巴马香猪不同生长阶段的肠道菌群特征分析

在猪的生长发育过程中,肠道菌群的建立及其均衡结构的维持对猪的健康生长具有重要作用,了解仔猪不同生长阶段肠道菌群的结构和功能可为指导其不同阶段的营养调控和饲养管理提供理论基础.本实验采集巴马香猪0 d(初生)、16 d(哺乳期)和40 d(保育期)3个生长阶段的粪便样品,采用16S rRNA基因高通量测序方法,分析巴马香...     

鸭胚胎发育过程中肠道菌群的演替规律研究

肠道内定植有种类繁多的微生物,其在维持稳态、调节宿主免疫系统及影响宿主生理发育过程中发挥积极作用,对畜禽生长发育和健康有重要的影响。胚胎期肠道菌群对禽类具有重要意义。本研究以鸭为模型,通过对不同胚龄鸭盲肠进行组织学观察,并对不同胚胎发育阶段的鸭胚胎整个肠道进行16s?rRNA测序。结果显示：随着鸭胚龄的增长,肠腔体积不断增加,肠绒毛数量增加。16天的鸭胚胎肠道微生物与出壳第一天雏鸭肠道微生物结构存在显著差异。在胚胎期,肠道微生物主要富集乳酸菌、布劳特氏菌、粪杆菌、拟杆菌、无色杆菌5种菌属,而出壳后,肠道微生物主要富集罗姆布茨菌、中慢生根瘤菌、藤黄色单胞菌3种菌属。说明随着鸭胚胎及肠道发育,肠道微生物结构及丰度存在差异,为禽类胚胎期的肠道微生物定植研究提供参考,也为微生态制剂在畜牧业生产中的合理开发与应用奠定理论基础。     

枯草芽孢杆菌与乳酸杆菌联合应用对断奶仔猪肠道菌群的影响

旨在研究枯草芽孢杆菌与乳酸杆菌联合应用对断奶仔猪肠道菌群的影响。采用Illumina MiSeq测序平台的16S rRNA测序技术分析不同处理后仔猪肠道菌群的变化。结果表明:处理组多样性指数Shannon指数均高于对照组(P0.05),Simpson指数均低于对照组(P0.05);门水平分类上拟杆菌门和厚壁菌门为优势菌群,拟杆菌门在联合益生菌组中的比例最高(61.6%),对照组中最低(43.3%);属水平分类上联合益生菌组与对照组相比存在显著性差异的菌群是颤螺菌属和瘤胃球菌属(P0.05)。结果提示,枯草芽孢杆菌与乳酸杆菌联合应用可以改善断奶仔猪肠道菌群结构,促进肠道内有益菌群的生长。     

鸭疫里默氏菌感染对鸭肠道菌群结构的影响

试验旨在分析鸭疫里默氏菌（RA）感染不同时期鸭肠道菌群结构变化规律,探讨鸭疫里默氏菌对鸭肠道微生物的影响及引起鸭致病的可能机制。采用细菌16S V4-V5区扩增通用引物,扩增鸭疫里默氏菌未感染组（鸭疫里默氏菌感染0 d组）,鸭疫里默氏菌感染后1、2、3、5、9和14 d的鸭直肠内容物样本DNA,将扩增得到的产物进行DNA建库后基于Ion S5^TMXL测序平台测序。测序得到的Raw Reads数据总量为4 710 688条序列,平均每个样本84 119条序列。共注释到数据库的操作分类单元（OTUs）数目为4 528。Alpha多样性分析结果表明,菌群多样性指数Shannon和Simpson在鸭疫里默氏菌感染组和未感染组间差异不显著（P>0.05）,菌群丰富度指数Chao1、Ace、Observed-species和PD-whole-tree在鸭疫里默氏菌感染后0~5 d逐渐降低,从5~14 d又逐渐增加,尤其在鸭疫里默氏菌感染后3和5 d均显著低于未感染组（P<0.05）。Beta多样性分析表明,未感染组与6个时间点的感染组间菌群差异均显著（P<0.05）,其中,未感染组与感染后3 d的物种差异最大,之后依次为感染后2、5、9、1和14 d。物种丰度聚类热图显示,在未感染组和不同时间感染组,物种丰度相对较高的微生物菌属均不同。在门水平,鸭疫里默氏菌感染组主要以厚壁菌门（Firmicutes）、unidentified-Bacteria、拟杆菌门（Bacteroidetes）、梭杆菌门（Fusobacteria）及变形菌门（Proteobacteria）为主;在属水平,Bacteroides在感染组和未感染组均为优势菌属,感染组中弯曲杆菌属（Campylobacter）和梭杆菌属（Fusobacterium）明显增加。本试验分析了鸭疫里默氏菌未感染组和感染不同时间组肠道菌群的差异,寻找到一些特征菌属,可为鸭疫里默氏菌的致病性研究提供理论依据。     

丁酸梭菌后期干预对番鸭回肠和盲肠菌群结构的影响

本试验旨在通过16S r RNA基因测序技术研究饲料中添加丁酸梭菌对番鸭后期回肠和盲肠菌群结构的影响。试验选取49日龄番鸭360羽,随机分为两个组,每组9个重复,每个重复20羽。对照组饲喂基础饲粮（C组）,试验组饲喂基础饲粮添加2×109CFU/kg丁酸梭菌（CB组）,试验期为21 d。试验结束后,每个重复随机取1羽番鸭进行屠宰并测定腹脂、胸肌、腿肌重量,采集回肠和盲肠内容物,采用16S rRNA基因测序技术分析其菌群结构。结果表明：与C组相比,CB组番鸭的体重无显著变化（P> 0.05）,腹脂率与C组相比显著上升19.5%(P <0.05)。16S rRNA基因测序结果表明,α多样性中各组差异并不显著。在门水平上,厚壁菌门（Firmicutes）、梭杆菌门（Fusobacteria）、拟杆菌门（Bacteroidetes）、变形菌门（Proteobacteria）、放线菌门（Actinobacteria）为番鸭回肠和盲肠的优势菌门;与C组相比,CB组回肠中厚壁菌门、梭杆菌门相对丰度增加,而拟杆菌门相对丰度减少;此外,在盲肠中变形菌门丰度有减少的趋势。在属水平上,回肠优势属...     

猪不同发育阶段肠道微生物菌群特征分析

为研究不同生长发育阶段猪肠道微生物菌群结构与特征的差异,本研究将50头28日龄体重8 kg左右的杜×长×大断奶仔猪随机分为5栏,分别在第60、90、120、150、180日龄饲喂前,从每栏随机挑选5头猪,每头采取100 g左右的新鲜粪样,采用16S rRNA高通量测序技术对微生物多样性进行研究。结果显示:通过菌群分类学分析发现,不同时期猪肠道微生物分布于22个门、42个纲、74个目、119个科、321个属和579个种,厚壁菌门(Firmicutes)、拟杆菌门(Bacteroides)、螺旋体门(Spirochaetae)为主要优势菌门,不同时期的特异菌群显著差异;对丰度值前30的肠道菌群与血液免疫抗体浓度进行相关性关联分析发现,IL-2浓度与12个菌群存在显著相关性,IL-6浓度与14个菌群存在显著相关性,IgG浓度与12个菌群存在显著相关性,IgM浓度与11个菌群存在显著相关性,IgA浓度与26个菌群存在显著相关性。综上表明,猪肠道微生物菌群结构与组成在不同生长发育阶段均存在显著差异,对猪免疫性能具有重要作用。     

16S rRNA基因测序分析犬骨癌的癌内菌群特征

本研究旨在分析患骨癌犬的癌组织的菌群特征及其与癌旁组织菌群的构成差异,进而探究癌内菌群对犬骨癌发生发展的影响。提取癌组织与癌旁组织菌群的基因组总DNA,进行高通量测序,结合数据分析两者的菌群特征,并利用Tax4Fun对其菌群进行功能预测。结果发现,2组菌群的丰富度指数(Ace、Chao1)和多样性指数(Shannon、Simpson)无显著性差异(P>0.05)。相对丰度方面,2组样本在门水平的菌群主要是变形菌门、拟杆菌门和厚壁菌门,其中癌组织的拟杆菌门(t=0.114,P=0.039)、广古菌门(t=0.067,P=0.017)、脱硫菌门(t=0.019,P=0.002)以及螺旋菌门(t=0.021,P=0.072)显著高于癌旁组织;在属水平上主要由绿脓杆菌属、乳杆菌和链球菌属等组成,其中癌组织的甲烷杆菌属(t=0.495,P=0.02)、互营杆菌属(t=0.495,P=0.004)以及Sarcina属(t=0.436,P=0.011)显著高于癌旁组织,且癌旁组织中不含有Sarcina属。PCoA图提示2组肠道菌群有显著性差异;LDA差异贡献分析发现2组之间共有27个物种存在显...     

以16S rRNA为基础的检测技术在肠道菌群研究中的应用

肠道微生态菌群是一个非常复杂的微生态系统。胃肠菌群对于宿主的健康和生产成绩非常重要。依赖于以细菌分离培养为主的传统分析方法已经远远不能适应深入研究的需要。近些年围绕16S rRNA发展起来的分子方法在肠道微生态菌群研究中的应用越来越广,本文将就这些方法的应用情况作一简述。     

多形拟杆菌对仔猪肠道菌群的影响

多形拟杆菌在健康动物和人体的粪便中数量可达3.2×109cfu/g,是绝对的优势菌,多形拟杆菌在帮助宿主吸收多糖以及提高营养利用率、调控脂肪积累、加快肠道黏膜的血管形成和提高宿主的免疫力、维持肠道微生态平衡等方面均有着非常重要的作用。本实验从健康的猪肠道中分离多形拟杆菌,采用了生理生化实验进行鉴定。本文通过研究多形拟杆菌对仔猪肠道菌群的影响,对提升猪肉品质,增加猪肉瘦肉率和预防仔猪腹泻,维持仔猪肠道微生物态平衡有很大的借鉴意义。     

Analysis of Microbiota Structure and Bacteroides Distribution in Different Intestinal Segments in Duck

This study aimed to analyze the microbiota composition and diversity and the distribution of Bacteroides in duodenal, jejunal, ileal and caecal contents in healthy ducks. The contents of duodenum, jejunum, ileum and cecum were collected aseptically from 20 healthy adult Gaoyou ducks (70-day-old, half male and female), and the bacterial DNA of intestinal contents were extracted. The IonS5TMXL platform was used for 16S rRNA high-throughput sequencing, the microbiota structure and abundance, as well as the distribution of Bacteroides were analyzed. The results showed that the microbiota abundance in duodenal and jejunal contents was significantly higher than that in ileal and caecal contents (P<0.05), the microbiota diversity in ileal contents was the lowest. The microbiota structure in duodenal and jejunal contents was similar, they were different from that in ileum, and especially cecum. The dominant phyla in the intestinal contents of healthy duck were Bacteroidetes, Firmicutes, Proteobacteria and Fusobacteria. The relative abundance of these phyla were different in different intestinal segment contents. The different microbial species were colonized in different intestinal segments, and the differential phyla in duodenum, jejunum, ileum and cecum were Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, respectively. There were 28 kinds of Bacteroides species in duck intestine, among them, B. acidifaciens, B. barnesiae, B. caccae, B. caecicola, B. coprocola, B. sp and B. luti were significantly clustered in the cecum, and B. caecigallinarum, B. plebeius and B. barnesiae were dominantly colonized in duck cecum. The results indicate that intestinal space significantly affects the microbiota abundance and diversity, and different intestinal segments were colonized by differential microorganism, which is consistent with the intestinal segment niche and function. In the cecum, the dominant colonization of Bacteroides may be related to its physiological and biochemical functions.     

诱导冬眠期间野生达乌尔黄鼠肠道菌群结构和功能适应变化

本试验对野生达乌尔黄鼠诱导冬眠期间肠道菌群的结构和功能变化进行了研究,旨在探究诱导冬眠期间野生达乌尔黄鼠肠道菌群如何发挥其功能以帮助机体维持正常的生理功能,为今后进一步研究其作用机制提供依据.适应性喂养14 d后,将8只野生达乌尔黄鼠随机分为2组,对照组饲养于室温,诱导冬眠组饲养于4℃无光照环境,2组均饲喂标准鼠饲粮,...     

Factors Influencing Equine Gut Microbiota: Current Knowledge

Gastrointestinal microbiota play a crucial role in nutrient digestion, maintaining animal health and welfare. Various factors may affect microbial balance often leading to disturbances that may result in debilitating conditions such as colic and laminitis. The invention of next-generation sequencing technologies and bioinformatics has provided valuable information on the effects of factors influencing equine gut microbiota. Among those factors are nutrition and management (e.g., diet, supplements, exercise), medical substances (e.g., antimicrobials, anthelmintics, anesthetics), animal-related factors (breed and age), various pathological conditions (colitis, diarrhea, colic, laminitis, equine gastric ulcer syndrome), as well as stress-related factors (transportation and weaning). The aim of this review is to assimilate current knowledge on equine microbiome studies, focusing on the effect of factors influencing equine gastrointestinal microbiota. Decrease in microbial diversity and richness leading to decrease in stability; decrease in Lachnospiraceae and Ruminococcaceae family members, which contribute to gut homeostasis; increase in Lactobacillus and Streptococcus; decrease in lactic acid utilizing bacteria; decrease in butyrate-producing bacteria that have anti-inflammatory properties may all be considered as a negative change in equine gut microbiota. Shifts in Firmicutes and Bacteroidetes have often been observed in the literature in response to certain treatments or when describing healthy and unhealthy animals; however, these shifts are inconsistent. It is time to move forward and use the knowledge now acquired to start manipulating the microbiota of horses.     

育肥猪粪便菌群结构及其与生长速度的相关性分析

【目的】 研究育肥猪的生长速度与粪便微生物之间的作用关系,寻找与猪生长速度相关的微生物菌群。【方法】 选取50头出生重相近的仔猪,在相同饲养环境中进行饲养管理,生病猪及时转出试验组,125日龄时按体重由高到低排序,把体重最高和最低的4头猪分别分为体重高（51.30 kg±2.57 kg,HW）、低（36.90 kg±2.50 kg,LW）组,通过16S rRNA测序,对125日龄生长育肥猪的粪便微生物区系多样性、群落组成及与生长速度的关联性进行分析。【结果】 Alpha多样性分析显示,两组间均无显著差异（P>0.05）。主成分分析结果显示,HW和LW组中能够明显区分菌群结构。粪便微生物结构组成分析表明,HW和LW组的优势菌门均为厚壁菌门、拟杆菌门和螺旋体门,优势菌属为密螺旋体属、乳杆菌属、链球菌属和未被培养菌属Muribaculaceae菌。LW组中拟杆菌门丰度极显著高于HW组（P<0.01）,纤维杆菌门丰度显著高于HW组（P<0.05）,而髌骨细菌门丰度显著低于HW组（P<0.05）。对粪便微生物结构组成进行差异分析发现,HW组检测到16个特有菌门,LW组检测到1个特有菌门和24个特有菌属。将肠道菌群与生长速度进行相关性分析,共发现10个菌门,18个属与体重（BW）和平均日增重（ADG）呈正相关,7个菌门和12个属与BW和ADG呈负相关。【结论】 相同日龄不同生长速度的猪粪便微生物的区系结构存在显著差异,差异菌群可能对猪的生长速度起到了一定的调控作用,本研究结果为研发益生菌和提高猪生长速度提供了参考依据。     

腹泻犊牛与健康犊牛粪便菌群结构组成与功能研究

本研究旨在探究腹泻与健康犊牛粪便微生物的结构组成与分布特征,筛选出一些可作为评价犊牛腹泻参考指标的特异性菌群。试验采集10份腹泻和10份健康夏南牛犊牛的粪便样本并提取粪便总DNA,运用16S rRNA高通量测序技术,比较腹泻组和健康组在微生物多样性方面（组成及结构）存在的差异,获得两组间具有统计学差异的Biomarker,并对差异功能基因进行注释。结果表明,腹泻犊牛粪便微生物的多样性小于健康犊牛;在门水平上,与健康组相比,腹泻组犊牛粪便中微生物相对丰度显著升高的是变形菌门和梭杆菌门,螺旋菌门显著降低（P<0.05）;在属水平上,与健康组相比,腹泻组犊牛粪便微生物中埃希氏-志贺菌属、梭杆菌属、乳杆菌属和梭状芽孢杆菌属相对丰度明显升高,不可培养拟杆菌目S24-7群、拟普雷沃菌属和普雷沃氏菌科的菌属显著降低（P<0.05）。通过对COG功能预测分析,腹泻组在翻译、核糖体结构和起源类群明显降低。通过KEGG代谢途径分析,腹泻组粪便中显著升高的代谢通路是碳水化合物代谢和外源性物质降解和代谢,显著降低的代谢通路分别是细胞增殖和死亡、复制和修复、翻译和转录（P<0.05）。本研究分析了腹泻组和健康组之间的优势菌群,筛选出可以作为犊牛腹泻参考指标的10个Biomarker,并对功能差异基因进行注释,为进一步研究犊牛腹泻的治疗及预防奠定了基础。     

Isolation,Identification, 16S rRNA Gene Sequencing and Genetic Evolution Analysis of Aeromonas aeruginosa from Duck

【Objective】 The experiment was aimed to study the pathogenic bacteria of acute death of ducklings in a duck farm in Henan province and its phylogenetic status.【Method】 The liver and spleen of dead ducks in the diseased duck farm were collected.The bacterial morphology, Gram-staining, biochemical characteristics, sequence analysis of 16S rRNA gene, drug sensitivity test and pathogenicity test were carried out.【Results】 The isolated bacteria grew on blood agar medium with smooth, convex, milky white and α-hemolytic Gram-positive cocci.Biochemical test results showed that the isolated bacteria were positive for maltose, sucrose, raffinose, nitrate reduction reaction, MP-VP test, urea, lysine decarboxylase, ornithine decarboxylase and aescin, and negative for xylose, lactose, glucose, sorbitol, hydrogen sulfide, citrate, peptone, mannitol, phenylalanine and methyl red.The results of 16S rRNA gene sequencing and BLAST comparison results showed that the 16S rRNA gene sequence of the isolated strain was 94.8%-99.9% similar to that of Aerococcus viridans published on NCBI, and the similarity with strains Mnlv1, Mnlv2 and W66 was the highest, up to 99.9%.The similarity with strain GXBl-1 was the lowest, which was 94.8%.Phylogenetic tree analysis showed that the isolated bacteria belonged to the same genus and group on the same branch as strains of Aerococcus viridans FL09, 15MS and Mnlv2 etc., and had the closest genetic relationship with FL09.The results of drug sensitivity showed that the isolated strain was sensitive to fosfomycin, ampicillin and amoxicillin, moderately sensitive to penicillin, neomycin and amikacin, it was resistant to rifampicin, neomycin, bacitracin, erythromycin and enrofloxacin.The results of pathogenicity test showed that the strain was lethal and increased with the increase of inoculation concentration.【Conclusion】 This study determined that the pathogen causing the acute death of ducklings in a duck farm in Henan province was Aerococcus viridans, which provided a reference basis for clinical diagnosis and treatment of the diseases caused by this bacteria.     

牦牛胃肠道微生物影响因素的研究进展

胃肠道是牦牛重要的消化吸收器官,瘤胃和肠道中的微生物对牦牛的健康生长和繁殖发育具有重要作用。目前,大多基于高通量测序技术分析牦牛胃肠道微生物群落的组成、分布、多样性和功能预测等。本文综述了国内外有关牦牛胃肠道微生物的研究性论文,阐述了不同饲粮、年龄、海拔等对牦牛胃肠道微生物的影响,以期为牦牛的生产养殖提供理论依据。