Exploring the bovine rumen bacterial community from birth to adulthood

The mammalian gut microbiota is essential in shaping many of its host''s functional attributes. One such microbiota resides in the bovine digestive tract in a compartment termed as the rumen. The rumen microbiota is necessary for the proper physiological development of the rumen and for the animal''s ability to digest and convert plant mass into food products, making it highly significant to humans. The establishment of this microbial population and the changes occurring with the host''s age are important for understanding this key microbial community. Despite its importance, little information about colonization of the microbial populations in newborn animals, and the gradual changes occurring thereafter, exists. Here, we characterized the overall bovine ruminal bacterial populations of five age groups, from 1-day-old calves to 2-year-old cows. We describe the changes occurring in the rumen ecosystem after birth, reflected by a decline in aerobic and facultative anaerobic taxa and an increase in anaerobic ones. Some rumen bacteria that are essential for mature rumen function could be detected as early as 1 day after birth, long before the rumen is active or even before ingestion of plant material occurs. The diversity and within-group similarity increased with age, suggesting a more diverse but homogeneous and specific mature community, compared with the more heterogeneous and less diverse primary community. In addition, a convergence toward a mature bacterial arrangement with age was observed. These findings have also been reported for human gut microbiota, suggesting that similar forces drive the establishment of gut microbiotas in these two distinct mammalian digestive systems.     

New microbiota found in sputum from patients with community-acquired pneumonia

Community-acquired pneumonia （CAP） is a major concern in hospitals and the bacterial community of which has not been systemically discussed yet. Sputum from patients in the acute stages is a kind of accessible sample reflecting its fea- tures. In our study, we analyzed 45 sputum samples from 45 patients with CAP. Eighteen sputum samples from healthy people were chosen as the controls. Pyrosequencing of the 16s rDNA V3 hypervariable regions of aH the bacteria con- tained in the sputum was used as a culture-independent method to disclose the community constitution. Also, our published data for hospital-acquired pneumonia （HAP） in sputum was used for comparison. By pyrosequencing, 〉90,000 DNA reads were detected. After being analyzed by tools in the Ribosomal Database Project, the reads were clas- sified into five main phyla and 〉100 genera. At the phyla level, the reads＇ distribution of CAP is similar to that of healthy people and at genera level, the occurrence of each genus possesses their feature in three categories. Genera such as Streptococcus and Neisseria showed stability in their percentages, indicating that such genera are rarely affected by exogenous bacteria or antibiotics. The role of other genera such as Moraxella and Rothia in CAP should be emphasized. According to our analysis, the bacterial communities of CAP are with slight change when compared with those of healthy people, but have a large gap between HAP. Meanwhile, Rothia might be an important endogenous pneumonia-causing factor.     

包埋法固定化对硫氧化微生物菌群结构和功能的影响

【目的】为探讨包埋法固定化过程对硫氧化菌群硫化物去除能力及菌群微生物群落结构的影响,【方法】以聚乙烯醇-海藻酸钠-活性炭为载体,对硫氧化菌群进行了固定化,并采用富含硫化物的无机盐培养基,对比固定化与非固定化硫氧化菌群对硫化物的氧化去除能力。同时,利用PCR-DGGE技术,探讨硫氧化菌群在固定化前后以及在硫化物氧化去除过程中微生物群落结构变化。【结果】在对硫氧化菌群进行固定化之后,12 h之内对硫化物的最大去除能力从1000 mg/L下降为600 mg/L。硫氧化菌群的微生物群落结构发生了明显变化,但菌群中的硫氧化菌Catenococcus thiocycli未受影响,硫氧化菌Thioclava pacifica在菌群中的地位反而得到了强化。【结论】受制于底物在载体材料中的扩散迁移效率,硫氧化菌群对硫化物的氧化去除能力在固定化之后有所下降。由于不同微生物对固定化形成的微环境的适应能力以及对载体附着能力的不同,固定化对硫氧化菌群的微生物群落结构产生较大影响。     

高通量测序分析DNA提取引起的对虾肠道菌群结构偏差

【目的】通过高通量测序技术,评价不同DNA试剂盒提取引起的对虾肠道菌群结构偏差,了解健康凡纳滨对虾肠道菌群结构特征。【方法】分别以细菌、粪便和组织DNA试剂盒3次重复提取凡纳滨对虾肠道总DNA(分别编号为SIB,SIS和SIT),检测DNA含量、纯度及其16S r DNA V4区可扩增性,进一步采用Illumina Mi Seq高通量测序比较SIB和SIS样品菌群组成和多样性。【结果】细菌试剂盒提取的虾肠总DNA效果最好,粪便试剂盒次之,而组织试剂盒所提DNA含量低且难以被扩增。从SIB和SIS样品分别获得52151±5085和55296±5147条有效序列,同一(46800条)测序深度下,SIS样品OTU(operational taxonomic unit)数量和Shannon多样性指数均显著高于SIB的,而SIB样品间OTU重复性则优于SIS样品间的。从SIB和SIS样品鉴定的优势门一致,均包括变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)、浮霉菌门(Planctomycetes)、放线菌门(Actinobacteria)和蓝细菌门(Cyanobacteria),但不同分类水平上绝大多数优势菌群丰度在两种样品间差异明显。【结论】高通量测序分析表明对虾肠道菌群结构因DNA提取方法不同而呈现显著偏差;本研究健康凡纳滨对虾肠道核心菌群主要由发光杆菌属(Photobacterium),乳球菌属(Lactococcus),弧菌属(Vibrio),Aliivibrio和3个分类未定属构成。     

乳酸链球菌素对瘤胃体外发酵、甲烷生成及功能菌群数量的影响北大核心CSCD

【目的】旨在通过体外静态模拟瘤胃发酵法研究乳酸链球菌素(NI)对瘤胃发酵、甲烷生成及功能菌群数量的影响。【方法】以不添加任何添加剂处理做阴性对照(NC),以莫能菌素(MON,5μmol/L)做阳性对照,试验组NI添加水平分别为3(NI-3)、9(NI-9)和27 mg/100 m L(NI-27),每个处理4个重复,分别于培养后的0、3、6、9、12、24 h测定产气量和甲烷产量。培养24 h后,采集发酵液样品,用于发酵参数和菌群数量的测定。【结果】与NC组相比,添加NI和MON均能显著降低产气量和甲烷产量(P<0.05);添加NI对pH值、干物质消失率(DMD)和有机物消失率(OMD)无显著影响(P>0.05);NI-9处理组与NC组相比氨态氮浓度显著降低(P<0.05),而NI-3和NI-27组氨氮浓度没有显著变化(P>0.05);相比而言,MON处理组DMD、OMD和氨氮浓度与NC组相比均显著降低(P<0.05),而pH值与其他各处理组相比没有差异(P>0.05);与NC组相比,NI各处理组和MON组乙酸浓度及乙丙比均显著降低(P<0.05),丙酸浓度显著提高(P<0.05)。功能菌方面,qPCR结果显示添加NI和MON对总菌和拟杆菌门数量均无显著影响(P>0.05);与NC相比,添加NI对原虫、甲烷菌、真菌和厚壁菌门数量均无显著影响(P>0.05),而MON组原虫、甲烷菌、真菌和厚壁菌门数量显著降低(P<0.05);NI和MON处理均显著提高了硫还原菌和C.aminophilum数量(P<0.05),但C.sticklandii数量不受影响(P>0.05)。【结论】添加适宜浓度的NI可降低瘤胃甲烷与氨的生成,但并不影响饲料消化,这种发酵模式的改变可能与瘤胃功能菌群数量与多样性的变化密切相关。     

Focus: Microbiome: Human Microbiota and Ophthalmic Disease

The human ocular surface, consisting of the cornea and conjunctiva, is colonized by an expansive, diverse microbial community. Molecular-based methods, such as 16S rRNA sequencing, has allowed for more comprehensive and precise identification of the species composition of the ocular surface microbiota compared to traditional culture-based methods. Evidence suggests that the normal microbiota plays a protective immunological role in preventing the proliferation of pathogenic species and thus, alterations in the homeostatic microbiome may be linked to ophthalmic pathologies. Further investigation of the ocular surface microbiome, as well as the microbiome of other areas of the body such as the oral mucosa and gut, and their role in the pathophysiology of diseases is a significant, emerging field of research, and may someday enable the development of novel probiotic approaches for the treatment and prevention of ophthalmic diseases.     

Effect of high fibre diets formulated with different fibrous ingredients on performance,nutrient digestibility and faecal microbiota of weaned piglets

The aim of the experiment on 180 weaned piglets (8.9 kg body weight) was to investigate the influence of high fibre diets formulated with different fibrous ingredients on performance, nutrient digestibility, diarrhoea incidence and numbers of faecal microbiota. The dietary treatments included a Control diet and five high fibre diets formulated with different fibre sources including wheat bran, soybean hulls, naked oat hulls, palm kernel expeller and bamboo fibre. The high fibre diets averaged 14.6% neutral detergent fibre with different non-starch polysaccharides (NSP) components and were fed ad libitum for 28 d. Faecal samples were collected during the last 3 d of the experiment and the apparent total tract digestibility of nutrients and fibre components were determined. Pigs fed the Control and wheat bran diets had a higher (p ≤ 0.05) average daily gain (ADG) than pigs fed the palm kernel expeller and bamboo meal diets. The reduced ADG for pigs appeared to be related to reductions in the digestibility of gross energy and dry matter, respectively. The feed-to-gain ratio was significantly higher (p ≤ 0.05) for pigs fed the fibre diets. The digestibility of NSP components was different among the treatments. The diarrhoea incidence was not affected by treatments. The abundance of faecal bifidobacteria was significantly higher (p ≤ 0.05) for pigs fed the wheat bran diet than for pigs fed the bamboo meal diet. It was concluded that the diets formulated with different fibre sources when fed to weaned piglets have different effects on pig performance, nutrient digestibility and numbers of faecal microbiota. The wheat bran diet rich in arabinoxylans enabled a better performance than the other tested diets with fibre addition.     

Tracing microbiota changes in yamahai-moto,the traditional Japanese sake starter

Sake is made from steamed rice, malted rice, and water. Sake production begins with the preparation of a small-scale starter (moto); the quality of moto significantly influences the flavor and richness of sake. In the traditional starter, yamahai-moto, the growth of naturally occurring lactic acid bacteria represses the putrefactive micro-organisms, whereas in the modern starter, sokujo-moto, this is achieved by adding lactic acid. In this study, the successive change in bacterial flora of yamahai-moto was analyzed by pyrosequencing 16S ribosomal RNA genes. Lactobacillus was dominant throughout the process (93–98%). Nitrate-reducing bacteria that have been generally assumed to be the first colonizers of yamahai-moto were scarcely found in the early stage, but Lactobacillus acidipiscis dominated. Lactobacillus sakei drastically increased in the middle stage. This is the first report, though one case study, to show how the early stage microbiota in Japanese yamahai-moto is varyingly controlled without nitrate-reducing bacteria using next-generation sequencing.     

从肠道菌群角度认识阿尔茨海默病的潜在发病机制

过去10年中,人们逐渐认识到肠道微生物群的多样性及菌群平衡在维护宿主健康中发挥的作用。肠道微生物及其代谢产物通过一系列的生化、免疫和生理功能环节与宿主进行交流,从而影响宿主的稳态和健康。阿尔茨海默病(Alzheimer’s disease,AD)是一种复杂的神经退行性疾病,其易感性和发展过程受年龄、遗传和表观遗传等因素的影响。研究发现,肠道微生物群的紊乱(组成改变和易位)与神经系统疾病(AD)有关,胃肠道通过肠脑轴与中枢神经系统进行沟通,包括对神经的直接作用、内分泌途径和免疫调控方式。动物模型、粪便菌群移植及益生菌干预为肠道菌群与AD的相关性提供了证据。外漏的细菌代谢产物可能直接损害神经元功能,也可能诱发神经炎症,促进AD的发病。本文主要综述了肠道微生物群与AD的关联和作用机制,以期为通过改善肠道菌群结构预防AD的可能干预措施提供依据。     

The role of intestinal microbiota in cardiovascular disease

Accumulating evidence has indicated that intestinal microbiota is involved in the development of various human diseases, including cardiovascular diseases (CVDs). In the recent years, both human and animal experiments have revealed that alterations in the composition and function of intestinal flora, recognized as gut microflora dysbiosis, can accelerate the progression of CVDs. Moreover, intestinal flora metabolizes the diet ingested by the host into a series of metabolites, including trimethylamine N‐oxide, short chain fatty acids, secondary bile acid and indoxyl sulfate, which affects the host physiological processes by activation of numerous signalling pathways. The aim of this review was to summarize the role of gut microbiota in the pathogenesis of CVDs, including coronary artery disease, hypertension and heart failure, which may provide valuable insights into potential therapeutic strategies for CVD that involve interfering with the composition, function and metabolites of the intestinal flora.