The effect of regular or reduced‐fat distillers grains with solubles on rumen methanogenesis and the rumen bacterial community

Aims

The effect of feeding dried distillers grains with solubles (DDGS) or reduced‐fat DDGS (RFDG) on ruminal methanogenesis and the rumen bacterial community of dairy cattle was evaluated.

Methods and Results

Treatments were CONT, a diet with no distillers grains; DG, inclusion of 20% DDGS; rfDG, inclusion of 20% RFDG; and MIX, inclusion of 10% DDGS and 10% RFDG. Methane emission was measured; rumen bacterial community was evaluated by sequencing the V4 region of the 16S rRNA gene. Total methane production remained unaffected. However, feeding distillers grains tended to reduce methanogenesis per unit of feed intake, decreased the abundance of the phylum Bacteroidetes and tended to increase Firmicutes. The abundance of Prevotellaceae positively correlated with feed intake; methane emission was positively correlated with the abundance of Prevotellaceae and was negatively correlated with the abundance of Succinivibrionaceae.

Conclusions

DDGS or RFDG may reduce methanogenesis per unit of feed intake; shifts in the abundance of predominant ruminal bacterial families may influence methane formation, likely because of their role on hydrogen liberation and utilization pathways.

Significance and Impact of the Study

Replacing corn and soybean meal with DDGS or RFDG in dairy rations may reduce the proportion of dietary energy wasted as methane, without detrimental effects on the overall bacterial population.     

油菜叶绿体16S rRNA基因前导顺序的一级结构

质粒pBN119的3.2kb BamHI片段的PvuⅡ-BglⅡ片段全顺序长为840bp,其中含油菜叶绿体16S rRNA基因5′端的140bp。通过寻找GTTC顺序,发现在395至468位核苷酸之间是tRNA~(Val)基因;在73至118位核苷酸之间是一个蛋白阅读框。和已发表的玉米叶绿体16S rRNA前导顺序进行比较,同样存在三个相应的大肠杆菌RNA聚合酶的结合位点。和大肠杆菌的启动子及相应基因作比较,表明叶绿体基因组具有很明显的原核性,但其tRNA~(Val)基因没有CCA3′顺序。在16S rRNA基因、tRNA~(Val)基因及蛋白阅读框的5′端附近均能找到一个比较稳定的茎环结构。我们推测这些茎环结构可能和位于反问重复顺序上的某些基因的转录调节有关。     

Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen

Microbial colonization is central to ruminal degradation of dietary material yet little is known about the dynamics of this process. The aim of this study was to characterize the initial stages of bacterial colonization of forage, and to assess the impact that different postsample processing and analysis methods had on the results obtained. Bacterial 16S rRNA gene-based analysis of damaged, nonconserved perennial ryegrass, incubated in sacco in the bovine rumen, required the development and validation of new quantitative PCR and denaturing gradient gel electrophoresis (DGGE) primers. Analysis with previously available primer sets was compromised due to dominant amplification of forage-derived chloroplast 16S rRNA genes. DGGE analysis of incubated samples demonstrated that a diverse and consistent population of ruminal bacteria colonized rapidly. Postsampling methodologies did not affect overall population profiles whereas the washing method appeared to influence bacterial numbers. However, regardless of processing methodology, bacterial numbers increased rapidly within 5 min, stabilizing after 15 min of incubation. These findings reveal for the first time the dynamics of bacterial colonization of forage within the rumen.     

油菜叶绿体16SrRNA基因的一级结构分析

本文报道了油菜叶绿体16S rRNA基因的全顺序及其5′端上游的156bp和3′端下游的101bp的核苷酸顺序。油菜叶绿体16s rRNA基因长为1491bp,和烟草、玉米相比,同源程度分别为98.5％、96.1％。油菜叶绿体16S rRNA基因5′端上游及3′端下游的顺序能互补而形成一个较大的茎环结构,但与烟草相比,由于3′端下游顺序有79bp的缺失,因此,该结构中的茎部分大小仅为烟草的二分之一。     

Defining seasonal marine microbial community dynamics

Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.     

HRT and nutrients affect bacterial communities grown on recirculation aquaculture system effluents

In a recirculation aquaculture system the drumfilter effluent can be used as substrate for heterotrophic bacterial production, which can be recycled as feed. Because the bacteria might contain pathogens, which could reduce its suitability as feed, it is important to characterize these communities. Bacteria were produced in growth reactors under different conditions: 7 h hydraulic retention time (HRT) vs. 2 h, sodium acetate vs. molasses, and ammonia vs. nitrate. The community of the drumfilter effluent was different from those found in the reactors. However, all major community components were present in the effluent and reactor broths. HRT influenced the bacteria community, resulting in a DGGE profile dominated by a band corresponding to an Acinetobacter sp.-related population at 2 h HRT compared to 7 h HRT, where bands indicative of alpha-proteobacterial populations most closely related to Rhizobium and Shinella spp. were most abundant. Molasses influenced the bacterial community. It was dominated by an Aquaspirillum serpens-related population. Providing total ammonia nitrogen (TAN) in addition to nitrate led to the occurrence of bacteria close to Sphaerotilus spp., Flavobacterium mizutaii and Jonesia spp. It was concluded from these results that a 6-7 h HRT is recommended, and that the type of substrate is less important, and results in communities with a comparably low pathogenic risk.     

Diversity of endophytic bacterial communities in poplar grown under field conditions

Bacterial endophytes may be important for plant health and other ecologically relevant functions of poplar trees. The composition of endophytic bacteria colonizing the aerial parts of poplar was studied using a multiphasic approach. The terminal restriction fragment length polymorphism analysis of 16S rRNA genes demonstrated the impact of different hybrid poplar clones on the endophytic community structure. Detailed analysis of endophytic bacteria using cultivation methods in combination with cloning of 16S rRNA genes amplified from plant tissue revealed a high phylogenetic diversity of endophytic bacteria with a total of 53 taxa at the genus level that included Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The community structure displayed clear differences in terms of the presence and relative proportions of bacterial taxa between the four poplar clones studied. The results showed that the genetic background of the hybrid poplar clones corresponded well with the endophytic community structure. Out of the 513 isolates and 209 clones identified, Actinobacteria, in particular the family Microbacteriaceae, made up the largest fraction of the isolates, whereas the clone library was dominated by Alpha- and Betaproteobacteria. The most abundant genera among the isolates were Pseudomonas and Curtobacterium, while Sphingomonas prevailed among the clones.     

A comparison of ammonia-oxidiser populations in eutrophic and oligotrophic basins of a large freshwater lake

A combination of PCR amplification and oligonucleotide probing was used to investigate the populations of ammonia-oxidisers of the -Proteobacteria in the eutrophic and oligotrophic basins of Lake Windermere, a large temperate lake in the English Lake District. Numbers of ammonia-oxidisers (MPN) in the Windermere lakewater were low (< 100 cells ml^–1) throughout the year with the exception of peaks in August, which coincided with stratification, and November in the South Basin where overturn may have introduced ammonia-oxidising bacteria into the water column. Sediment samples contained larger populations of ammonia oxidisers, usually ca. 10⁴ per g. dry weight, which remained relatively constant throughout the seasonal cycle in both Basins. DNA was recovered from lakewater and sediment samples and Nitrosospiraand N. europaea-eutrophalineage16S rRNA genes amplified in a nested PCR reaction, with confirmation of identity by oligonucleotide hybridisation. Nitrosospira 16S rDNA was readily detected in all samples and therefore found to be ubiquitous. In contrast, nitrosomonad DNA of the N. europaea-eutropha lineage could only be detected in the oligotrophic North Basin. Enrichment cultures of lakewater samples only exhibited nitrification at low (0.67 mM) and medium (5 mM) ammonium concentrations, whilst sediment enrichments nitrified at all concentrations tested including high (12.5 mM) ammonium medium. These data suggest that ammonia-oxidiser populations may be physiologically distinguished between lakewater and sediment, and that species distribution in a single lake is non-uniform.     

一株降解煤油菌株的筛选与鉴定

本文通过从污水处理厂活性污泥中分离得到一株高效降解轻油(煤油)细菌5092-2,通过形态学、16S rRNA鉴定该菌为Mangroveibacter sp.。进一步对其生长条件进行了研究,发现该菌在23℃到38℃、pH为5.0到9.0范围内生长无明显差异。在温度为35℃,pH 7.2~7.4,160 r/min培养7 d,菌株降解煤油的能力达到52.3%,具有进一步研究的价值。     

基于高通量测序的宏基因组学技术在动物胃肠道微生物方面的研究进展

微生物在自然界普遍存在,且具有降解植物细胞壁的特殊功能。动物胃肠道寄生的微生物与宿主生长发育和机体代谢密切相关,可以帮助动物将植物源性物质转化为机体所需要的营养物质。基于高通量测序的宏基因组学技术和分析方法的改进,使人们对复杂环境中微生物的研究更加方便、透彻。而宏基因组学技术应用于动物胃肠道微生物的研究,则有助于挖掘胃肠道微生物基因库并筛选其中的功能基因。这不仅对动物生长发育调控、疾病预防等基础研究具有重要意义,而且在工业生产及食品安全等领域也发挥着重要作用。就基于高通量测序技术的宏基因组技术在动物胃肠道微生物分类、功能应用等方面的研究进行了梳理和综述,旨在为动物科学生产及微生物发酵等相关领域的研究工作提供科学指导。     

一株硫酸盐还原菌的分离鉴定和系统发育分析

从处理硫酸盐废水的厌氧折流板反应器中分离得到一株硫酸盐还原菌D11, 该菌株革兰氏反应阴性, 无芽孢, 菌体杆状稍有弯曲, 宽度在0.6 μm~0.8 μm, 长度在1.8 μm~3.3 μm之间, 有极生单鞭毛, 能运动, 接触酶阳性, 氧化酶阴性。菌株生长的pH范围介于6.0~8.0之间, 最适pH为7.0, 生长温度范围为25°C~37°C, 最适温度为30°C。能够以葡萄糖、蔗糖、乙酸、乳酸、乙醇和丙二醇为唯一碳源生长, 不能利用丙三醇、丁醇、琥珀酸和苹果酸。菌株DNA的G+C含量为62.7 mo     

10种常见细菌基因检测膜条的研制

以16S rRNA基因为检测靶基因,设计10种常见细菌的DNA探针,将探针固定于硝酸纤维素膜条;PCR扩增细菌的16S rRNA基因片段并标记生物素后与膜条杂交;采用碱性磷酸酶标记的链亲和素检测生物素标记,以NBT/BCIP显色。该膜条不仅能单独检测10种细菌中的任何一种,也能同时检测5种细菌。该方法具备高通量、低成本、快速、准确等特点,具有良好的临床应用前景。     

The Use of Terminal Restriction Fragment Length Polymorphism (T-RFLP) for the Characterisation of Microbial Communities in Marine Sediments

Terminal Restriction Fragment Length Polymorphism (T-RFLP) of PCR amplified 16S rRNA genes was used to investigate microbial communities in the sediments of Ria Formosa, Portugal. Five replicates of surface sand sediments were collected at an artificial inlet to the sea, between June 2001 and July 2002. Restriction enzymes Msp1 and Hha1 provided 57 different terminal fragments (T-RFs). The sediments were essentially dominated by the same ribotypes throughout the year, with seasonal shifts attributed to minor ribotypes. Principal component analysis of the T-RFs profile revealed no consistent pattern of temporal variation and no consistent grouping of replicate sediment samples. The results suggest that the small-scale spatial variability outweighs the seasonal variability. Phylogenetic affiliations suggested that the dominant bacteria were representatives of the α-Proteobacteria group.     

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。     

基于16S rDNA扩增子测序技术揭示真胃左方变位对奶牛粪便微生物的影响

[目的]本试验旨在测定产后健康奶牛和罹患真胃左方变位(left displacement of the abomasum, LDA)奶牛粪便中微生物菌群的变化,以期探讨LDA发生与菌群的关联性,评估其对机体代谢的潜在影响.[方法]采用16S rDNA高通量测序技术,测定10头健康奶牛(Health)、10头真胃左方变位...     

Rethinking microbial diversity analysis in the high throughput sequencing era

The analysis of amplified and sequenced 16S rRNA genes has become the most important single approach for microbial diversity studies. The new sequencing technologies allow for sequencing thousands of reads in a single run and a cost-effective option is split into a single run across many samples. However for this type of investigation the key question that needs to be answered is how many samples can be sequenced without biasing the results due to lack of sequence representativeness? In this work we demonstrated that the level of sequencing effort used for analyzing soil microbial communities biases the results and determines the most effective type of analysis for small and large datasets. Many simulations were performed with four independent pyrosequencing-generated 16S rRNA gene libraries from different environments. The analysis performed here illustrates the lack of resolution of OTU-based approaches for datasets with low sequence coverage. This analysis should be performed with at least 90% of sequence coverage. Diversity index values increase with sample size making normalization of the number of sequences in all samples crucial. An important finding of this study was the advantage of phylogenetic approaches for examining microbial communities with low sequence coverage. However, if the environments being compared were closely related, a deeper sequencing would be necessary to detect the variation in the microbial composition.