Abiotic Environmental Factors Affecting the Formation of Microbial Biofilms

Biofilms are aform of existence of bacteria in the environment, due to which bacteria can expand the boundaries of their habitats during contamination of different surfaces under diverse conditions. The most important environmental factors affecting biofilms are discussed. These factors include temperature, osmolarity, the concentration of ferrous iron ions, the availability of nutrients, the quality of materials on which biofilms are formed, and light and theambient acidity.     

Intestinal NADPH Oxidase 2 Activity Increases in a Neonatal Rat Model of Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is a complication of prematurity. The etiology is unknown, but is related to enteral feeding, ischemia, infection, and inflammation. Reactive oxygen species production, most notably superoxide, increases in NEC. NADPH oxidase (NOX) generates superoxide, but its activity in NEC remains unknown. We hypothesize that NOX-derived superoxide production increases in NEC. Newborn Sprague-Dawley rats were divided into control, formula-fed, formula/LPS, formula/hypoxia, and NEC (formula, hypoxia, and LPS). Intestinal homogenates were analyzed for NADPH-dependent superoxide production. Changes in superoxide levels on days 0-4 were measured. Inhibitors for nitric oxide synthase (L-NAME) and NOX2 (GP91-ds-tat) were utilized. RT-PCR for eNOS, NOX1, GP91^phox expression was performed. Immunofluorescence studies estimated the co-localization of p47^phox and GP91^phox in control and NEC animals on D1, D2, and D4. NEC pups generated more superoxide than controls on D4, while all other groups were unchanged. NADPH-dependent superoxide production was greater in NEC on days 0, 3, and 4. GP91-ds-tat decreased superoxide production in both groups, with greater inhibition in NEC. L-NAME did not alter superoxide production. Temporally, superoxide production varied minimally in controls. In NEC, superoxide generation was decreased on day 1, but increased on days 3-4. GP91^phox expression was higher in NEC on days 2 and 4. NOX1 and eNOS expression were unchanged from controls. GP91^phox and p47^phox had minimal co-localization in all control samples and NEC samples on D1 and D2, but had increased co-localization on D4. In conclusion, this study proves that experimentally-induced NEC increases small intestinal NOX activity. All components of NEC model are necessary for increased NOX activity. NOX2 is the major source, especially as the disease progresses.     

Mucosa-Associated Bacterial Diversity in Necrotizing Enterocolitis

Background

Previous studies of infant fecal samples have failed to clarify the role of gut bacteria in the pathogenesis of NEC. We sought to characterize bacterial communities within intestinal tissue resected from infants with and without NEC.

Methods

26 intestinal samples were resected from 19 infants, including 16 NEC samples and 10 non-NEC samples. Bacterial 16S rRNA gene sequences were amplified and sequenced. Analysis allowed for taxonomic identification, and quantitative PCR was used to quantify the bacterial load within samples.

Results

NEC samples generally contained an increased total burden of bacteria. NEC and non-NEC sample sets were both marked by high inter-individual variability and an abundance of opportunistic pathogens. There was no statistically significant distinction between the composition of NEC and non-NEC microbial communities. K-means clustering enabled us to identify several stable clusters, including clusters of NEC and midgut volvulus samples enriched with Clostridium and Bacteroides. Another cluster containing both NEC and non-NEC samples was marked by an abundance of Enterobacteriaceae and decreased diversity among NEC samples.

Conclusions

The results indicate that NEC is a disease without a uniform pattern of microbial colonization, but that NEC is associated with an abundance of strict anaerobes and a decrease in community diversity.     

Gastroenteritis with Necrotizing Enterocolitis in Premature Babies

Eleven premature babies developed necrotizing enterocolitis in an epidemic of gastroenteritis and salmonella infection. This occurred in one of two premature baby wards over a period of 10 weeks. All affected babies had severe gastroenteritis and six had salmonella infection. No cases of necrotizing enterocolitis occurred in the unaffected ward during the same period. All other possible factors which might have predisposed to necrotizing enterocolitis occurred with equal frequency in both wards.There seems little doubt that infection was the significant factor in the pathogenesis.     

Neonatal Necrotizing Enterocolitis: Clinical and Radiological Features

Necrotizing enterocolitis is an uncommon but dangerous disease in premature infants. Ten cases, seen over a three-year period at the Stanford University Medical Center, represented an incidence of 0.4 percent. The patients, six of whom died, derived from a general population, in contrast to the large series of patients reported in the literature in which the incidence was from 0.9 percent to 3.7 percent.^3-6The initial symptoms—rapid respiration, periodic breathing, lethargy and irritability—were identical to those which occurred in numerous infants who had respiratory disease. Subsequent symptoms (abdominal distension, in 100 percent; vomiting, 80 percent; apneic spells, 70 percent; jaundice, 70 percent; guaic-positive stools, 60 percent) were those of nonspecific acute abdominal disease.The radiologist first made the diagnosis in 90 percent of cases. Interstitial air in the wall of the gut and the retroperitoneum, and portal vein gas were the most diagnostic radiographic features. Barium contrast studies were not helpful, and in one case led to the erroneous diagnosis of small bowel volvulus.Plain abdominal radiographs must be taken of all premature infants with symptoms of nonspecific acute abdominal disease. If the radiographs are negative, but symptoms continue, they should be repeated at frequent intervals, for early diagnosis is critical to institution of proper therapy.     

环境因素对L-异亮氨酸发酵的影响

通过 5L自控发酵罐发酵实验 ,结合发酵过程中菌生长形态的变化 ,对L -异亮氨酸补料分批发酵进行研究 ,研究了环境因素对黄色短杆菌 (Brevibacteriumflavum)TJCN - 1的影响 ,优化出发酵最佳控制条件 ,提出分阶段发酵控制模式 ,对L -异亮氨酸生产有指导意义。     

Necrotizing Enterocolitis (NEC) and the Risk of Intestinal Stricture: The Value of C-Reactive Protein

Necrotizing enterocolitis (NEC) is a severe complication frequently seen during the neonatal period associated with high mortality rate and severe and prolonged morbidity including Post-NEC intestinal stricture. The aim of this study is to define the incidence and risk factors of these post-NEC strictures, in order to better orient their medicosurgical care. Sixty cases of NEC were retrospectively reviewed from a single tertiary center with identical treatment protocols throughout the period under study, including systematic X-ray contrast study. This study reports a high rate of post-NEC intestinal stricture (n = 27/48; 57% of survivors), either in cases treated surgically (91%) and after the medical treatment of NEC (47%). A colonic localization of the strictures was more frequent in medically-treated patients than in those with NEC treated surgically (87% vs. 50%). The length of the strictures was significantly shorter in case of NEC treated medically. No deaths were attributable to the presence of post-NEC stricture. The mean hospitalization time in NICU and the median age at discontinuation of parenteral nutrition were longer in the group with stricture, but this difference was not significant. The median age at discharge was significantly higher in the group with stricture (p = 0.02). The occurrence of post-NEC stricture was significantly associated with the presence of parietal signs of inflammation and thrombopenia (<100 000 platelets/mm³). The mean maximum CRP concentration during acute phase was significantly higher in infants who developed stricture (p<0.001), as was the mean duration of the elevation of CRP levels (p<0.001). The negative predictive value of CRP levels continually <10 mg/dL for the appearance of stricture was 100% in our study. In conclusion, this retrospective and monocentric study demonstrates the correlation between the intensity of the inflammatory syndrome and the risk of secondary intestinal stricture, when systematic contrast study is performed following NEC.     

Longitudinal Analysis of the Premature Infant Intestinal Microbiome Prior to Necrotizing Enterocolitis: A Case-Control Study

Necrotizing enterocolitis (NEC) is an inflammatory disease of the newborn bowel, primarily affecting premature infants. Early intestinal colonization has been implicated in the pathogenesis of NEC. The objective of this prospective case-control study was to evaluate differences in the intestinal microbiota between infants who developed NEC and unaffected controls prior to disease onset. We conducted longitudinal analysis of the 16S rRNA genes of 312 samples obtained from 12 NEC cases and 26 age-matched controls with a median frequency of 7 samples per subject and median sampling interval of 3 days. We found that the microbiome undergoes dynamic development during the first two months of life with day of life being the major factor contributing to the colonization process. Depending on when the infant was diagnosed with NEC (i.e. early vs. late onset), the pattern of microbial progression was different for cases and controls. The difference in the microbiota was most overt in early onset NEC cases and controls. In proximity to NEC onset, the abundances of Clostridium sensu stricto from Clostridia class were significantly higher in early onset NEC subjects comparing to controls. In late onset NEC, Escherichia/Shigella among Gammaproteobacteria, showed an increasing pattern prior to disease onset, and was significantly higher in cases than controls six days before NEC onset. Cronobacter from Gammaproteobacteria was also significantly higher in late onset NEC cases than controls 1-3 days prior to NEC onset. Thus, the specific infectious agent associated with NEC may vary by the age of infant at disease onset. We found that intravenously administered antibiotics may have an impact on the microbial diversity present in fecal material. Longitudinal analysis at multiple time points was an important strategy utilized in this study, allowing us to appreciate the dynamics of the premature infant intestinal microbiome while approaching NEC at various points.     

454测序法在环境微生物生态研究中的应用

传统的Sanger测序技术虽已成熟,但其速度和成本的限制满足不了大规模测序的要求。第二代高通量测序技术结合了乳胶微粒和皮升级反应的454焦磷酸测序法,作为一种高通量测序技术,具有分析结果准确、高速、高灵敏度和高自动化的特点。对454测序法的技术原理和操作步骤进行了介绍,对近年来运用该方法在环境微生物生态研究领域的进展进行了综述。     

微生物发酵产氢的影响因素分析*

随着环保要求的愈益严格和化石能源的日益短缺,氢作为清洁高效的可再生能源日益受到人们的重视。微生物发酵产氢可以利用可再生的生物质,符合可持续发展的要求。针对影响微生物发酵产氢的因素,总结了国内外在该领域的研究成果,重点介绍了产氢微生物、营养物、产物和工艺操作条件等方面对发酵产氢的影响,同时还阐述了以有机废弃物为基质时的发酵产氢影响因素。     

Low Abdominal NIRS Values and Elevated Plasma Intestinal Fatty Acid-Binding Protein in a Premature Piglet Model of Necrotizing Enterocolitis

To identify early markers of necrotizing enterocolitis (NEC), we hypothesized that continuous abdominal near-infrared spectroscopy (A-NIRS) measurement of splanchnic tissue oxygen saturation and intermittent plasma intestinal fatty-acid binding protein (pI-FABP) measured every 6 hours can detect NEC prior to onset of clinical symptoms. Premature piglets received parenteral nutrition for 48-hours after delivery, followed by enteral feeds every three hours until death or euthanasia at 96-hours. Continuous A-NIRS, systemic oxygen saturation (SpO₂), and heart rate were measured while monitoring for clinical signs of NEC. Blood samples obtained at 6-hour intervals were used to determine pI-FABP levels by ELISA. Piglets were classified as fulminant-NEC (f-NEC), non-fulminant-NEC (nf-NEC) and No-NEC according to severity of clinical and histologic features. Of 38 piglets, 37% (n=14) developed nf-NEC, 18% (n=7) developed f-NEC and 45% (n=17) had No-NEC. There were significant differences in baseline heart rate (p=0.008), SpO₂ (p<0.001) and A-NIRS (p<0.001) among the three groups. A-NIRS values of NEC piglets remained lower throughout the study with mean for f-NEC of 69±3.8%, 71.9±4.04% for nf-NEC, and 78.4±1.8% for No-NEC piglets (p<0.001). A-NIRS <75% predicted NEC with 97% sensitivity and 97% specificity. NEC piglets demonstrated greater variability from baseline in A-NIRS than healthy piglets (10.1% vs. 6.3%; p=0.04). Mean pI-FABP levels were higher in animals that developed NEC compared to No-NEC piglets (0.66 vs. 0.09 ng/mL;p<0.001). In f-NEC piglets, pI-FABP increased precipitously after feeds (0.04 to 1.87 ng/mL;p<0.001). pI-FABP levels increased in parallel with disease progression and a value >0.25ng/mL identified animals with NEC (68% sensitivity and 90% specificity). NIRS is a real-time, non-invasive tool that can serve as a diagnostic modality for NEC. In premature piglets, low A-NIRS in the early neonatal period and increased variability during initial feeds are highly predictive of NEC, which is then confirmed by rising plasma I-FABP levels. These modalities may help identify neonates with NEC prior to clinical manifestations of disease.     

Intestinal Fatty Acid-Binding Protein as a Diagnostic Marker for Complicated and Uncomplicated Necrotizing Enterocolitis: A Prospective Cohort Study

Background

Early NEC symptoms are non-specific and diagnostic tests lack discriminative power. Intestinal fatty acid-binding protein (I-FABP), mainly located in small bowel enterocytes, is released into the blood following NEC-associated enterocyte disruption. Aim of this prospective cohort trial was to determine the diagnostic value of I-FABP measured in plasma (I-FABPp) and urine (I-FABPu) for the presence of NEC, to evaluate I-FABP levels during NEC development, and to assess its prognostic value for the progression from suspected to complicated disease.

Methods

Between 2010 and 2012 we prospectively enrolled neonates with suspected NEC. We measured I-FABP levels eight-hourly from onset of suspected NEC for at least 48 hours, or until surgery. NEC diagnosis was confirmed radiologically or during operation. We defined NEC as complicated if it resulted in surgery and/or death. We determined disease course and diagnostic I-FABP cut-off points.

Results

The study comprised 37 neonates (24M, 13F), gestational age 28 (24–36) weeks, birth weight 1190 (570–2,400) grams. We found significantly higher I-FABPp and I-FABPu levels in NEC patients (n = 22) than in patients with other diagnoses (n = 15). Cut-off values for diagnosing NEC were 9 ng/mL I-FABPp and 218 ng/mL I-FABPu, with corresponding likelihood ratios (LRs) of 5.6 (95% CI 0.89–35) and 5.1 (95% CI 0.73–36), respectively. I-FABP levels were highest in the first eight hours after symptom onset and gradually decreased over time. Cut-off values for complicated disease were 19 ng/mL I-FABPp and 232 ng/mL I-FABPu, with LRs of 10 (95% CI 1.6–70) and 11 (95% CI 1.6–81), respectively.

Conclusions

Both plasma and urinary I-FABP levels specifically identify NEC in preterm infants prior to appearance of diagnostic radiological signs suggestive for NEC. Moreover, serial I-FABP measurements accurately predict development of complicated disease.     

Environmental Factors Affecting Productivity of Brown-Headed Nuthatches

Abstract: Understanding the link between habitat use and components of fitness can yield useful insight into the environmental conditions necessary for population maintenance and can help promote effective habitat management. This information is especially important for species that are in decline or otherwise of conservation concern. Populations of brown-headed nuthatches (Sitta pusilla), an obligate cavity nester, have declined throughout their range, primarily due to extensive habitat loss and degradation. To help guide habitat management for this species, we identified habitat features associated with variation in the number of offspring fledged within 2 populations in southern Florida, USA. The most important predictor of productivity was the date on which a nest attempt began, with earlier nests producing more fledglings. The number of large pine (Pinus elliottii var. densa) snags and, to a lesser extent, the number of small pine trees surrounding a nest site were positively associated with productivity. We recommend that land managers in southern Florida focus on providing abundant large pine snags because doing so will increase productivity and also may increase nest-site availability and the percentage of individuals that breed each year. Prescribed burning may be an effective way to increase the abundance of large pine snags; however, land managers should exercise caution when doing so because of the trade-off between snag recruitment and snag consumption that accompanies the use of fire. We lack the data required to predict the fire-return interval that optimizes this trade-off, but until these data are available we recommend increasing the spatial heterogeneity in fire-return interval and lengthening the fire-return interval in some areas to 5-6 years.     

Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake

Agricultural activities, including stock-farming, planting industry, and fish aquaculture,can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear.Hence, in this work, we selected Honghu Lake as a typical lake that is influenced by agriculture activities. We collected water and sediment samples from 18 sites, which span a wide range of areas from impacted and less-impacted areas. We performed a geospatial analysis on the composition of microbial communities associated with physicochemical properties and antibiotic pollution of samples. The co-occurrence networks of water and sediment were also built and analyzed. Our results showed that the microbial communities of impacted and less-impacted samples of water were largely driven by the concentrations of TN, TP, NO_3^--N, and NO_2^--N, while those of sediment were affected by the concentrations of Sed-OM and Sed-TN. Antibiotics have also played important roles in shaping these microbial communities: the concentrations of oxytetracycline and tetracycline clearly reflected the variance in taxonomic diversity and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Furthermore, for samples from both water and sediment, large differences of network topology structures between impacted and less-impacted were also observed. Our results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu Lake.     

Environmental Factors That Control Microbial Perchlorate Reduction

As part of a study to elucidate the environmental parameters that control microbial perchlorate respiration, we investigated the reduction of perchlorate by the dissimilatory perchlorate reducer Dechlorosoma suillum under a diverse set of environmental conditions. Our results demonstrated that perchlorate reduction by D. suillum only occurred under anaerobic conditions in the presence of perchlorate and was dependent on the presence of molybdenum. Perchlorate reduction was dependent on the presence of the enzyme chlorite dismutase, which was induced during metabolism of perchlorate. Anaerobic conditions alone were not enough to induce expression of this enzyme. Dissolved oxygen concentrations less than 2 mg liter⁻¹ were enough to inhibit perchlorate reduction by D. suillum. Similarly to oxygen, nitrate also regulated chlorite dismutase expression and repressed perchlorate reduction by D. suillum. Perchlorate-grown cultures of D. suillum preferentially reduced nitrate in media with equimolar amounts of perchlorate and nitrate. In contrast, an extended (40 h) lag phase was observed if a similar nitrate-perchlorate medium was inoculated with a nitrate-grown culture. Perchlorate reduction commenced only when nitrate was completely removed in either of these experiments. In contrast to D. suillum, nitrate had no inhibitory effects on perchlorate reduction by the perchlorate reducer Dechloromonas agitata strain CKB. Nitrate was reduced to nitrite concomitant with perchlorate reduction to chloride. These studies demonstrate that microbial respiration of perchlorate is significantly affected by environmental conditions and perchlorate reduction is directly dependent on bioavailable molybdenum and the presence or absence of competing electron acceptors. A microbial treatment strategy can achieve and maintain perchlorate concentrations below the recommended regulatory level, but only in environments in which the variables described above can be controlled.     

荧光原位杂交技术及其在环境微生物生态学中的应用研究

荧光原位杂交技术是一种能够同时对微生物进行定性、定量和研究微生物群落空间分布情况的有力工具。简要介绍了荧光原位杂交技术的方法,并对其在人为创制环境和自然环境中特征性微生物种群及群落生态学中的应用研究进行了讨论,指出了该种技术在应用中存在的问题与缺陷,最后对荧光原位杂交技术在堆肥微生物生态中的应用及与其他方法的组合应用进行了展望。     

综合应用ITS及16SrDNA进行环境微生物生态研究

提出并介绍一种研究微生物生态的新方法.该方法将克隆测序和RISA图谱技术有机结合.其技术关键是PCR扩增的目标片段包含全长ITS和部分16S rDNA片段,既可利用16S rDNA进行系统发育分析,又可测定ITS片段大小并与RISA图谱进行比对定位.分析过程简单经济,易于操作,普通分子生物实验室即可实现.     

FoxP3+ Regulatory T Cells Attenuate Experimental Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) results from severe intestinal inflammation in premature infants. FoxP3⁺ regulatory T cells (Tregs) are central to gut homeostasis. While Treg proportions are significantly reduced in the ileums of premature infants with NEC, it is unknown whether they play a critical function in preventing NEC. This study investigated Treg development in newborn rat pups and their role in experimental NEC induction. Utilizing an established rat model of experimental NEC, the ontogeny of T cells and Tregs in newborn pups was characterized by flow cytometry. To investigate the functions of Tregs, newborn pups were given Tregs harvested from adult rats prior to NEC induction to assess clinical improvement and mechanisms of immune regulation. The results revealed that there were few Treg numbers in the terminal ileums of newborn rats and 8-fold reduction after NEC. Adoptive transfer of Tregs significantly improved weight loss, survival from 53% to 88%, and NEC incidence from 87% to 35%. The Tregs modulated the immune response as manifested in reduced CD80 expression on antigen presenting cells and decreased T cell activation within the mesenteric lymph nodes. These findings suggest that while Tregs are present in the intestines, their numbers might be insufficient to dampen the excessive inflammatory state in NEC. Adoptive transfer of Tregs attenuates the severity of NEC by limiting the immune response. Strategies to enhance Tregs have a therapeutic potential in controlling the development of NEC.