Changes In Microbial Populations Research Articles

Evaluation of Bacterial Contamination Sources in Meat Production Line

AbstractBacterial contamination during slaughtering process is a safety problem and concern for shelf life in meat production. We compare two different slaughter lines, sheep and cattle samples from Iranian slaughterhouse using PCR‐denaturing gradient gel electrophoresis (DGGE) analysis for evaluation the sources of bacterial contaminations.Bacterial diversity was significantly different between and within cattle and sheep slaughter lines. Samples are contaminated most frequently with Salmonella enterica (28% and 30%), Enterococcus fecalis (18% and 20%), Escherichia coli (13% and 14%) and Pseudomonas fluorescens (8% and 6%), either on equipment surfaces after general cleaning and sanitizing treatments (56%).Biodiversity of carcasses samples is increased during skinning and evisceration process and may indicate similar sources of contamination from hides and rectums of the animal to carcasses and environment.Practical Applications16S rDNA based denaturing gradient gel electrophoresis‐PCR is a method for assessment of microbial diversity, source of contaminations and changes of microbial population in slaughterhouses.

Changes of Soil Microbial Population and Structure Under Short-term Application of an Organically Enhanced Nitrogen Fertilizer

Changes of Soil Microbial Population and Structure Under Short-term Application of an Organically Enhanced Nitrogen Fertilizer

복합항균제제를 첨가한 생면의 미생물학적 및 이화학적 품질 특성

This study was conducted to investigate the effects of natural preservatives (G3, G3-1, F3, and F3-1) using Cordyceps militaris on improvement of food quality and safety of noodle during storage. Wheat flour noodle were prepared using three different concentrations of natural preservatives (0.100, 0.200, and 0.400%). Changes in microbial populations, pH value, titratable acidity, and sensory evaluation were measured during storage at 12±2℃ for 3 days. Overall, use of natural preservatives resulted in lower levels of total mesophilic bacteria, coliform, yeast and mold in noodle compared to the control. In particular, natural preservatives using 2× MIC concentrations (0.400%) of F3 and F3-1 were effective at maintaining levels of total mesophilic bacteria for noodle during storage. The pH values of noodle made with F3 and F3-1 were higher than the others. The titratable acidity of noodle with natural preservatives did not significantly change during storage. In sensory evaluation, appearance, color, and overall acceptability of noodle with F3 and F3-1 were preferred than the control. These results could provide useful information for developing an alternative preservation method to improve food quality and shelf-life of noodle using natural preservatives.

Wastewater ammonia removal using an integrated fixed-film activated sludge-sequencing batch biofilm reactor (IFAS-SBR): Comparison of suspended flocs and attached biofilm

Integrated fixed-film activated sludge (IFAS) that combines the activated sludge (suspended flocs) and attached biofilm has been applied in municipal wastewater treatment to promote nitrification. This study investigated the changes in reactor performance and bacterial community structure in response to different organic loadings (500, 250, 150 mg/L COD) in an integrated fixed-film activated sludge (IFAS) reactor operated under sequencing batch mode. Changes of bacterial population in the suspended flocs and attached biofilm were compared. Biomass in the suspended flocs and in biofilm decreased as the organic loading decreased. The specific nitrification rate was highest when COD was only 150 mg/L in the feeding, which highlighted the effects of competition between heterotrophic bacteria and autotrophic bacteria over oxygen and space. Besides, lack of carbon sources limited denitrification activities. The percentages of nitrifying related genes over total genes were higher in biofilms as compared to those in activated sludge flocs, indicating biofilm was a more favorable habitat for nitrifiers. In addition, extracellular polymeric substance (EPS) in biofilm and suspended flocs changed differently in response to the organic loading changes, which might also be related to the microbial population changes.

Salt-tolerant microorganisms treating hypersaline organic wastewater and the microbial population dynamics

ABSTRACT Halotolerant microorganism was domesticated and used for the treatment of hypersaline organic wastewater containing acetone and dichloroethane. The degradation performance and the microbial population changes of the activated sludge were investigated. The degradation performance of the domesticated activated sludge for acetone and dichloroethane (94.3% and 88.4%) was much better than the un- domesticated activated sludge (17.8% and 74.1%). The main strains in domesticated sludge were salt-tolerant strains for organics degradation, indicating that the microbial community has been effectively domesticated and cultured.

Vaginal microbial communities from synchronized heifers and cows with reproductive disorders.

To evaluate changes in the resident microbial population in the cranial vaginal mucosa induced by a progesterone-releasing intravaginal device (PRID) compared to the vaginal microbiota of cows with reproductive disorders. Vaginal discharge was evaluated by clinical examination and a Vaginitis Diagnosis Score was performed by exfoliative cytology. All samples classified as positive and some classified as negative by clinical evaluation were later diagnosed as positive for vaginitis by cytological analysis. Bacterial diversity profiles were performed by PCR-DGGE and clustered according to the reproductive health status of the specimens, revealing a correspondence between the structures of the communities in the vagina and the clinical profile. Representative bands from each group were sequenced and identified as Ruminococcus sp., Dialister sp., Escherichia sp./Shigella sp., Virgibacillus sp., Campylobacter sp., Helcoccoccus sp., Staphylococcus sp., Bacillus sp., Actinopolymorpha sp., Exiguobacterium sp., Haemophilus sp./Histophilus sp., Aeribacillus sp., Porphyromonas sp., Lactobacillus sp. and Clostridium sp. Our results contribute to the knowledge of the vaginal microbiome in synchronized heifers showing positive or negative clinical vaginitis. This study contributes to the understanding of a dynamic vaginal colonization by bacterial consortiums during the synchronization with a widely used PRID protocol. Also, the results reveal the presence of well-known metritis-related pathogens as well as emerging uterine opportunistic pathogens. The provided information will allow to carry out further studies to elucidate functional roles of these native micro-organisms in the bovine reproductive tract.

Plasmids from Shiga Toxin-Producing Escherichia coli Strains with Rare Enterohemolysin Gene ( ehxA ) Subtypes Reveal Pathogenicity Potential and Display a Novel Evolutionary Path

Bacterial plasmids are known to be key agents of change in microbial populations, promoting the dissemination of various traits, such as drug resistance and virulence. This study determined the genetic makeup of virulence plasmids from rare enterohemolysin subtype D and E Shiga toxin-producing E. coli strains. We demonstrated that ehxA subtype D plasmids represent a novel E. coli virulence plasmid, and although subtype D plasmids were derived from nonclinical isolates, they encoded a variety of virulence determinants that are associated with pathogenic E. coli In contrast, subtype E plasmids, isolated from strains recovered from severely ill patients, carry only a few virulence determinants. The results of this study reemphasize the plasticity and vast diversity among E. coli plasmids. This work demonstrates that, although E. coli strains of certain serogroups may not be frequently associated with disease, they should not be underestimated in protecting human health and food safety.

Biotransformation of 6:2 polyfluoroalkyl phosphates (6:2 PAPs): Effects of degradative bacteria and co-substrates

Polyfluoroalkyl phosphates (PAPs), a group of fluorotelomer alcohol (FTOH)-based surfactants commonly used in water- and grease-proof food contact paper, have been suggested as a direct source of human exposure to health-concerned perfluoroalkyl carboxylic acids (PFCAs). This study investigated factors affecting biotranformation of 6:2 polyfluoroalkyl phosphates (6:2 PAPs) by three known FTOH-degrading Pseudomonas strains (Pseudomonas butanovora, P. oleovorans, and P. fluorescens DSM 8341) under different co-substrate conditions and compared to that by activated sludge samples. The three pure strains transformed 6:2 PAPs into eight different per- and poly-fluoroalkyl carboxylic acids (PFCAs) and/or PFCA precursors. P. fluorescens DSM 8341 produced 5:2 sFTOH [CF3(CF2)4CH(OH)CH3] and P. oleovorans produced 5:2 ketone [CF3(CF2)4C(O)CH3] as the primary transformation product, respectively, with citrate having a minimal impact on the transformation. P. butanovora with lactate produced more diverse transformation products than those by any two strains. Activated sludge was more efficient at transforming 6:2 PAPs and produced more transformation products including PFHpA [CF3(CF2)5COOH] and PFPeA [CF3(CF2)3COOH], with 5:2 sFTOH as the most abundant product on day 30. The abundance of the alkane hydroxylase (alkB) gene related to alkane oxidation, the changes of total microbial population as well as their community structure in activated sludge during 6:2 PAPs biotransformation were also investigated.

Effects of corn silage and grass silage in ruminant rations on diurnal changes of microbial populations in the rumen of dairy cows

Here, we examined diurnal changes in the ruminal microbial community and fermentation characteristics of dairy cows fed total mixed rations containing either corn silage (CS) or grass silage (GS) as forage. The rations, which consisted of 52% concentrate and 48% GS or CS, were offered for ad libitum intake over 20 days to three ruminal-fistulated lactating Jersey cows during three consecutive feeding periods. Feed intake, ruminal pH, concentrations of short chain fatty acids and ammonia in rumen liquid, as well as abundance change in the microbial populations in liquid and solid fractions, were monitored in 4-h intervals on days 18 and 20. The abundance of total bacteria and Fibrobacter succinogenes increased in solids in cows fed CS instead of GS, and that of protozoa increased in both solid and liquid fractions. Feeding GS favored numbers of F. succinogenes and Selenomonas ruminantium in the liquid fraction as well as the numbers of Ruminobacter amylophilus, Prevotella bryantii and ruminococci in both fractions. Minor effects of silage were detected on populations of methanogens. Despite quantitative changes in the composition of the microbial community, fermentation characteristics were less affected by forage source. These results suggest a functional adaptability of the ruminal microbiota to total mixed rations containing either GS or CS as the source of forage. Diurnal changes in microbial populations were primarily affected by feed intake and differed between species and fractions, with fewer temporal fluctuations evident in the solid than in the liquid fraction. Interactions between forage source and sampling time were of minor importance to most of the microbial species examined. Thus, diurnal changes of microbial populations and fermentative activity were less affected by the two silages.

Biodiversity of Living, Non-marine, Thrombolites of Lake Clifton, Western Australia

ABSTRACTLake Clifton in Western Australia is recognized as a critically endangered ecosystem and the only thrombolite reef in the southern hemisphere. There have been concerns that increases in salinity and nutrient run-off have significantly impacted upon the thrombolite microbial community. Here we used cultivation-independent molecular approaches to characterize the microbial diversity of the thrombolites at Lake Clifton. The most dominant phyla currently represented are the Proteobacteria with significant populations of Bacteroidetes and Firmicutes. Cyanobacteria, previously invoked as the main drivers of thrombolite growth, represent only a small fraction (∼1–3% relative abundance) of the microbial community. We report an increase in salinity and nitrogen levels at Lake Clifton that may be contributing to a change in dominant microbial populations. This heightens concerns about the long-term health of the Lake Clifton thrombolites; future work is needed to determine if phyla now dominating this system are capable of the required mineral precipitation for continued thrombolite growth.

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment

Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane® 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions.

Identification of abiotic and biotic reductive dechlorination in a chlorinated ethene plume after thermal source remediation by means of isotopic and molecular biology tools

Thermal tetrachloroethene (PCE) remediation by steam injection in a sandy aquifer led to the release of dissolved organic carbon (DOC) from aquifer sediments resulting in more reduced redox conditions, accelerated PCE biodegradation, and changes in microbial populations. These changes were documented by comparing data collected prior to the remediation event and eight years later. Based on the premise that dual C-Cl isotope slopes reflect ongoing degradation pathways, the slopes associated with PCE and TCE suggest the predominance of biotic reductive dechlorination near the source area. PCE was the predominant chlorinated ethene near the source area prior to thermal treatment. After thermal treatment, cDCE became predominant. The biotic contribution to these changes was supported by the presence of Dehalococcoides sp. DNA (Dhc) and Dhc targeted rRNA close to the source area. In contrast, dual C-Cl isotope analysis together with the almost absent VC 13C depletion in comparison to cDCE 13C depletion suggested that cDCE was subject to abiotic degradation due to the presence of pyrite, possible surface-bound iron (II) or reduced iron sulphides in the downgradient part of the plume. This interpretation is supported by the relative lack of Dhc in the downgradient part of the plume. The results of this study show that thermal remediation can enhance the biodegradation of chlorinated ethenes, and that this effect can be traced to the mobilisation of DOC due to steam injection. This, in turn, results in more reduced redox conditions which favor active reductive dechlorination and/or may lead to a series of redox reactions which may consecutively trigger biotically induced abiotic degradation.Finally, this study illustrates the valuable complementary application of compound-specific isotopic analysis combined with molecular biology tools to evaluate which biogeochemical processes are taking place in an aquifer contaminated with chlorinated ethenes.

Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals

While changes in gut microbial populations have been described in human immuno-deficiency virus (HIV)-infected patients undergoing antiretroviral therapy (ART), the mechanisms underlying the contributions of gut bacteria and their molecular agents (metabolites and proteins) to immune recovery remain unexplored. To study this, we examined the active fraction of the gut microbiome, through examining protein synthesis and accumulation of metabolites inside gut bacteria and in the bloodstream, in 8 healthy controls and 29 HIV-infected individuals (6 being longitudinally studied). We found that HIV infection is associated to dramatic changes in the active set of gut bacteria simultaneously altering the metabolic outcomes. Effects were accentuated among immunological ART responders, regardless diet, subject characteristics, clinical variables other than immune recovery, the duration and type of ART and sexual preferences. The effect was found at quantitative levels of several molecular agents and active bacteria which were herein identified and whose abundance correlated with HIV immune pathogenesis markers. Although, we cannot rule out the possibility that some changes are partially a random consequence of the disease status, our data suggest that most likely reduced inflammation and immune recovery is a joint solution orchestrated by both the active fraction of the gut microbiota and the host.

Changes in Microbial Populations of WPC34 and WPC80 Whey Protein During Long-Term Storage

The effect of ambient relative humidity (70 and 90%, RH) and temperature and a 70 and 90% RH and temperatures (25, 30 and 35C) on microbial spoilage of whey protein concentrate (WPC34) and whey protein concentrate (WPC80) stored for up to 18 months were investigated. WPC34 and 80 were packaged in bags marked as standard (Std) and high performance (HP), and every 3 months changes in the behavior of aerobic mesophilic bacteria, yeast and mold and lipolytic bacteria were monitored. Initial populations of aerobic mesophilic bacteria in WPC80 and WPC34 averaged 2.7 and 1.6 log CFU/g, respectively. Yeast and mold populations of WPC34 in HP bags increased slightly during storage at 30 and 35C in a 70 and 90% RH, respectively, while lipolytic associated bacteria were not determined in the same samples. The pH of samples in all bags declined while water activity (aw) slightly increased during storage especially at higher RH and temperatures. Pratical Applications Information on the effect of adverse long-term storage conditions on whey protein concentrate (WPC) is needed for effective supply of this product to Africa and other semi-arid regions. This study investigated differences between ambient relative humidity storage, temperatures and type of bags on native microbial population, water activity and pH of WPC. It also, provides WPC manufacturers a better insight with regards to storage conditions and type of bags that can maintain longer shelf life. The data from this study could be used for quality control purposes and or development of a better bag suited for storage above ambient conditions.

Assessment of the biodegradability of selected sulfa drugs in two polluted rivers in Poland: Effects of seasonal variations, accidental contamination, turbidity and salinity

The aim of our study was to assess the aerobic biodegradation of four selected sulfonamides (sulfanilamide, sulfamethoxazole, sulfadiazine and sulfathiazole) using water samples drawn from highly polluted rivers. Additionally, we aimed to identify the factors that have a significant effect on the process efficiency.The 19 water samples were collected from Brynica and Czarna Przemsza rivers (in Poland) at the same location at approximately monthly intervals. A characteristic feature of the results is the presence of significant differences between the rates of sulfonamides biodegradation in particular samples.The sulfonamide most resistant to biodegradation was sulfamethoxazole, whereas sulfathiazole was most biodegradable. Seasonal variations and related microbial population changes had the most significant effects on sulfonamides biodegradation, e.g., the studied process was highly inhibited during wintertime. A decrease in the biodegradation rate in the river water could be caused by an accidental water pollution by industrial wastewater with heavy metals, an increase in salinity and a decrease in pH, and turbidity.

Enhanced bioreduction of iron and arsenic in sediment by biochar amendment influencing microbial community composition and dissolved organic matter content and composition

Biochar derived from the pyrolysis at 500°C with fresh biogas slurry and residue, was conducted to investigate its potential role in mediating the speciation and mobilization of As(V) and Fe(III) from arsenic-contaminated tailing mine sediment, with consideration of the changes in microbial populations and dissolved organic matter (DOM). The reduction of As(V) (10–13%) and Fe(III) (12–17%) were partly in response to biochar abiotically causing desorption and reduction effect, but were predominantly (87–90% and 83–88% for As(V) and Fe(III)) attributed to biochar stimulating biological reduction. The level of As(III) released from sediment upon biochar amendment (656.35±89.25μgL−1) was significantly higher than the level released without biochar amendment (98.06±19.38μgL−1) after 49 days incubation. Although a low level of Fe(II) (0.81±0.07mgL−1) was determined in the solution when amending with biochar, most of released Fe(II) (166.25±40.25mgL−1) was formed as biochar-Fe(II)minerals composite. More importantly, biochar stimulated the DOM bioavailability in association with bacterial activities mediating As(V) and Fe(III) reduction. High-throughput sequencing results indicated biochar application shifted the soil microbial community and increased the relative abundance of As(V)-/Fe(III)-reducing bacteria, mostly Geobacter, Anaeromyxobacter, Desulfosporosinus and Pedobacter. The discovery of biochar-bacteria-DOM consortium may broaden new understanding into speciation and mobilization of metals, which arouses attention to exploit feasible bioremediation for metal-contaminated sediment.

Bardoxolone Methyl Prevents High-Fat Diet-Induced Colon Inflammation in Mice.

Obesity induces chronic, low-grade inflammation, which increases the risk of colon cancer. We investigated the preventive effects of Bardoxolone methyl (BARD) on high-fat diet (HFD)-induced inflammation in a mouse colon. Male C57BL/6J mice (n=7) were fed a HFD (HFD group), HFD plus BARD (10 mg/kg) in drinking water (HFD/BARD group), or normal laboratory chow diet (LFD group) for 21 weeks. In HFD mice, BARD reduced colon thickness and decreased colon weight per length. This was associated with an increase in colon crypt depth and the number of goblet cells per crypt. BARD reduced the expression of F4/80 and CD11c but increased CD206 and IL-10, indicating an anti-inflammatory effect. BARD prevented an increase of the intracellular pro-inflammatory biomarkers (NF-қB, p NF-қB, IL-6, TNF-α) and cell proliferation markers (Cox2 and Ki67). BARD prevented fat deposition in the colon wall and prevented microbial population changes. Overall, we report the preventive effects of BARD on colon inflammation in HFD-fed mice through its regulation of macrophages, NF-қB, cytokines, Cox2 and Ki67, fat deposition and microflora.

Combined application of rice husk biochar and fly ash improved the yield of lowland rice

The effects of rice husk biochar (BC) and coal fly ash (FA) on growth and yield of rice and soil properties were investigated in a lowland rice soil. All growth parameters and yield were positively influenced by the integrated application of BC, FA and chemical fertilisers compared with sole application of chemical fertilisers. Yield increase was 16.4% when BC+FA was applied together with 50% of the recommended dose of nitrogen (N) compared with the recommended dose of N, phosphorus and potassium (NPK). Post-harvest soil analysis suggested that BC and FA both act as a supplier, as well as a reservoir of nutrients. Accumulation of heavy metals in soil and plant parts after harvest was below the toxicity threshold for plants and humans. There was also no significant change in microbial population compared with the initial soil. Therefore, combined application of BC and FA supplemented with chemical fertilisers could be recommended to improve soil fertility and crop productivity without affecting the soil quality.

In vitro extraction and fermentation of polyphenols from grape seeds (Vitis vinifera) by human intestinal microbiota.

The effects of several parameters on the extraction yield of total polyphenols from grape seeds by pressurized liquid extraction were investigated. The highest recovery of total polyphenols occurred at 80 °C within 5 min, and a single extraction allowed a recovery of more than 97% of total polyphenols. Following the purification with macroporous resin, the effects of grape polyphenols (>94.8%) on human intestinal microbiota were monitored over 36 h incubation by fluorescence in situ hybridization, and short-chain fatty acids (SCFAs) were measured by HPLC. The result showed that the grape polyphenols promoted the changes in the relevant microbial populations and shifted the profiles of SCFAs. Fermentation of grape polyphenols resulted in a significant increase in the numbers of Bifidobacterium spp. and Lactobacillus-Enterococcus group and inhibition in the growth of the Clostridium histolyticum group and the Bacteroides-Prevotella group, with no significant effect on the population of total bacteria. The findings suggest that grape polyphenols have potential prebiotic effects on modulating the gut microbiota composition and generating SCFAs that contribute to the improvements of host health.

유류오염 토양 내 석유계 탄화수소 화합물의 분해에 대한 퇴비의 시용 효과

BACKGROUND: Petroleum-contaminated soil from leaking above- and underground storage tanks and spillage during transport of petroleum products is widespread environmental problem in recent years. Application of compost may be the most promising, cost-effective, and eco-friendly technology for soil bioremediation because of its advantages over physical and chemical technology. The objective of this study was to evaluate effect of compost application on degradation of total petroleum hydrocarbon (TPH) in petroleum hydrocarbon-contaminated soil. METHOD AND RESULTS: An arable soil was artificially contaminated by diesel, and compost was applied at the different rate of 0, 10, 30, and 50 Mg/ha. Concentration of TPH in the soil decreased as application rate of compost increased. Degradation efficiency was highest at compost 30 Mg/ha; however, it slightly decreased with compost 50 Mg/ha. Kinetic modeling was performed to estimate the rates of chemical reaction. The correlation coefficient (R2) values for the linear plots using the second-order model were higher than those using the first-oder model. Compost 30 and 50 Mg/ha had the fastest TPH degradation rate in the second-order model. Change of microbial population in soil with compost application was similar to that of TPH. Microbial population in the soil increased as application rate of compost increased. Increasing microbial population in the contaminated soil corresponded to decreased in TPH concentration. CONCLUSION: Conclusively, compost application for soil bioremediation could be an effective response to petroleum hydrocarbon-contaminated soil. The increase in microbial population with compost suggested that compost application at an optimum rate might enhance degradation of TPH in soil.