不同性别和生长阶段对克氏原螯虾肠道菌群多样性的影响

为研究性别和生长阶段对克氏原螯虾(Procambarus clarkii)肠道菌群的影响, 实验对来自虾塘的雌雄成虾肠道样品及来自实验室养殖的幼虾和成虾的肠道样品进行了16S rRNA高通量测序分析。结果表明, 不同性别间克氏原螯虾肠道菌群的多样性和功能均没有显著性差异(独立样本t检验: P>0.05), 其优势菌群在门水平上均包括厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)和拟杆菌门(Bacteroidetes)等; 属水平上包括拟杆菌属(Bacteroidia)、希瓦氏菌属(Shewanella)、梭菌属(Clostridium)和柠檬酸杆菌属(Citrobacter)等; 但各优势菌群在个体间的丰度差异较大, 且在成虾阶段趋于保守, 属肠道常驻菌群。幼虾肠道菌群的Alpha多样性显著高于成虾(独立样本t检验: P<0.05)。在门水平上, 优势菌群较为一致, 包括变形菌门、拟杆菌门、厚壁菌门和放线菌门(Actinobacteria)。成虾厚壁菌门与拟杆菌门的比例高于幼虾, 表明成虾分解食物和吸收营养的潜力更强。在属水平上, 成虾和幼虾肠道中均存在大量的黄杆菌属(Flavobacterium)、拟杆菌属和氢噬胞菌属(Hydrogenophaga), 这些菌属可以帮助机体进行多种营养代谢, 成虾肠道中与碳水化合物代谢相关的菌群多于幼虾。PICRUSt功能预测显示, 在克氏原螯虾肠道中, 营养代谢功能相关的菌群相对丰度最高, 而成虾肠道菌群代谢碳水化合物的功能显著高于幼虾。实验表明, 在野外虾塘养殖下的克氏原螯虾的肠道菌群不论是在群落多样性、物种丰度还是菌群功能预测上, 都未体现出性别间的差异, 且肠道菌群的个体差异较大; 但在不同生长阶段间, 克氏原螯虾肠道微生物的群落多样性、丰度及功能都有显著差异, 相比于幼虾, 成虾肠道菌群多样性降低, 多种代谢功能升高。     

高通量测序分析小头裸裂尻鱼皮肤和肠道的微生物多样性

【目的】解析小头裸裂尻鱼不同部位的微生物群落结构、物种组成、多样性特征以及菌群功能差异。【方法】通过Illumina MiSeq扩增子高通量测序,分析小头裸裂尻鱼皮肤黏膜、肠道黏膜和肠道内容物3个部位微生物菌群组成差异,并通过Tax4Fun预测菌群潜在功能。【结果】皮肤黏膜微生物α多样性最高,其Shannon指数显著高于肠道黏膜(P<0.05)和肠道内容物(P<0.001)。主坐标分析表明,皮肤黏膜微生物显著区别于其他2个部位。在门水平小头裸裂尻鱼3个部位相对丰度前五的微生物类群均为放线菌门(Actinobacteria)、变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、绿弯菌门(Chloroflexi)和蓝藻门(Cyanobacteria),其中肠道内容物中放线菌门相对丰度(46.53%)显著高于肠道黏膜(29.23%,P<0.05)和皮肤黏膜(25.83%,P<0.01);肠道黏膜中变形菌门的相对丰度(40.33%)显著高于肠道内容物(26.10%,P<0.05)。对各部位相对丰度前10的菌群进行分析发现,小头裸裂尻鱼皮肤黏...     

室内饲养对高原鼠兔肠道微生物群落构建过程的影响

群落生态构建过程是近年来微生物群落生态学的研究热点。室内饲养可引起肠道菌群的剧烈变化,这种改变是否会影响群落的构建过程,一直未见报道。本文以高原鼠兔 (Ochotona curzoniae) 为对象,采用16S rRNA测序技术,探讨室内饲养和野生高原鼠兔肠道微生物群落在结构、功能以及群落构建过程等方面的差异。结果表明,在繁殖季节,室内饲养组的群落多样性指数和均匀度指数均显著低于野外组;群落丰度指数和群落覆盖度指数在非繁殖季节显著高于繁殖季节。拟杆菌门 (Bacteroidetes) 在室内饲养组显著富集,而厚壁菌门 (Firmicute) 和浮霉菌门 (Planctomycetes) 在野外组显著富集;在野外组,Epsilonbacteraeota和软壁菌门 (Tenericutes) 在繁殖季节显著富集。菌群功能分析显示,室内饲养组与野生组在细胞通讯和心血管疾病通路存在显著差异;野外组繁殖季节与非繁殖季节肠道菌群功能在氨基酸代谢、碳水化合物代谢和脂质代谢等通路存在显著差异。中性模型拟合结果表明,室内饲养明显降低了菌群构建的随机过程。野外组生理状态也会降低菌群构建的随机性。本研究证明室内饲养和宿主生理状态均会对高原鼠兔肠道菌群组成及群落构建产生影响,此结果为实现高原鼠兔室内繁殖提供了新的理论基础。     

利福平对红裸须摇蚊幼虫肠道微生物群落结构及功能的潜在影响北大核心

【目的】摇蚊是水生生态系统中重要的昆虫种类之一,其肠道微生物与个体生长发育、环境适应等过程密切相关,本研究旨在探究抗生素处理对摇蚊幼虫肠道微生物群落结构及功能的潜在影响。【方法】利用16S rRNA基因扩增子测序技术对利福平处理的红裸须摇蚊(Propsilocerus akamusi)幼虫肠道内容物中的菌群进行分析和比较,应用Tax4Fun法对其肠道菌群功能进行预测。【结果】利福平处理能够改变红裸须摇蚊幼虫肠道群落结构和多样性,宿主肠道菌群中拟杆菌门(Bacteroidota)(P<0.05)以及脱铁杆菌门(Deferribacterota)(P<0.001)的相对丰度显著上升,而变形菌门(Proteobacteria)与厚壁菌门(Firmicutes)相对丰度有所下降。在属水平上,利福平处理使耶尔森菌属(Yersinia)、假单胞菌属(Pseudomonas)、脱硫弧菌属(Desulfovibrio)的相对丰度有所降低,其中脱硫弧菌属(Desulfovibrio)显著降低。与此同时,共线性网络分析表明利福平处理后细菌群落稳定性大幅下降,菌种之间关联性显著减弱。通过京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)通路注释预测出红裸须摇蚊幼虫肠道菌群基因与基因信息处理、新陈代谢、人类疾病等功能相关,利福平处理可以使肠道菌群基因的抗药性功能显著上升,而内分泌和代谢疾病功能显著下降。【结论】研究结果揭示了抗生素利福平对红裸须摇蚊幼虫肠道细菌群落结构及功能的潜在影响,为进一步探索摇蚊肠道菌群发挥的必要作用奠定理论基础。     

乌鲁木齐市3~5岁儿童口腔微生物与肠道微生物的构成差异

目的探索乌鲁木齐市3～5岁儿童口腔微生物与肠道微生物的菌群构成及多样性等差异。方法从本团队前期流行病学调查的乌鲁木齐市3～5岁儿童中,按调查时间顺序随机抽取12名儿童。分别收集唾液及粪便样本共计24份,分为口腔微生物组和肠道微生物组。利用16S V3-V4区设计引物来进行PCR扩增,使用MiSeq测序仪进行二代测序,比较两组的微生物构成及多样性差异。结果门水平上:放线菌门(t=5.98,P0.001)、变形菌门(z=20.0,P=0.005)、TM7(z=78.0,P0.001)在口腔中丰度较高;厚壁菌门(z=134.0,P0.001)在肠道中丰度较高。厚壁菌门/拟杆菌门的值在肠道中较大(z=113.0,P=0.017)。属水平上:罗斯菌属、普雷沃菌属、链球菌属为口腔中丰度较高的菌属;粪杆菌属、Ruminococcaceae、拟杆菌属为肠道中丰度较高的菌属(P0.001)。奈瑟菌属、卟啉单胞菌属等仅存在于口腔中。Catenibacterium、肠杆菌属等仅存在于肠道中。菌群功能显示:在细胞运动(z=136.0,P0.001)、碳水化合物代谢(t=-4.71,P0.001)等方面表现出肠道组占优势;在遗传信息的翻译(t=8.17,P0.001)、神经退行性疾病(z=78.0,P0.001)等方面表现出口腔组占优势。结论放线菌门、变形菌门、TM7在口腔中丰度较高;厚壁菌门在肠道中丰度较高。口腔和肠道微生物在菌群功能上差异较大。奈瑟菌属、卟啉单胞菌属、Catenibacterium等可能为某些全身系统性疾病的标志性菌属。     

基于16S rRNA基因高通量测序的 太原地区健康成年人肠道菌群结构分析

目的探讨太原地区健康成年人的肠道菌群结构及多样性。方法采集太原地区20份健康成年人的粪便样本,提取DNA、构建菌群16S rRNA基因克隆文库、高通量测序并进行生物信息学分析。结果测序获得优质序列1 383 680条,平均序列为69 184条±551条,归类于455个OTUs;所有样本共含有10个菌门,101个菌属,141种菌;其中核心菌门3个,依次为拟杆菌门(63.13%)、厚壁菌门(31.14%)和变形菌门(5.10%),占所有样本微生物总量的99.37%;丰度最高的前10个菌属依次为拟杆菌属(43.34%)、普氏菌属(15.51%)、栖粪杆菌属(4.92%)、罗氏菌属(4.73%)、毛螺菌属(3.27%)、萨特菌属(2.50%)、粪球菌属(2.38%)、布劳特菌属(2.31%)、瘤胃球菌属(2.18%)和副杆状菌属(1.61%),占样本微生物总量的82.75%,未分类的菌属占6.84%。结论健康成年人肠道微生物群落复杂,但主要菌群相对稳定,为进一步研究人体肠道菌群结构与功能提供了参考依据。     

三种跳虫肠道菌群的多样性分析及功能预测

【目的】跳虫在土壤生态系统中发挥着重要的作用。本研究旨在调查Sinella(Coecobrya)oligoseta,Proisotoma minuta和Tomocerus missus 3种跳虫肠道菌群的结构和多样性以及潜在功能。【方法】采用16S rDNA扩增子测序法对以上3种跳虫成虫肠道内容物中的菌群进行分析和比较;应用Tax4Fun法对其肠道菌群基因进行功能预测。【结果】3种跳虫中成虫肠道菌群多样性最高的是T.missus,最低的是S.(C.)oligoseta。在门水平上3种跳虫成虫肠道中最主要的菌群均为变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes),放线菌门(Actinobacteria)也具有较高的丰度;在属水平上S.(C.)oligoseta肠道中假单胞菌属Pseudomonas的丰度(16.21%)明显高于P.minuta和T.missus肠道中的丰度(分别为0.87%和1.37%);P.minuta肠道中弧菌属Vibrio的丰度(25.81%)明显高于S.(C.)oligoseta和T.missus肠道中的丰度(分别为3.35%和0.004%)。另外,KEGG pathway注释预测出3种跳虫成虫肠道菌群基因功能涉及碳水化合物和氨基酸代谢、传染性疾病和耐药性。【结论】S.(C.)oligoseta,P.minuta和T.missus这3种跳虫肠道菌群在门水平上的核心菌群相同,而在属水平上的优势菌属丰度存在较大差异,其影响因素应该包括物种自身遗传特点及栖息地环境中微生物种类和数量的不同。在这3种跳虫肠道内发现放线菌,有利于新型放线菌的开发及其代谢产物的利用,并且它们的肠道内很可能存在耐药性和致病性菌株,这为跳虫肠道菌群的功能研究指引了新方向。     

饥饿及恢复喂食对日本医蛭肠道菌群多样性的影响

为了研究饥饿及恢复喂食对日本医蛭肠道微生物菌群的影响, 采用高通量测序技术分析了正常组、饥饿30d、恢复喂食7d以及恢复喂食14d的日本医蛭肠道微生物菌群特征及多样性的变化。结果显示: 日本医蛭核心菌群门水平上, 主要集中于变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes), 属水平核心菌群有气单胞菌属(Aeromonas)、Mucinivorans属、拟杆菌属(Bacteroides)、丹毒丝菌属(Erysipelothrix)等。饥饿及恢复摄食, 对气单胞菌属、Mucinivorans属在内的核心菌群多样性及丰度产生了一定的影响。本研究为揭示日本医蛭肠道菌群组成以及研究日本医蛭消化道微生物功能奠定了基础。     

不同养殖场林麝肠道微生物组成和功能的差异

肠道疾病是养殖林麝(Moschus berezovskii)常见疾病。动物肠道微生物伴随宿主进化并与胃肠道构成了复杂的微生态系统。为探究不同饲养环境对圈养林麝肠道微生物组成和功能的影响,本研究对采自国内5个不同养殖场的215份粪便样品进行了16S rRNA基因高通量测序,对比分析不同养殖场林麝肠道微生物组成、多样性和功能的差异。结果显示,厚壁菌门和拟杆菌门是未喂食复合益生菌的祁连县养殖场林麝肠道菌群的绝对优势菌门,而喂食复合益生菌的甘肃两当县和陕西凤县的4家养殖场林麝肠道菌群的绝对优势菌门为厚壁菌门和变形菌门。不同养殖场林麝肠道菌群组成、优势菌门、优势菌属、潜在致病菌、代谢及疾病相关功能均有显著差异。祁连县养殖场林麝肠道微生物的α多样性和疾病相关功能表达量显著低于其他养殖场,并以肠型2为主,其主导菌为厚壁菌门、UCG-005和拟杆菌属;两当县和凤县的4家养殖场林麝肠道菌群潜在致病菌相对丰度较低。本研究推测食物组成差异可能是导致不同养殖场林麝肠道微生物差异的主要因素,复合益生菌的使用可能是导致α多样性和潜在致病菌下降的重要因素。该结果可为林麝的人工养殖和有效管理提供科学依据,也对人工饲养...     

峨眉山藏酋猴mtDNA控制区序列变异及种群遗传多样性

为更有效地保护藏酋猴Macaca thibetana野生种群,本文测定了来自峨眉山藏酋猴8个亚群体的47个样品mtDNA控制区5'端505 bp的序列,发现了27个变异位点(5.74%),定义了4种单倍型,其单倍型多样性(h)为0.236±0.079、核苷酸多样性(π)为0.00902±0.00354,单倍型之间的序列差异平均为0.623%,平均核苷酸差异(K)为4.274,单倍型序列之间变异较大,种群中的核苷酸多样性较高;将峨眉山的藏酋猴看成一个种群与同为四川地区的马边群体及安徽的黄山群体的相应序列进行比较,结果显示峨眉山藏酋猴种群mtDNA控制区序列与马边群体间的差异性较小,而与黄山群体间的差异性较大。分子方差分析(AMOVA)表明,90.04%的遗传变异发生在种群之间,仅有9.96%的变异发生在种群内。进一步分析表明,藏酋猴各地理种群间均不同程度地存在着一定的遗传分化(Fst=0.9004,P<0.05),种群间基因交流较贫乏(Nm<1)。基于最大似然法和邻接法构建的系统发生树均支持四川地区的藏酋猴种群和安徽黄山种群分别聚为不同的类群,支持将它们归入各自的管理单元;而本研究中的四川地区藏酋猴在系统发生树上也分为2个亚支,但这2个亚支并未与地理分布成完全的对应关系,应归为一个管理单元加以保护。     

Effects of diet,habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis)

The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6–5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome composition. Additionally, we examined the influence of habitat types (forest versus savanna) and diet types (crop‐raiding versus noncrop‐raiding) on the microbiome within L. africana. We found 58 bacterial orders, representing 16 phyla, across all African elephant samples. The most common phyla were Firmicutes, Proteobacteria, and Bacteroidetes. The microbiome of L. africana was dominated by Firmicutes, similar to other hindgut fermenters, while the microbiome of L. cyclotis was dominated by Proteobacteria, similar to more frugivorous species. Alpha diversity did not differ across species, habitat type, or diet, but beta diversity indicated that microbial communities differed significantly among species, diet types, and habitat types. Based on predicted KEGG metabolic pathways, we also found significant differences between species, but not habitat or diet, in amino acid metabolism, energy metabolism, and metabolism of terpenoids and polyketides. Understanding the digestive capabilities of these elephant species could aid in their captive management and ultimately their conservation.     

Human gut microbiota and bifidobacteria: from composition to functionality

The human gut is the home of an estimated 10(18) bacterial cells, many of which are uncharacterized or unculturable. Novel culture-independent approaches have revealed that the majority of the human gut microbiota consists of members of the phyla Bacteroidetes and Firmicutes. Nevertheless the role of bifidobacteria in gut ecology illustrates the importance of Actinomycetes and other Actinobacteria that may be underestimated. The human gut microbiota represents an extremely complex microbial community the collective genome of which, the microbiome, encodes functions that are believed to have a significant impact on human physiology. The microbiome is assumed to significantly enhance the metabolism of amino and glycan acids, the turnover of xenobiotics, methanogenesis and the biosynthesis of vitamins. Co-colonisation of the gut commensals Bifidobacterium longum and Bacteroides thetaiotaomicron in a murine model system revealed that the presence of bifidobacteria induced an expansion in the diversity of polysaccharides targeted for degradation by Bacteroides and also induced host genes involved in innate immunity. In addition, comparative analysis of individual human gut microbiomes has revealed various strategies that the microbiota use to adapt to the intestinal environment while also pointing to the existence of a distinct infant and adult-type microbiota.     

转基因鲤鱼与对照鲤肠道微生物群落差异研究

以转“全鱼”生长激素基因鲤(Cyprinus carpio L.)和野生对照鲤为对象, 采用454高通量测序技术对其肠道微生物16S rRNA基因进行测序并分析了3个不同发育阶段微生物群落结构的变化, 进而探讨了转基因鲤与对照鲤肠道微生物群落的差异。基于转基因鲤和对照鲤不同发育时期(6日龄、2月龄、5月龄)肠道微生物群落组成的DCA排序分析显示, 2月龄转基因鲤与对照鲤肠道微生物组成不同。Alpha多样性及均匀度都显示转基因鲤肠道微生物多样性高于对照鲤。从门水平的比较分析发现, 转基因鲤肠道中存在较多的厚壁菌门(Firmicutes)细菌, 而对照鲤中拟杆菌门(Bacteroidetes)细菌较多, 其中2月龄转基因鲤肠道内Bacteroidetes/Firmicutes比值低于对照鲤。研究结果表明, 在所分析的3个发育时期, 转基因鲤的肠道微生物组成与对照鲤相比发生了改变, 且在2月龄时存在差异。该研究为进一步揭示转基因鱼肠道微生物与宿主的相互影响和作用机制提供了很好的参考。     

Metagenome plasticity of the bovine abomasal microbiota in immune animals in response to Ostertagia ostertagi infection

Infections in cattle by the abomasal nematode Ostertagia ostertagi result in impaired gastrointestinal function. Six partially immune animals were developed using multiple drug-attenuated infections, and these animals displayed reduced worm burdens and a slightly elevated abomasal pH upon reinfection. In this study, we characterized the abomasal microbiota in response to reinfection using metagenomic tools. Compared to uninfected controls, infection did not induce a significant change in the microbial community composition in immune animals. 16S rRNA gene-based phylogenetic analysis identified 15 phyla in the bovine abomasal microbiota with Bacteroidetes (60.5%), Firmicutes (27.1%), Proteobacteria (7.2%), Spirochates (2.9%), and Fibrobacteres (1.5%) being the most predominant. The number of prokaryotic genera and operational taxonomic units (OTU) identified in the abomasal microbial community was 70.8±19.8 (mean ± SD) and 90.3±2.9, respectively. However, the core microbiome comprised of 32 genera and 72 OTU. Infection seemingly had a minimal impact on the abomasal microbial diversity at a genus level in immune animals. Proteins predicted from whole genome shotgun (WGS) DNA sequences were assigned to 5,408 Pfam and 3,381 COG families, demonstrating dazzling arrays of functional diversity in bovine abomasal microbial communities. However, none of COG functional classes were significantly impacted by infection. Our results demonstrate that immune animals may develop abilities to maintain proper stability of their abomasal microbial ecosystem. A minimal disruption in the bovine abomasal microbiota by reinfection may contribute equally to the restoration of gastric function in immune animals.     

基于高通量测序技术研究水貂远端肠道细菌群落组成

【目的】研究水貂远端肠道微生物群落组成及其多样性。【方法】通过高通量测序技术研究水貂远端肠内容物细菌的组成和多样性。【结果】从10只健康水貂远端肠道内容物样品中得到146 287高质量序列代表17个菌门、167个细菌属。水貂肠道细菌以厚壁菌门(59.99%)、拟杆菌门(16.2%)、梭杆菌门(11.5%)、放线菌门(5.9%)和变形菌门(5.3%)为主,其中厚壁菌门最为丰富。厚壁菌门中的梭菌目是最丰富的目,而梭菌目中的链球菌占有50%以上的OTUs,是最大的细菌属。【结论】水貂肠道内存在复杂的微生物区系,这对进一步研究水貂对营养物质吸收利用提供了理论基础。     

Characterization of the gut microbiota in early life stages of pikeperch Sander lucioperca

This study characterized the gastrointestinal microbiome of nine juvenile farmed pikeperch Sander lucioperca using a metagenomics approach based on bacterial 16S rRNA gene sequencing. Potential changes in the gut microbiota during 2 months of S. lucioperca juvenile life were investigated. Results revealed that gut microbiota was dominated by Proteobacteria (95–92%), while other phyla Firmicutes (1–1·5%) and Actinobacteria (0·9–1·5%) were less abundant. At the family level, fish‐gut microbiota were dominated by Enterobacteriaceae, which constituted c. 83% of all DNA sequence reads. Such a situation was present in all of the examined fish except one, which showed a different proportion of particular microbial taxa than the other fish. In this fish, a higher relative abundance (%) of Fusobacteria (21·0%), Bacteroidetes (9·5%) and Firmicutes (7·5%) was observed. There were no significant differences in the gut microbiome structure at different stages of development in the examined fish. This may indicate that Proteobacteria inhabiting the gut microbiota at an early stage of life are a necessary component of the pikeperch microbiome that may support proper nutrition of the fish. The information obtained on the gut microbiome could be useful in determining juvenile S. lucioperca health and improving rearing conditions by welfare monitoring in aquaculture.     

Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers

Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens.     

Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene

The intestinal tract houses one of the richest and most complex microbial populations on the planet, and plays a critical role in health and a wide range of diseases. Limited studies using new sequencing technologies in horses are available. The objective of this study was to characterize the fecal microbiome of healthy horses and to compare the fecal microbiome of healthy horses to that of horses with undifferentiated colitis. A total of 195,748 sequences obtained from 6 healthy horses and 10 horses affected by undifferentiated colitis were analyzed. Firmicutes predominated (68%) among healthy horses followed by Bacteroidetes (14%) and Proteobacteria (10%). In contrast, Bacteroidetes (40%) was the most abundant phylum among horses with colitis, followed by Firmicutes (30%) and Proteobacteria (18%). Healthy horses had a significantly higher relative abundance of Actinobacteria and Spirochaetes while horses with colitis had significantly more Fusobacteria. Members of the Clostridia class were more abundant in healthy horses. Members of the Lachnospiraceae family were the most frequently shared among healthy individuals. The species richness reported here indicates the complexity of the equine intestinal microbiome. The predominance of Clostridia demonstrates the importance of this group of bacteria in healthy horses. The marked differences in the microbiome between healthy horses and horses with colitis indicate that colitis may be a disease of gut dysbiosis, rather than one that occurs simply through overgrowth of an individual pathogen.     

Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya

The mosquito gut represents an ecosystem that accommodates a complex, intimately associated microbiome. It is increasingly clear that the gut microbiome influences a wide variety of host traits, such as fitness and immunity. Understanding the microbial community structure and its dynamics across mosquito life is a prerequisite for comprehending the symbiotic relationship between the mosquito and its gut microbial residents. Here we characterized gut bacterial communities across larvae, pupae and adults of Anopheles gambiae reared in semi-natural habitats in Kenya by pyrosequencing bacterial 16S rRNA fragments. Immatures and adults showed distinctive gut community structures. Photosynthetic Cyanobacteria were predominant in the larval and pupal guts while Proteobacteria and Bacteroidetes dominated the adult guts, with core taxa of Enterobacteriaceae and Flavobacteriaceae. At the adult stage, diet regime (sugar meal and blood meal) significantly affects the microbial structure. Intriguingly, blood meals drastically reduced the community diversity and favored enteric bacteria. Comparative genomic analysis revealed that the enriched enteric bacteria possess large genetic redox capacity of coping with oxidative and nitrosative stresses that are associated with the catabolism of blood meal, suggesting a beneficial role in maintaining gut redox homeostasis. Interestingly, gut community structure was similar in the adult stage between the field and laboratory mosquitoes, indicating that mosquito gut is a selective eco-environment for its microbiome. This comprehensive gut metatgenomic profile suggests a concerted symbiotic genetic association between gut inhabitants and host.     

基于16S rDNA高通量测序的短尾猴口腔微生物多样性

口腔微生物群落结构是维持机体健康的重要因素,了解动物口腔微生物多样性有助于认识和理解动物的生态学适应。本研究以栖息于安徽黄山的短尾猴为研究对象,采用非损伤性取样法收集了鱼鳞坑YA1群体中19个短尾猴口腔样本,采用改进高盐提取法提取微生物DNA,利用Illumina Miseq测序平台对微生物16S rDNA V3-V4区扩增产物进行双端测序,分析微生物群落结构多样性。研究共获得206 533条优质序列,发现4 685个OTU,归属20个门、310个属。结果表明：短尾猴口腔微生物物种丰富,以变形菌门(Proteobacteria,占总条带44.58%)、厚壁菌门(Firmicutes, 30.28%)、拟杆菌门(Bacteroidetes, 12.27%)、梭杆菌门(Fusobacteria, 7.72%) 和放线菌门(Actinobacteria,3.70%)为主;24个微生物属在所有样本中均有分布,为其核心微生物属;短尾猴口腔中存在大量与口腔疾病相关的微生物和多种低丰富度的潜在病原菌。本研究为进一步研究短尾猴口腔微生物群落结构形成与适应性提供了基础资料,也提示在保护和管理野生猴群中需要应对人畜共患病传播的潜在风险。