探讨4种非营养性饲料添加剂对澳洲淡水龙虾（Cherax quadricarinatus）肝胰腺消化酶活力、免疫功能及离体消化率的影响，筛选出适宜的饲料添加剂，为非营养性添加剂在饲料中的应用和研究提供理论依据。分别以柠檬酸（S-Ⅰ）、复合酶制剂（S-Ⅱ）、植物乳杆菌加枯草芽孢杆菌（S-Ⅲ）、根瘤菌加枯草芽孢杆菌（S-Ⅳ）作为非营养性添加剂，配制4种等氮等脂等能饲料，喂养澳洲淡水龙虾14 d后，取样测定其肝胰腺消化酶（胰蛋白酶、脂肪酶和淀粉酶）活力、免疫功能［碱性磷酸酶（AKP）、酸性磷酸酶（ACP）、超氧化物歧化酶（SOD）活力和总抗氧化能力（T-AOC）］及离体消化率（干物质消化率、蛋白质离体消化率和总氨基酸转化效率）等相关指标。结果表明，S-Ⅰ可以显著提高澳洲淡水龙虾肝胰腺的淀粉酶、AKP和SOD活力（P<0. 05），S-Ⅱ可以显著提高其淀粉酶和胰蛋白酶活力以及免疫功能（P<0. 05）；而S-Ⅲ和S-Ⅳ在消化酶活力和免疫功能上均显著提高（P<0. 05）。在4种非营养性饲料添加剂对澳洲淡水龙虾离体消化率的影响中，S-Ⅳ的干物质消化率、蛋白质离体消化率和总氨基酸转化效率均值最高。S-Ⅲ和S-Ⅳ对消化酶活力、免疫功能及离体消化率的影响比S-Ⅰ和S-Ⅱ的高，并且S-Ⅳ的离体消化率比S-Ⅲ高，因此在这4种非营养性添加剂中优先选择S-Ⅳ。

从健康珍珠龙胆石斑鱼肠道中分离纯化获得4株疑似枯草芽孢杆菌（Bacillus subtilis）菌株（B1、B2、B3和B4），并进行了菌落形态、菌株理化性质、16S rDNA序列和产酶能力分析等方面的研究。结果表明，在理化性质方面，4株菌的试验结果均符合枯草芽孢杆菌的生化特性，并结合菌落形态，初步证明4株分离菌可能均为枯草芽孢杆菌；同时，基因序列比对结果显示，4株菌的16S rDNA序列与已知的枯草芽孢杆菌序列相似性≥99%，最终鉴定均为枯草芽孢杆菌。经过产酶能力的试验研究发现，4株菌都具有产纤维素酶、淀粉酶和蛋白酶的能力，且B3菌株同其他3株菌相比，其产纤维素酶、淀粉酶和蛋白酶的能力均较强。因此，本试验选取B3作为具有益生菌潜力的菌株。

The present study evaluated the in vitro and in vivo antagonistic effect of Bacillus against the pathogenic vibrios.Cell-free extracts of Bacillus subtilis BT23 showed greater inhibitory effects against the growth of Vibrio harveyi isolated by agar antagonism assay from Penaeus monodon with black gill disease. The probiotic effect of Bacillus was tested by exposing shrimp to B. subtilis BT23 at a density of 106-108 cfu ml-1 for 6 d before a challenge with V. harveyi at 103-104 cfu ml-1 for 1 h infection. The combined results of long- and short-term probiotic treatment of B. subtilis BT23 showed a 90% reduction in accumulated mortality.This study reports that pathogenic vibrios were controlled by Bacillus under in vitro and in vivo conditions.Results indicated that probiotic treatment offers a promising alternative to the use of antibiotics in shrimp aquaculture.

We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.

Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.

Gut microbiota typically occupy habitats with definable limits/borders that are comparable to oceanic islands. The gut therefore can be regarded as an 'island' for the assembly of microbial communities within the 'sea' of surrounding environments. This study aims to reveal the ecological mechanisms that govern microbiota in the fish gut 'island' ecosystem. Taxonomic compositions, phylogenetic diversity, and community turnover across host development were analyzed via the high-throughput sequencing of 16S rRNA gene amplicons. The results indicate that the Shannon diversity of gut microbiota in the three examined freshwater fish species all significantly decreased with host development, and the dominant bacterial taxa also changed significantly during host development. Null model and phylogenetic-based mean nearest taxon distance (MNTD) analyses suggest that host gut environmental filtering led to the assembly of microbial communities in the fish gut 'island'. However, the phylogenetic clustering of local communities and deterministic processes that governed community turnover became less distinct as the fish developed. The observed mechanisms that shaped fish gut microbiota seemed to be mainly shaped by the gut environment and by some other selective changes accompanying the host development process. These findings greatly enhance our understanding of stage-specific community assembly patterns in the fish gut ecosystem.© 2016 The Authors Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

The assembly of resident microbial communities is an important event in animal development; however, the extent to which this process mirrors the developmental programs of host tissues is unknown. Here we surveyed the intestinal bacteria at key developmental time points in a sibling group of 135 individuals of a model vertebrate, the zebrafish (Danio rerio). Our survey revealed stage-specific signatures in the intestinal microbiota and extensive interindividual variation, even within the same developmental stage. Microbial community shifts were apparent during periods of constant diet and environmental conditions, as well as in concert with dietary and environmental change. Interindividual variation in the intestinal microbiota increased with age, as did the difference between the intestinal microbiota and microbes in the surrounding environment. Our results indicate that zebrafish intestinal microbiota assemble into distinct communities throughout development, and that these communities are increasingly different from the surrounding environment and from one another.

To reveal the effects of fish genotype, feeding habits and serum physiological index on the composition of gastrointestinal microbiota, eight fish species with four different feeding habits were investigated.The V1 to V3 regions of 16S rRNA gene were analysed by high-throughput sequencing (454 platform) to compare the gut microbiota of different fish species. A total of 551 995 high-quality sequences with an average length of 463 bp were obtained from the 48 samples. No significant difference was observed among the detected sequences obtained from fishes with different feeding habits (One-way anova, F = 1·003, P = 0·400), but the number of OTUs among different feeding habits was significantly different (One-way anova, F = 7·564, P < 0·001). Additionally, significant correlations were detected between the fish genotype and microbial composition (partial Mantel test, all P values = 0·001) in the stomach, foregut and hindgut. Moreover, different core intestinal microbiota was also noticed in the eight fish species with different feeding habits.Feeding habits and genotype clearly affected the gastrointestinal microbiota of fish. Moreover, the evolutionary process shaped the serum physiological indexes of fish.This study provided much important information for developing commercial fish feeds.© 2014 The Society for Applied Microbiology.

To study the effects of Bacillus subtilis supplementation in a high-fat diet on the gut microbiota and nonalcoholic fatty liver disease in grass carp (Ctenopharyngodon idella), juveniles (60 ± 5 g) were fed three diets: (a) a control diet (CON), (b) a high-fat diet (HFD) and (c) a high-fat diet supplemented with B. subtilis (HFD + BS). After 8 weeks of feeding, fish growth, serum biochemical indices and total liver lipid content were measured, and gut microbiota analysis was performed using the MiSeq250 high-throughput sequencing platform. The results of this study showed that B. subtilis could improve growth and blood serum indices and reduce lipid deposition in the fish liver, preventing fatty liver disease. A grass carp model of fatty liver induced by a high-fat diet was successfully established. Moreover, B. subtilis altered the intestinal microbiota of HFD-fed grass carp, making it more similar to that of the control group. This study revealed the important effects of B. subtilis on grass carp with fatty liver induced by a high-fat diet and provides the foundation for the application of probiotics in grass carp farming.