracts are only modestly over-represented in the two bacteria.     

Amplicon-based profiling of bacteria in raw and secondary treated wastewater from treatment plants across Australia

In this study, we investigated the use of Illumina high-throughput sequencing of 16S ribosomal RNA (rRNA) amplicons to explore microbial diversity and community structure in raw and secondary treated wastewater (WW) samples from four municipal wastewater treatment plants (WWTPs A–D) across Australia. Sequence reads were analyzed to determine the abundance and diversity of bacterial communities in raw and secondary treated WW samples across the four WWTPs. In addition, sequence reads were also characterized to phenotypic features and to estimate the abundance of potential pathogenic bacterial genera and antibiotic-resistant genes in total bacterial communities. The mean coverage, Shannon diversity index, observed richness (S _obs), and abundance-based coverage estimate (ACE) of richness for raw and secondary treated WW samples did not differ significantly (P > 0.05) among the four WWTPs examined. Generally, raw and secondary treated WW samples were dominated by members of the genera Pseudomonas, Arcobacter, and Bacteroides. Evaluation of source contributions to secondary treated WW, done using SourceTracker, revealed that 8.80–61.4% of the bacterial communities in secondary treated WW samples were attributed to raw WW. Twenty-five bacterial genera were classified as containing potential bacterial pathogens. The abundance of potentially pathogenic genera in raw WW samples was higher than that found in secondary treated WW samples. Among the pathogenic genera identified, Pseudomonas and Arcobacter had the greatest percentage of the sequence reads. The abundances of antibiotic resistance genes were generally low (<0.5%), except for genes encoding ABC transporters, which accounted for approximately 3% of inferred genes. These findings provided a comprehensive profile of bacterial communities, including potential bacterial pathogens and antibiotic-resistant genes, in raw and secondary treated WW samples from four WWTPs across Australia and demonstrated that Illumina high-throughput sequencing can be an alternative approach for monitoring WW quality in order to protect environmental and human health.