美国鲥鱼对我国淡水生态系统的潜在入侵风险

近年来美国鲥鱼已被引入到我国的上海和广东等地进行水产养殖。本实验报道了在纯淡水人工养殖条件下美国鲥鱼的繁殖和生长情况。人工养殖鲥鱼的生长速度接近美国北卡罗莱纳州沿岸野生鲥鱼的生长速度,而高于特拉华河野生鲥鱼的生长速度;人工养殖的2龄鲥鱼既可以在养殖池中自然产卵,也可以通过注射激素人工诱导产卵,其平均受精率、孵化率和仔鱼17天内的存活率分别约15%、75%和54%。这一结果表明,尽管鲥鱼是在海水中进行繁殖的洄游性鱼类,但在生长环境适宜的淡水条件下同样可以正常生长,并达到性成熟和繁育后代,有可能在适宜的淡水水体中形成自我维持的种群。结合本实验结果和美国鲥鱼的其他生物学特性,本文认为美国鲥鱼在我国天然水体生态系统中具有潜在的入侵性。     

基于16S rRNA基因扩增子测序分析日本囊对虾肠道菌群结构与功能的特征

【背景】肠道菌群在对虾的生理活动中起关键作用。日本囊对虾是我国海水养殖虾类中的主要品种之一,迄今为止有关其肠道菌群结构与功能的研究还鲜有报道。【目的】利用高通量测序技术探究日本囊对虾肠道菌群的组成结构与功能作用,揭示虾体肠道菌群与外源菌群结构间的相关性。【方法】60 d的养殖周期结束后,分别采集日本囊对虾肠道样品(归为虾肠组,n=3)、养殖水体样品(归为水体组,n=3)和对虾饲料样品(归为饲料组,n=3),提取各样品总DNA进行16SrRNA基因扩增子测序,基于生物信息学方法分析与比较样品间的菌群结构特征,并使用PICRUSt软件预测日本囊对虾肠道菌群功能。【结果】3组样品测序共获得822 713条有效序列,抽平处理后可聚类为3 416个OTU。虾肠组样品中有28.49%、59.30%的OTU可以依次在水体组、饲料组样品中检测到。门水平上,虾肠组样品中的优势菌门为变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)和梭杆菌门(Fusobacteria)。水体组、饲料组与虾肠组样品中的优势菌门结构不尽相同,但均由变形菌门和拟杆菌门组成。属水平上,虾肠组样品中的优势菌属包括弧菌属(Vibrio)、另类弧菌属(Aliivibrio)、假交替单胞菌属(Pseudoalteromonas)、假黄棕杆菌属(Pseudofulvibacter)、科尔韦尔氏菌属(Colwellia)、小纺锤状菌属(Fusibacter)、发光杆菌属(Photobacterium)、脱硫弧菌属(Desulfovibrio)、嗜冷杆菌属(Psychrobacter)以及弓形杆菌属(Arcobacter)。水体组和饲料组中检出的核心菌属结构与虾肠组相比有明显差异,其中海命菌属(Marivita)和假单胞菌属(Pseudomonas)分别为养殖水体及对虾饲料样品中的最优势菌属。PICRUSt预测结果显示,日本囊对虾肠道菌群的基因功能主要与新陈代谢类功能有关,包含氨基酸代谢、碳水化合物代谢与能量代谢等。【结论】日本囊对虾肠道菌群与其他种类对虾肠道菌群的结构间存在共性,其形成在一定程度上受到了外源菌群的干预,并在虾体的日常代谢活动中发挥了一定的作用。     

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...     

Bacterial biota of shrimp intestine is significantly modified by the use of a probiotic mixture: a high throughput sequencing approach

The use of probiotics is a common practice of current shrimp aquaculture. Despite the immunophysiological responses that have been measured in shrimp exposed to probiotics, no information is currently available on the effect of this practice on the intestinal microbiota. The objective of this work was to evaluate the effect of a probiotic mixture on the intestinal microbiota of shrimp cultured under farm conditions. A culture-independent method based on high-throughput-sequencing (16S rRNA) was used to examine intestinal bacterial communities. A traditional system (without probiotics) was used as the reference. Targeted metagenomics analysis revealed that the probiotic mixture was based on bacteria in the phyla Proteobacteria and Firmicutes. A total of 23 species of bacteria were detected in the probiotic mixture; of these, 11 were detected in the intestine of shrimp reared in both systems, and 12 were novel for the system. Eight of the novel species were detected in shrimp cultured with the probiotic mixture; however, none of these novel species were related to marine or inclusively aquacultural environments, and only one (Bacillus subtilis) was recognized as probiotic for shrimp. The use of the probiotic mixture modified the bacterial profile of the shrimp intestine; however, most of the bacteria incorporated into the intestine were nonindigenous to the marine environment with no previous evidence of probiotic effects on any marine organism. The use of this probiotic mixture may represent a risk of causing environmental imbalances, particularly because farms using these types of probiotic mixtures discharge their effluents directly into the ocean without prior treatment.     

Comparative study on the gut microbiotas of four economically important Asian carp species

Gut microbiota of four economically important Asian carp species(silver carp, Hypophthalmichthys molitrix; bighead carp,Hypophthalmichthys nobilis; grass carp, Ctenopharyngodon idella; common carp, Cyprinus carpio) were compared using 16 S rRNA gene pyrosequencing. Analysis of more than 590,000 quality-filtered sequences obtained from the foregut, midgut and hindgut of these four carp species revealed high microbial diversity among the samples. The foregut samples of grass carp exhibited more than 1,600 operational taxonomy units(OTUs) and the highest alpha-diversity index, followed by the silver carp foregut and midgut. Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria were the predominant phyla regardless of fish species or gut type. Pairwise(weighted) UniFrac distance-based permutational multivariate analysis of variance with fish species as a factor produced significant association(P0.01). The gut microbiotas of all four carp species harbored saccharolytic or proteolytic microbes, likely in response to the differences in their feeding habits. In addition, extensive variations were also observed even within the same fish species. Our results indicate that the gut microbiotas of Asian carp depend on the exact species, even when the different species were cohabiting in the same environment. This study provides some new insights into developing commercial fish feeds and improving existing aquaculture strategies.     

The Microbial Community in the Feces of the White Rhinoceros (Ceratotherium simum) as Determined by Barcoded Pyrosequencing Analysis

As a non-ruminant herbivore, the white rhinoceros has the ability to utilize fibrous plant matter through microbial fermentation in the hindgut. So far, there has been no report using molecular techniques to study the gut microbiota of the white rhinoceros. We used barcoded pyrosequencing to characterize 105,651 sequences of 16S rRNA genes obtained from fecal samples from five white rhinoceroses. Results showed that Firmicutes and Bacteroidetes were the predominant phyla in the samples, which were comprised largely of unclassified bacteria. The microbiota of one animal treated with drug therapy differed from those in other healthy animals, and was dominated by Aerococcus -related bacteria. The core microbiota in the healthy rhinoceros were dominated by phyla Firmicutes and Bacteroidetes, represented by the Ruminococcaceae, Lachnospiraceae, Rikenellaceae and Prevotellaceae families. The present work provides a phylogenetic framework for understanding the complex microbial community of the rhinoceros; however, further studies are required to link the distinctive microbiota with their digestive role in the hindgut of the white rhinoceros.     

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(F...     

不同生长阶段舜皇山土猪肠道微生物组成与多样性

目的 挖掘肠道微生物在舜皇山土猪耐粗饲及抗病等方面的作用,为舜皇山土猪的饲养与保护以及益生菌的开发提供理论依据.方法 采集3个生长阶段的舜皇山土猪粪便样品,各4～5组,进行16SrDNA V3-V4区基因高通量测序,分析其微生物的组成及多样性.结果 舜皇山土猪肠道微生物主要由拟杆菌门(Bacteroides)、厚壁菌门...     

冬眠对达乌尔黄鼠盲肠菌群的影响

冬眠哺乳动物的肠道微生物会发生季节性变化,同时在冬眠期间动物处于禁食状态,对肠道微生物的多样性和组成也产生影响。本研究通过16S rRNA基因高通量测序分析达乌尔黄鼠育肥阶段 (起始育肥期、快速育肥期、育肥完成期) 和冬眠阶段 (冬眠早期、冬眠晚期、出眠期) 共6个时期盲肠菌群的多样性、组成和功能,并通过冗余分析 (RDA) 探究其生理特征与菌群组成和功能之间的关系,揭示达乌尔黄鼠盲肠菌群的季节性变化。菌群组成的分析显示达乌尔黄鼠盲肠菌群主要由厚壁菌门 (Firmicutes)、拟杆菌门 (Bacteroidetes) 和疣微菌门 (Verrucomicrobia) 组成。与其他时期相比,冬眠早期厚壁菌门的相对丰度减少,拟杆菌门和疣微菌门的相对丰度增加。在Alpha多样性中,起始育肥期、快速育肥期和冬眠早期的Chao1和ACE指数显著低于出眠期,育肥完成期的Simpson指数显著低于快速育肥期 (P < 0.05) 。通过加权和非加权的UniFrac距离矩阵的主坐标分析发现盲肠菌群均显示出了明显的季节性聚类。PICRUSt分析中,丁酸代谢等代谢通路在育肥阶段富集,冬眠阶段集中在氮代谢等相关通路中。RDA分析显示达乌尔黄鼠不同时期的生理特征与其盲肠菌群的组成和功能显著相关。本研究表明,冬眠使达乌尔黄鼠盲肠菌群的多样性和相对丰度发生改变,盲肠菌群组成和功能的变化调节了达乌尔黄鼠的生理代谢,使达乌尔黄鼠适应季节性的环境变化。     

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico

Although the gut microbiota is known to provide many beneficial functions to animal hosts, such as aiding in digestion, fat metabolism, and immune function, relatively little is known about the gut microbiota of passerines. Gut microbes may have both beneficial and detrimental impacts on the fitness of migratory passerines; however physiological and morphological changes associated with prolonged migratory flight may cause disruptions of the stable microbiota and potentially a loss of function. Fecal samples were collected from Swainson's thrushes Catharus ustulatus and gray catbirds Dumetella carolinensis immediately after crossing the Gulf of Mexico during spring migration and before crossing during fall, and microbiota communities were analyzed using next‐generation sequencing. Microbiota communities were generally dominated by Firmicutes and Proteobacteria, with potential pathogens as well as potentially beneficial bacteria identified in all birds. Energetic condition of migrants was not significantly related to overall microbiota community structure though it cannot be conclusively stated that migratory flight does not impact the microbiota. Spring and fall migrants showed clear differences in microbiota communities, indicating that environmental factors influence the gut microbiota of these species more than host genetics.     

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae

The gut microbiota of fish larvae evolves fast towards a complex community. Both host and environment affect the development of the gut microbiota; however, the relative importance of both is poorly understood. Determining specific changes in gut microbial populations in response to a change in an environmental factor is very complicated. Interactions between factors are difficult to separate and any response could be masked due to high inter-individual variation even for individuals that share a common environment. In this study we characterized and quantified the spatio-temporal variation in the gut microbiota of tilapia larvae, reared in recirculating aquaculture systems (RAS) or active suspension tanks (AS). Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. However, when individuals were reared in replicate RAS, gut microbiota differed significantly. The highest variation was observed between individuals reared in different types of system (RAS vs. AS). Our data suggest that under experimental conditions in which the roles of deterministic and stochastic factors have not been precisely determined, compositional replication of the microbial communities of an ecosystem is not predictable.     

Planktonic bacteria in white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) aquaculture ponds in a salt-alkaline region

Aquaculture in salt-alkaline regions is encouraged in China, and culture of many aquatic species has been introduced into these areas. In this study, we cultured two species, white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) separately in aquaculture ponds in a salt-alkaline region in northwest China and assessed the impacts of the aquaculture operations on the planktonic bacterial community in the culture ponds. Culture of both species decreased the planktonic bacterial diversity and altered the bacterial community structure in the aquaculture ponds compared with the source water. Among the 10 dominant bacterial phyla, 8 were significantly correlated with environmental parameters; the exception was Actinobacteriota, the most dominant phylum, and Firmicutes. Proteobacteria and Bacteroidota abundances showed significant positive correlations with alkalinity, whereas Patescibacteria, Cyanobacteria, Planctomycetota, and Verrucomicrobiota abundance were positively correlated with salinity. Linear regression analysis showed that alkalinity was positively correlated with bacterial beta diversity and salinity was negatively correlated with that. In addition, white shrimp aquaculture significantly lowered the alkalinity, which suggests that culture of this species in inland salt-alkaline regions is a potential dealkalization solution.     

Host and environmental influences on the gut bacterial community of carabid beetles in distinct paddy fields

The relationship between the gut bacterial communities of carabid beetles and their habitats holds implications for understanding ecological dynamics. This study examined the gut bacterial communities of two carabid beetle species, Chlaenius pallipes and Pheropsophus jessoensis, in terraced and flat paddy fields. Differences in gut bacterial communities were evident at the species level and were based on habitat. Specifically, P. jessoensis had a greater presence of Firmicutes and Proteobacteria in terraced fields but more Actinobacteria in flatland fields. In comparison, C. pallipes consistently showed high levels of Firmicutes in both habitats. These differences were reflected at class and genus levels, emphasizing the role of host specificity in shaping gut microbiota. Alpha diversity metrics indicated that P. jessoensis hosted a more diverse bacterial community than C. pallipes. Terraced fields, however, showed slightly reduced diversity in P. jessoensis, suggesting environmental effects on microbial populations. Beta diversity analysis using Bray–Curtis distances differentiated the bacterial communities of the two beetles. Multivariate analysis of variance reinforced these findings. Insights from the Sloan neutral model indicate that environmental factors predominantly influence bacterial community assembly through stochastic processes. Functionally, metabolism was highlighted, indicating the role of gut bacteria in beetle metabolic processes. Notably, energy metabolism varied between field types, revealing environmental effects on gut bacterial functions. This study offers in-depth insights into interactions between host-specific and environmental factors influencing gut bacterial communities of carabid beetles, contributing to a broader understanding of microbial ecology and the roles of environment and host in microbiota dynamics.     

成年与未成年圈养林麝粪便菌群多样性的比较

本研究旨在解析林麝未成年组(n=10)和成年组(n=10)之间的菌群差异。收集林麝新鲜粪便,提取总DNA,利用带标签的通用引物扩增16S rRNA V3-V4区,使用Illumina Miseq 300PE测序平台对扩增产物进行Miseq双端测序,通过计算ACE和Shannon等多样性指数,以及微生物组成成分和距离聚类分析,揭示组成结构与差异。α多样性分析表明成年组微生物的多样性丰富度略高于未成年组,但不存在显著差异性(P>0.05)。未成年组和成年组均是厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)和变形菌门(Proteobacteria)所占的比例较高。成年组Proteobacteria比例明显高,而Firmicutes比例较低。LEfSe分析表明有12个显著差异的细菌分类。两组在Firmicutes门存在显著差异的细菌较少,而在Proteobacteria上存在显著差异的细菌较多。本研究证明在不同年龄阶段,微生物的丰富度和多样性不存在显著差异,细菌的组成成分也相同。但是在组成比例上存在差异性,间接反映了不同年龄阶段营养吸收的不同需求。     

Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture

Commensal bacteria control the micro-ecology of metazoan epithelial surfaces with pivotal effect on tissue homeostasis and host defense. In contrast to the upper respiratory tract, the lower respiratory tract of healthy individuals has largely been considered free of microorganisms. To understand airway micro-ecology we studied microbiota of sterilely excised lungs from mice of different origin including outbred wild mice caught in the natural environment or kept under non-specific-pathogen-free (SPF) conditions as well as inbred mice maintained in non-SPF, SPF or germ-free (GF) facilities. High-throughput pyrosequencing of reverse transcribed 16S rRNA revealed metabolically active murine lung microbiota in all but GF mice. The overall composition across samples was similar at the phylum and family level. However, species richness was significantly different between lung microbiota from SPF and non-SPF mice. Non-cultivatable Betaproteobacteria such as Ralstonia spp. made up the major constituents and were also confirmed by 16S rRNA gene cloning analysis. Additionally, Pasteurellaceae, Enterobacteria and Firmicutes were isolated from lungs of non-SPF mice. Bacterial communities were detectable by fluorescent in situ hybridization (FISH) at alveolar epithelia in the absence of inflammation. Notably, higher bacterial abundance in non-SPF mice correlated with more and smaller size alveolae, which was corroborated by transplanting Lactobacillus spp. lung isolates into GF mice. Our data indicate a common microbial composition of murine lungs, which is diversified through different environmental conditions and affects lung architecture. Identification of the microbiota of murine lungs will pave the path to study their influence on pulmonary immunity to infection and allergens using mouse models.     

水产养殖环境微生物研究进展

近年来,水产养殖产业的迅猛发展在带来巨大经济效益的同时,也使周边水质持续恶化。在水产养殖中,微生物在生态平衡和环境保护方面的作用日益明显。着重介绍了养殖水域菌落结构的持续性变化、微生物在水产养殖中的作用以及水产养殖水域微生物群系组成变化的原因,并阐述了改善养殖水环境的生物修复技术,旨在为水产养殖环境微生物的相关研究及其管理提供参考依据。     

Interspecific comparison of the fecal microbiota structure in three Arctic migratory bird species

The gut microbiota of birds is known to be characterized for different species, although it may change with feeding items. In this study, we compared the gut microbiota of birds with different feeding behaviors in the same habitat. We collected fecal samples from three Arctic species, snow buntings Plectrophenax nivalis, sanderlings Calidris alba, and pink‐footed geese Anser brachyrhynchus that are phylogenetically quite distant in different families to evaluate effects of diet on gut microbiota. Also, we characterized the prevalence of fecal bacteria using the Illumina MiSeq platform to sequence bacterial 16S rRNA genes. Our NMDS results showed that fecal bacteria of snow buntings and sanderlings were significantly distant from those of pink‐footed geese. Although all three birds were occupied by three bacterial phyla, Proteobacteria, Firmicutes, and Bacteroidetes, dominant taxa still varied among the species. Our bacterial sequences showed that snow buntings and sanderlings were dominated by Firmicutes and Bacteroidetes, while pink‐footed geese were dominated by Proteobacteria. In addition, the bacterial diversity in snow buntings and sanderlings was significantly higher than that in pink‐footed geese. Our results suggest that insectivorous feeding diet of snow buntings and sanderlings could be responsible for the similar bacterial communities between the two species despite the distant phylogenetic relationship. The distinctive bacterial community in pink‐footed geese was discussed to be related with their herbivorous diet.     

First Glimpse of Gut Microbiota of Quarantine Insects in China

Quarantine insects are economically important pests that frequently invade new habitats. A rapid and accurate monitoring method to trace the geographical sources of invaders is required for their prevention, detection, and eradication. Current methods based on genetics are typically time-consuming. Here, we developed a novel tracing method based on insect gut microbiota. The source location of the insect gut microbiota can be used to rapidly determine the geographical origin of the insect. We analyzed 179 gut microbiota samples from 591 individuals of 22 quarantine insect species collected from 36 regions in China. The gut microbiota of these insects primarily included Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, and Tenericutes. The diversity of the insect gut microbiota was closely associated with geographical and environmental factors. Different insect species could be distinguished based on the composition of gut microbiota at the phylum level. Populations of individual insect species from different regions could be distinguished based on the composition of gut microbiota at the phylum, class, and order levels. A method for determining the geographical origins of invasive insect species has been established; however, its practical application requires further investigations before implementation.     

Bacteria associated with Artemia spp. along the salinity gradient of the solar salterns at Eilat (Israel)

The crustacean genus Artemia naturally inhabits various saline and hypersaline environments and is the most frequently laboratory-hatched animal for live feed in mari- and aquaculture. Because of its high economic importance, Artemia-bacteria interactions were so far studied mostly in laboratory strains. In this study, we focused our attention on the Artemia-associated microbiota in its natural environment in the solar salterns of Eilat, Israel. We applied a culture-independent method (clone libraries) to investigate the bacterial community structure associated with Artemia in five evaporation ponds with salinities from slightly above seawater (5%) to the point of saturation (32%), in two different developmental stages: in nauplii and in the intestine of adult animals. Bacteria found in naupliar and adult stages were classified within the Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Cyanobacteria. The halophilic proteobacterial genera Halomonas spp. and Salinivibrio spp. dominated the Artemia microbiota in both stages in all ponds. We also analysed a clone library of entire adult animals, revealing a novel bacterial phylogenetic lineage. This is the first molecular study of bacteria associated with two developmental stages of Artemia along a salinity gradient.