Diversity of the resident microbiota in a thermophilic municipal biogas plant

Biogas plants continuously convert biological wastes mainly into a mixture of methane, CO₂ and H₂O—a conversion that is carried out by a consortium of bacteria and archaea. Especially in the municipal plants dedicated towards waste treatment, the reactor feed may vary considerably, exposing the resident microbiota to a changing variety of substrates. To evaluate how and if such changes influence the microbiology, an established biogas plant (6,600 m³, up to 600 m³ biogas per h) was followed over the course of more than 2 years via polymerase chain reaction–denaturing gradient gel electrophoresis of 16S rRNA genes and subsequent sequencing. Both the bacterial and the archaeal community remained stable over the investigation. Of the bacterial consortium, about half of the sequences were in decreasing order of occurrence: Thermoacetogenium sp., Anaerobaculum mobile, Clostridium ultunense, Petrotoga sp., Lactobacillus hammesii, Butyrivibrio sp., Syntrophococcus sucromutans, Olsenella sp., Tepidanaerobacter sp., Sporanaerobacter acetigenes, Pseudoramibacter alactolyticus, Lactobacillus fuchuensis or Lactobacillus sakei, Lactobacillus parabrevis or Lactobacillus spicheri and Enterococcus faecalis. The other half matched closely to ones from similar habitats (thermophilic anaerobic methanogenic digestion). The archaea consisted of Methanobrevibacter sp., Methanoculleus bourgensis, Methanosphaera stadtmanae, Methanimicrococcus blatticola and uncultured Methanomicrobiales. The role of these species in methane production is discussed.     

奶牛产后感染性子宫疾病对子宫和卵巢的影响研究进展

微生物入侵是引起奶牛产后子宫疾病的主要因素,产后子宫能检出丰富的微生物种群,主要包括公认的致病菌如大肠杆菌、隐秘脓杆菌、坏死梭杆菌等,机会病原菌如产气荚膜梭菌、肺炎克雷伯菌、微球菌等和潜在致病菌如消化链球菌、金黄色葡萄球菌等。近年来,运用分子微生态技术发现子宫中的微生物属于变形菌门、梭杆菌门、厚壁菌门、拟杆菌门和软壁菌门5个已知的门和一类未被培养的种群,其中拟杆菌属、梭菌属等种群与子宫疾病密切相关。细菌侵入子宫后,以大肠杆菌为代表的革兰氏阴性菌和以化脓隐秘杆菌为代表的革兰氏阳性菌可被子宫内膜细胞上的Toll样受体识别引起炎症反应,改变子宫前列腺素分泌类型,影响卵泡发育、黄体大小,降低血清中雌激素和孕激素浓度,造成奶牛不发情、不排卵,导致产犊间隔延长、产奶量和产犊数量下降,严重影响奶业经济效益。本文从产后奶牛子宫内主要病原菌的种类及其与子宫健康状态的关系、子宫内膜对病原菌的识别与先天免疫、子宫疾病对子宫和卵巢功能的影响等方面对国内外研究进展进行了综述。     

肥胖患者HFA小鼠模型的建立

目的研究肥胖患者的肠道菌群在无菌小鼠体内的定植规律。方法选取20只无菌KM小鼠,接种肥胖患者的粪便,构建菌群人源化(HFA)动物模型,利用变性梯度凝胶电泳技术(DGGE)评价患者肠道菌群在无菌小鼠体内的定植规律。结果 HFA小鼠菌群平均丰富度(richness,S)为12.04±3.68,肥胖患者的条带S为24,为HFA小鼠S的2倍;肥胖患者Shannon指数(H')为3.02,HFA小鼠平均H'为2.46±0.33;HFA小鼠与人肠道菌群的总相似度为26%;大部分雌性HFA小鼠与雄性HFA小鼠在聚类分析图上分离,且雄性HFA小鼠与患者更为相似。结论HFA小鼠体内能部分模拟肥胖患者的微生物区系,且与患者性别相同的小鼠模拟得更好。本实验建立的HFA模型为肥胖与肠道菌群关系的进一步研究提供新的选择。     

Characterization of the cultivable microbiota of sprouts and their potential for application as protective cultures

The microbiota of ten seeds and ready-to-eat sprouts produced thereof was characterized by bacteriological culture and denaturing gradient gel electrophoresis (DGGE) of amplified DNA fragments of the 16S rRNA gene. The predominant bacterial biota of hydroponically grown sprouts mainly consisted of enterobacteria, pseudomonades and lactic acid bacteria (LAB). For adzuki, alfalfa, mung bean, radish, sesame and wheat, the ratio of these bacterial groups changed strongly in the course of germination, whereas for broccoli, red cabbage, rye and green pea the ratio remained unchanged. Within the pseudomonades, Pseudomonas gesardii and Pseudomonas putida have been isolated and strains of the potentially pathogenic species Enterobacter cancerogenes and Pantoea agglomerans were found as part of the main microbiota on hydroponically grown sprouts. In addition to the microbiota of the whole seedlings, the microbiota of root, hypocotyl and seed leafs were examined for alfalfa, radish and mung bean sprouts. The highest and lowest total counts for aerobic bacteria were found on seed leafs and hypocotyls, respectively. On the other hand, the highest numbers for LAB on sprouts were found on the hypocotyl. When sprouting occurred under the agricultural conditions, e.g. in soil, the dominating microbiota changed from enterobacteria to pseudomonades for mung beans and alfalfa sprouts. No pathogenic enterobacteria have been isolated from these sprout types. Within the pseudomonades group, Pseudomonas jessenii and Pseudomonas brassicacearum were found as dominating species on all seedling parts from soil samples. In practical experiments, a strain of P. jessenii was found to exhibit a potential for use as protective culture, as it suppresses the growth of pathogenic enterobacteria on ready-to-eat sprouts.     

肠道菌群与心血管疾病关系研究进展

近年来,越来越多的研究表明肠道菌群在心血管疾病、2型糖尿病、肥胖等疾病的发病过程中起着主要作用,肠道菌群组成改变以及肠道菌群代谢物水平改变是导致疾病发生发展的重要因素,人们对肠道菌群与宿主之间的相互作用产生极大兴趣。本文系统总结了肠道菌群组成结构改变及肠道菌群代谢物改变与动脉粥样硬化、高血压、心肌梗死、心力衰竭等心血管疾病的相关性,阐明了肠道菌群可能是促进心血管疾病发病的原因之一。因此,通过改变饮食结构和使用抗生素、益生菌制剂及肠道菌群代谢物氧化三甲胺(TMAO)小分子抑制剂,来调控肠道菌群组成及代谢物水平有望作为心血管疾病治疗的新靶点。     

A comparative in vitro investigation into the effects of cooked meats on the human faecal microbiota

Protein fermentation is one of the important microbial activities in the human colon. Meat foods rich in protein provide substantial resource for this metabolic activity. However, little information exists on the relative impact of different meats on the composition and activities of the human gut microbiota. Similarly, little information is available on the confounding effects of cooking on these activities. In this study, beef, chicken and fish (salmon) were examined in vitro for their impact on the human faecal microbiota. The influence of cooking method was also investigated by using either frying or boiling. Upon fermentation over 48 h the Clostridium perfringens/histolyticum group increased significantly in number in the beef fermentations, either fried (p = 0.023) or boiled (p = 0.017). Cooking method appeared to influence Clostridium spp. growth, with higher numbers in fried meat compared to boiled meats after 5 h (p = 0.024) and 48 h (p = 0.003) fermentation. Significant differences between meat types were also seen for numbers of Bifidobacterium spp. at 48 h (p = 0.028), Bacteroides group at 24 h (p = 0.016) as well as Coriobacterium/Atopobium group at 10 h (p = 0.038). Most types of short chain fatty acids increased significantly in concentration over the experiment (p < 0.05). Significant differences between meat types were found in n-butyric acid production at 24, 30 and 48 h (p = 0.015, p = 0.024 and p = 0.035 respectively) and in i-valeric acid production at 10, 24, 30 and 48 h (p = 0.026, p = 0.002, p = 0.019 and p = 0.022 respectively). The concentration of i-valeric acid differed significantly between cooking methods at 24 h (p = 0.042). These findings suggest that both the type of meat and cooking process can influence fermentation profiles within the human gut microbiota. Interactions between ingested cooked meats and the gut microbiota may represent a novel corollary to mechanisms underlying the observed increased risk of intestinal and systemic diseases associated with high intake of certain meats/processed meats.     

Spotting the differences: Probing host/microbiota interactions with a dedicated software tool for the analysis of faecal outputs in Drosophila

The intestinal physiology of Drosophila melanogaster can be monitored in an integrative, non-invasive manner by analysing graphical features of the excreta produced by flies fed on a dye-supplemented diet. This assay has been used by various labs to explore gut function and its regulation. To facilitate its use, we present here a free, stand-alone dedicated software tool for the analysis of fly excreta. The Ultimate Reader of Dung (T.U.R.D.) is designed to offer a flexible environment for a wide range of experimental designs, with special attention to automation and high-throughput processing. This software detects the distinctive changes in acid-base and water balance previously reported to occur in response to dietary challenges and mating. We have used T.U.R.D. to test the contribution of the bacterial environment of the flies to various intestinal parameters including the established diet- and mating-triggered responses. To this end, we have analysed the faecal patterns of flies reared in germ-free conditions, upon re-association with controlled microbiota and subjected to food-borne or systemic, non-lethal bacterial infections. We find that the tested faecal outputs are unchanged in all these conditions, suggesting that the impact of the bacterial environment on the intestinal features highlighted by faecal deposit analysis is minimal.     

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

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The complex role of inflammasomes in the pathogenesis of Inflammatory Bowel Diseases – Lessons learned from experimental models

Inflammasomes are a large family of multiprotein complexes recognizing pathogen-associated molecular pattern molecules (PAMPs) and damage-associated molecular patterns (DAMPs). This leads to caspase-1 activation, promoting the secretion of mature IL-1β, IL-18 and under certain conditions even induce pyroptosis. Inflammatory Bowel Diseases (IBD) is associated with alterations in microbiota composition, inappropriate immune responses and genetic predisposition associated to bacterial sensing and autophagy. Besides their acknowledged role in mounting microbial induced host responses, a crucial role in maintenance of intestinal homeostasis was revealed in inflammasome deficient mice. Further, abnormal activation of these functions appears to contribute to the pathology of intestinal inflammation including IBD and colitis-associated cancer. Herein, the current literature implicating the inflammasomes, microbiota and IBD is comprehensively reviewed.