珠江口优势种鱼类肠道与水体中的微生物组成关系

为探讨河口鱼类肠道微生物与水环境中微生物的相互影响关系,选取了2019年冬季珠江口4种鱼类优势种凤鲚（Coilia mystus）、棘头梅童鱼（Collichthys lucidus）、鳓（Ilisha elongata）和短吻鲾（Leiognathus brevirostris）为研究对象,利用16S rRNA基因的高通量测序技术分析了鱼类肠道和水环境中的微生物群落。结果表明：鱼类肠道和水环境之间微生物组成差异明显,而4种鱼类肠道微生物组成无显著差异。鱼类肠道微生物均以变形菌门（Proteobacteria）和厚壁菌门（Firmicutes）为优势类群,而水体微生物以变形菌门和放线菌门（Actinobacteria）为主;鱼类肠道中优势微生物属为Bacteroides、Romboutsia和Faecalibacterium等（相对丰度≥2%）,而水环境中的微生物优势属为Candidatus＿Actinomarina（相对丰度21.2%）。四种鱼类物种的肠道微生物分别与水环境微生物之间的共有OTUs组成存在差异,共有的OTUs数量占棘头梅童鱼肠道总OTUs数量的比例最高（18.8%）,...     

Antithrombotic Activity of Heparinoid G2 and Its Derivatives from the Clam Coelomactra antiquata

Clam heparinoid G2 (60.25 kDa) and its depolymerized derivatives DG1 (24.48 kDa) and DG2 (6.75 kDa) prepared from Coelomactra antiquata have been documented to have excellent fibrinolytic and anticoagulant activity. In this study, to further explore the antithrombotic activity of G2, DG1 and DG2, azure A, sheep plasma, and clot lytic rate assays were used to determine their anticoagulant and thrombolytic activity in vitro. The results indicated that the anticoagulant titer of G2 was approximately 70% that of heparin and the thrombolytic activity of DG2 was greater than G2, DG1, and heparin activities. Moreover, in a carrageenan-induced venous thrombosis model, oral administration of G2 and DG1 each at 20 mg/kg and 40 mg/kg for 7 days significantly reduced blacktail thrombus formation, increased tissue-type plasminogen activator, fibrin degradation products, and D-dimer levels, decreased von Willebrand factor and thromboxane B2 levels, and restored phylum and genus abundance changes of intestinal bacteria. DG2 had no antithrombotic effect. At 20 mg/kg, G2, DG1, and heparin had comparable antithrombotic activities, and DG1 at 40 mg/kg had more muscular antithrombotic activity than G2. Thus, DG1 could be an antithrombotic oral agent owing to its more robust antithrombotic activity and lower molecular weight.     

Effect of organic acids–essential oils blend and oat fiber combination on broiler chicken growth performance,blood parameters,and intestinal health

This study evaluated the effect of organic acids–essential oils blend with or without oat hulls (OH) on growth performance, organ weights, blood parameters, gut morphology, microbiota, and short-chain fatty acids (SCFA) in broiler chickens. Day-old broiler chickens were randomly allocated to 4 dietary treatments consisting of 1) a corn-soybean meal-wheat based diet (BAS), 2) BAS + 0.05% bacitracin methylene disalicylate (BMD), 3) BAS + protected organic acids–essential oils at 300 g/1,000 kg of feed (OE), and 4) BAS + protected organic acids–essential oils at 300 g/1,000 kg of feed + 3% OH (OEOH), in 8 replicate groups. Feeding was in starter (d 0 to 14), grower (d 14 to 24), and finisher (d 24 to 36) phases. Body weight (BW), feed intake (FI), feed conversion ratio (FCR), and mortality were determined weekly. On d 36, 8 chickens per treatment were sampled for blood biochemistry, organ weights, cecal SCFA production, and microbiota. Treatments had no effect on FI and FCR at all phases. Both OE and OEOH treatments reduced (P < 0.001) the body weight gain of birds at the starter phase. Birds fed the OEOH treatment had higher (P < 0.001) gizzard weight, while those offered the BMD diet showed a tendency (P = 0.08) to have higher cecal weight. Birds in the OEOH treatment recorded increased ileal villus height and villus height-to-crypt depth ratio, as well as reduced duodenal crypt depth, while birds in the OE treatment had increased jejunal villus height and villus height-to-crypt depth ratio. Both OEOH and OE treatments increased the number of goblet cells produced in the duodenum and jejunum. Treatments had no effect on SCFA concentrations. Birds in the OE treatment recorded the lowest concentration of blood urea (P = 0.05) and cholesterol (P < 0.05). Both OE and OEOH treatments increased (P < 0.05) the relative abundance of potentially beneficial bacteria in the genus Firmicutes_unclassified, Ruminococcus, Turicibacter, and Erysipelotrichaceae_unclassified, while reducing (P < 0.001) the relative abundance of potentially harmful Coprobacillus. Conclusively, both protected organic acids–essential oils blend and its combination with oat fibers show potential as tools to achieve antibiotics reduction in broiler production.     

Microbial community diversity associated with the intestinal mucosa of farmed rainbow trout (Oncoryhnchus mykiss Walbaum)

Bacterial communities from the intestinal tract of rainbow trout were investigated to assess transient and resident microbial communities using both culture-based and culture-independent techniques. Viable counts attached to the intestinal mucosa were in the range of log 4.77–5.38 and log 6.67–6.79 CFU g⁻¹ in the intestinal contents. Pseudomonas spp. and Enterobacteriaceae constituted nearly 80% of the allochthonous population but <60% of the autochthonous populations. This coincided with an elevated mucosal level of a group of Gram-positive rods from ∼2% in the digesta to 25–35% on the mucosa. This group was identified by 16S rRNA as Arthrobacter aurescens and Janibacter spp. HTCC2649. Analysis of denaturing gradient gel electrophoresis banding patterns showed complex communities in all intestinal regions. Similarity coefficients showed that mucosal communities were ∼70% similar to digesta communities and yet due to the presence of bands found uniquely either in the digesta or on the mucosa, the communities are distinctly different. Scanning electron microscopy confirmed mucosal bacterial populations and highlighted a possible localized colonization between mucosal folds. The study highlights the complexity of resident microbial communities that have not been fully explored in previous rainbow trout studies; this is especially true with probiotic/prebiotic investigations.     

培养组学在动物肠道微生物应用的研究进展

肠道微生物被称为动物的“隐藏免疫器官”,不仅能参与宿主代谢还能影响宿主的免疫系统,对维持机体健康至关重要。作者主要介绍了培养组学的发展历程及其对动物肠道微生物研究的重要意义、传统微生物培养方法和分子生物学方法在研究微生物时各自的优、缺点。培养组学是基于传统微生物培养方法同时采用多种培养条件进行微生物培养,再辅以基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)和16S rRNA基因测序技术建立的一种新型微生物分离、鉴定方法,该方法将传统微生物培养技术与分子生物学技术的优点融为一体。该方法在挖掘“新微生物”的研究中,具有发现、找到并获得的优势;在微生物的研究中可定制分离目标菌株进行验证,并能通过丰富注释清楚地了解肠道微生物组。此外,分析了培养组学分别在家禽肠道、猪肠道、反刍动物肠道等动物肠道的研究应用现状,提出了环境条件对肠道微生物的影响,如人类接触对肠道菌群的影响、同物种不同性别肠道菌群的差异,以期为培养组学在动物肠道微生物的研究运用中提供参考。     

内蒙古锡林郭勒冬季放牧蒙古牛肠道微生物多样性和功能预测分析

为探究内蒙古锡林郭勒冬季放牧蒙古母牛肠道微生物组成及其功能,采集同一地区冬季(11、12月和次年1月)放牧蒙古母牛(各20头)直肠粪便样品,利用16SrRNA测序技术对其肠道菌群多样性进行分析及PICRUSt(Phylogenetic investigation of communities by reconstruction of unobserved states,PICRUSt)功能预测。结果显示,60份样品平均每样品测得90 075条序列,通过聚类共获得3 975个操作分类单元(Operational taxonomic units,OTU),84.60%的OTU注释到门水平;29.56%的OTU注释到属水平;在门水平和属水平,冬季放牧蒙古牛肠道中优势物种分别为厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)、拟杆菌属(Bacteroides)和艾克曼菌属(Akkermansia);随着天气逐渐变冷,食物短缺,蒙古牛肠道中厚壁菌门(Firmicutes)减少,而拟杆菌门(Bacteroidetes)增多;聚类分析发现,11月和12月蒙古牛肠道微生物群落较为相似,而与次年1月相比有明显差异;PICRUSt功能预测发现,随着天气逐渐变冷,免疫系统、环境适应性及细胞运动性相关通路丰度降低,氨基酸代谢通路丰度增加。综上,蒙古牛肠道菌群在适应食物短缺的冬季发挥着重要作用。     

Use of 16S rRNA gene sequencing analysis to characterize culturable intestinal bacteria in Atlantic salmon (Salmo salar) fed diets with cellulose or non-starch polysaccharides from soy

Duplicate groups of Atlantic salmon (Salmo salar L.), kept in seawater, were fed fish meal‐based cold‐pelleted diets. Diets with non‐starch polysaccharides (NSP), either cellulose, purified soybean NSP or extruded purified soybean NSP at a dietary level of 100 g kg^?1, were compared with a diet without supplemental NSP and a diet with soybean meal in a 28‐day feeding trial. Isolation and characterizations were limited to culturable bacteria and population levels of aerobic and facultative aerobic heterotrophic autochthonous (adherent) and allochthonous (transient) bacteria present in the mid and distal intestines of Atlantic salmon fed the five different diets estimated using traditional bacteriological techniques. The presence of an autochthonous microbiota was demonstrated using transmission electron microscopy. No significant effects of diet composition were observed on total population levels of culturable bacteria present in the digestive tract, but the study showed that the composition of the gut microbiota (autochthonous or allochthonous) was sensitive to dietary changes. A total of 752 culturable isolates from the intestines were characterized by biochemical and physiological properties. Of these, 188 isolates were further characterized by partial sequencing the 16S rRNA genes. Among these, 146 isolates belonged to 31 phylotypes that were >94% identical to previously described species. However, 42 isolates showed similarity <94% to species available at the National Center of Biotechnology Information. Several of the phylotypes identified in the present study have not been reported previously in the gastrointestinal (GI) tract of fish, including the Gram‐negative bacteria Gelidibacter salicanalis, Pseudoalteromonas elyakovii, Psychrobacter aquimaris, Psychrobacter cibarius, Psychrobacter fozii, Psychrobacter maritimus, Psychrobacter okhotskensis and Psychrobacter psychrophilus. Among the Gram‐positive bacteria identified were Arthrobacter bergeri, Arthrobacter psychrolactophilus, Arthrobacter rhombi, Bacillus pumilus, Bacillus subtilis, Exiguobacterium spp., Microbacterium oxydans, Planococcus maritimus, Sporosarcina ginsengisoli and several bacteria that have been described as unculturable previously. In addition, we identified Carnobacterium inhibens, a lactic acid bacterium that is not frequently isolated from the GI tract of fish. Psychrobacter cibarius was the dominant bacterial species and was isolated from the digestive tract of all fish investigated.     

Chitosan Oligosaccharides Alleviate Colitis by Regulating Intestinal Microbiota and PPARγ/SIRT1-Mediated NF-κB Pathway

Chitosan oligosaccharides (COS) have been shown to have potential protective effects against colitis, but the mechanism underlying this effect has not been fully elucidated. In this study, COS were found to significantly attenuate dextran sodium sulfate-induced colitis in mice by decreasing disease activity index scores, downregulating pro-inflammatory cytokines, and upregulating Mucin-2 levels. COS also significantly inhibited the levels of nitric oxide (NO) and IL-6 in lipopolysaccharide-stimulated RAW 264.7 cells. Importantly, COS inhibited the activation of the NF-κB signaling pathway via activating PPARγ and SIRT1, thus reducing the production of NO and IL-6. The antagonist of PPARγ could abolish the anti-inflammatory effects of COS in LPS-treated cells. COS also activated SIRT1 to reduce the acetylation of p65 protein at lysine 310, which was reversed by silencing SIRT1 by siRNA. Moreover, COS treatment increased the diversity of intestinal microbiota and partly restored the Firmicutes/Bacteroidetes ratio. COS administration could optimize intestinal microbiota composition by increasing the abundance of norank_f_Muribaculaceae, Lactobacillus and Alistipes, while decreasing the abundance of Turicibacte. Furthermore, COS could also increase the levels of propionate and butyrate. Overall, COS can improve colitis by regulating intestinal microbiota and the PPARγ/SIRT1-mediated NF-κB pathway.     

宏基因组测序分析野生林麝瘤胃、小肠和大肠微生物组成和抗生素抗性基因

本试验旨在研究野生林麝(Moschus berezovskii)瘤胃、小肠和大肠微生物组成和抗生素抗性基因.采集野生林麝消化道3个区段(瘤胃、小肠和大肠)的内容物进行宏基因组测序,并进行常规物种注释和抗生素抗性基因功能注释.结果表明:3个区段共有优势菌门为厚壁菌门(Firmicutes)和变形菌门(Proteobact...