Fermented Beverage Benefits: A Comprehensive Review and Comparison of Kombucha and Kefir Microbiome

Beverage fermentation is an ancient ritual that has been practised for millennia. It was slowly disappearing from households and communities due to the advancement of manufacturing technology and the marketing of soft drinks until the recent revival of the beverage fermentation culture due to an increase in the demand for health drinks amid the COVID-19 pandemic. Kombucha and kefir are two well-known fermented beverages that are renowned for their myriad of health benefits. The starter materials for making these beverages contain micro-organisms that act like microscopic factories producing beneficial nutrients that have antimicrobial and anticancer effects. The materials modulate the gut microbiota and promote positive effects on the gastrointestinal tract. Due to wide variations in the substrates and types of micro-organisms involved in the production of both kombucha and kefir, this paper compiles a compendium of the micro-organisms present and highlights their nutritional roles.

Functional diversity can facilitate the collapse of an undesirable ecosystem state

Biodiversity may increase ecosystem resilience. However, we have limited understanding if this holds true for ecosystems that respond to gradual environmental change with abrupt shifts to an alternative state. We used a mathematical model of anoxic-oxic regime shifts and explored how trait diversity in three groups of bacteria influences resilience. We found that trait diversity did not always increase resilience: greater diversity in two of the groups increased but in one group decreased resilience of their preferred ecosystem state. We also found that simultaneous trait diversity in multiple groups often led to reduced or erased diversity effects. Overall, our results suggest that higher diversity can increase resilience but can also promote collapse when diversity occurs in a functional group that negatively influences the state it occurs in. We propose this mechanism as a potential management approach to facilitate the recovery of a desired ecosystem state.

Causative Micro-Organisms in Necrotizing Fasciitis and their Influence on Inflammatory Parameters and Clinical Outcome

Background: Necrotizing fasciitis (NF) is a potentially fatal soft tissue infection. Four types of pathogens can be distinguished in the pathogen spectrum, although there are strong regional differences with regard to the most common pathogens. Patients and Methods: All cases of NF between 2003 and 2021 with an identified causative agent were analyzed retrospectively. The cases were divided into three groups: polymicrobial, gram-positive and gram-negative. Demographic factors, localization of infection, inflammatory parameters, and clinical outcome were compared between the three groups. Results: A total of 95 cases were analyzed, 41% of which were caused by multiple pathogens. A gram-positive pathogen was reported in 40% of cases and a gram-negative pathogen in 19%. There were significant differences between the three groups with respect to age (with patients in the gram-negative group being on average the oldest) and intensive care unit admissions (which was most frequent in the polymicrobial group). Conclusions: The pathogen spectrum of NF has rarely been studied in a large patient population. Gram-positive pathogens account for the majority of monomicrobial infections in our study. Nevertheless, we recommend calculated broad-spectrum antibiotic therapy given the high number of polymicrobial infections and gram-negative infections. Gram-negative infections may be associated with increased mortality, elevated procalcitonin levels, and are relatively frequent in NF of the lower extremities.

Evaluation of Culture Top transport systems for assessing the bacterial diversity of microbiota by culturomics as compared to a routine transport system

In recent years, metagenomics and then culturomics, which consists of the multiplication of media and culture conditions and the rapid identification of all bacterial colonies, have generated renewed interest in the human microbiota, and diseases associated with modifications in its composition in particular. The sample transport media included in diverse swab transport systems and the storage conditions are among the factors that influence the results of the culturomics. In this study, we compared the results of culturomics from paired skin, oral and rectal swabs from intensive care unit (ICU) patients using Culture Top sample transport medium as compared to our routine one. From 152 clinical samples, we were able to isolate and identify 45 600 colonies, belonging to 338 different bacterial species. The transport system Culture Top identified 282 different bacterial species, while 244 were identified by our routine system. Of these, 188 different bacterial species were commonly identified using both transport systems, while 94 (27.8 %) and 56 (16.5 %) were only identified using Culture Top and our routine system, respectively (P<0.001), but there was no significant difference in bacterial diversity at the genus or phylum level, or in terms of their type of respiration and cell wall. In conclusion, the Culture Top transport system appears to be complementary to our routine system, although it seems slightly superior in terms of isolated bacterial species.

Mechanistically acting anti-obesity compositions/formulations of natural origin: a patent review (2010-2021)

Introduction: Current health trends indicate that the rate of incidence of obesity has risen considerably. According to the World Health Organization (WHO) report 2017, the issue of obesity has grown to an epidemic proportion, with over 4 million people dying every year. Orlistat, a potent pancreatic lipase (PL) inhibitor for long-term treatment of obesity has been recently reported to cause hepatic and renal toxicities. Hence, there is a need to develop newer, safer and efficacious therapeutics that targets obesity and its associated disorders.Areas covered: The present article attempts to review patents on compositions of natural origin that include either combination of two or more lead NPs/whole extract(s)/ mixture of one or more NPs/extracts from various plants and micro-organisms. Patents that were granted during the period 2010 to 2021 have been considered.Expert opinion: The article highlights the recent trends in the rise of the global obesity population. Patents are classified based on the mechanism of action of extracts/NPs. It has been observed that in the years 2013, 2017 and 2019 maximum number of patents from China, South Korea, United States and Japan have been filed for the anti-obesity compositions.

Microbial contamination profile change over a 4-year period in nonoperated cleft soft palate

AIMS

Surgical site infection is a major concern in cleft soft palate. Knowledge of the type, number and antimicrobial resistance of pathogens present preoperatively contribute to treatment success. The aim of this study is to determine whether or not the microbial contamination (diversity) preoperatively has changed since 2015.

METHODS AND RESULTS

Swabs were taken from the surgical site in 103 consecutive patients who presented for primary repair of the soft palate cleft. These were sent for microscopy, culture and sensitivity testing. Swabs were taken before disinfecting the site. Results were tabled and compared with two previous studies from the same facility. Out of 103 patients, 100 patients showed positive cultures with 42 different pathogenic micro-organisms identified. Most dominant pathogen was Klebsiella pneumoniae, 45.6%, increased by 28% from the previous two studies, with 93.6% of these pathogens resistant to one or more antimicrobials. Most of the other identified pathogens showed an alarming increase in occurrence, with a wide resistance to antimicrobials.

CONCLUSIONS

The increase in number and diversity of microbial contamination as well as their resistance to antimicrobials is a real concern. Ways of preventing postoperative infection in a natural way need to be explored.

SIGNIFICANCE

Surgeons need to be aware of constant changes in micro-organisms.

Microbial production of beneficial indoleamines (serotonin and melatonin) with potential application to biotechnological products for human health

Micro-organisms have showed the ability to produce biologically active compounds associated with neurotransmission in higher organisms. In particular, serotonin- and melatonin-producing microbes are valuable sources for the development of eco-friendly bioproducts. Serotonin and melatonin are indoleamines that have received special attention due to their positive effects on human health. These biomolecules exert a critical role in several physiological or pathological processes, including some mental and neurological disorders. This article includes a review of the microbial production of serotonin and melatonin, their functions in micro-organisms and their potential uses as therapeutic and/or preventive agents to improve human health. A description of the quantification methods employed to detect indoleamines and the evidence found concerning their microbial production at laboratory and industrial scale-for application in biotechnological products-is also provided. The microbial ability to synthesize beneficial indoleamines should be further studied and harnessed, to allow the development of sustainable bioprocesses to produce foods and pharmaceuticals for human health.

Combined carbon flows through detritus, microbes, and animals in reference and experimentally enriched stream ecosystems

Tracking carbon (C) flow through ecosystems requires quantification of myriad biophysical processes, including C routing through microbial and metazoan food webs. Yet detailed organic matter budgets are rarely combined with simultaneous measurement of C flows supporting microbial and animal production. Here, we synthesize concurrent data sets on organic matter, microbes, and macroinvertebrates from two detritus-based stream ecosystems, one of which was subject to experimental nitrogen (N) and phosphorus (P) enrichment. Our synthesis provides new insights into C flow through forest stream ecosystems. Over 3 yr, the reference stream showed a striking balance of inputs and outputs, with a mean surplus of only 7 g C·m^-2 ·yr^-1 (~1% of annual inputs), presumably stored in sediments as fine particulate organic matter (FPOM). In contrast, N and P enrichment over 2 yr resulted in severe deficits of C (-576 g C·m^-2 ·yr^-1 or ~170% of annual inputs), a shortfall presumably met by stored C. Our data set provides an ecosystem-based estimate of the fate of forest litter C at ambient nutrient concentrations: 6.2% was leached as dissolved organic C, 40.6% and 8.5% flowed to litter-associated fungi and bacteria, respectively, 7.5% was consumed by macroinvertebrates, 1.8% was exported as coarse particles, and the remainder (35.4%) was presumably fragmented by biophysical processes. Our calculations also allowed an estimate of inputs into the heterogeneous FPOM pool, which is otherwise difficult to obtain. At naturally low nutrient concentrations, 50.7% was derived from fragmented litter, 39.1% from microbial biomass (mostly fungal), and 10.2% from macroinvertebrate egesta. Nutrient addition drove large changes in C fluxes in the experimental stream, especially in flows of leaf litter to fungi (×1.7 pretreatment) and macroinvertebrates (×2.7), and of FPOM to hydrologic export (×2.6). Our results underscore the key roles of both microbes and metazoans in controlling C flow through detritus-based ecosystems, as well as how release from persistent nutrient limitation may perturb steady-state conditions of C inputs vs. outputs. Our analysis also suggests areas for future research, including assessing the relative importance of stored vs. recycled C in fueling detrital food webs subject to altered nutrient regimes and other global-change drivers.

Possible food safety hazards of ready-to-eat raw fish containing product (sushi, sashimi)

It is undeniable that with the popularity of sushi and sashimi over the last decade the consumption of raw fish has extremely increased. Raw fish is very appreciated worldwide and has become a major component of human diet because of its fine taste and nutritional properties. Possible hazards concerning fish safety and quality are classified as biological and chemical hazards. They are contaminants that often accumulate in edible tissue of fish and transmit to humans via the food chain affecting the consumer's health. Although their concentration in fish and fishery products are found at non-alarming level of a daily basis period, they induce hazardous outcome on human health due to long and continuous consumption of raw fish. Regular sushi and sashimi eaters have to be aware of the contaminants found in the other components of their dish that often add up to acceptable residue limits found in fish. Hence, there is the urge for effective analytical methods to be developed as well as stricter regulations to be put in force between countries to monitor the safety and quality of fish for the interest of public health.

Polyester-based biodegradable plastics: an approach towards sustainable development

Non-degradability of conventional plastics, filling of landfill sites, raising water and land pollution and rapid depletion of fossil resources have raised the environmental issues and global concerns. The current demand and production of plastics is putting immense pressure on fossil resources, consuming about 6% of the global oil and is expected to grow up to 20%. The polyester-based biodegradable plastics (BPs) are considered as a remedy to the issue of plastics waste in the environment. BPs appear to manage the overflow of plastics by providing new means of waste management system and help in securing the non-renewable resources of nature. This review comprehensively presents the environmental burdens due to conventional plastics as well as production of polyester-based BPs as an alternative to conventional commodity plastics. The diversity of micro-organisms and their enzymes that degrade various polyester-based BPs (PLA, PCL, PHB/PHBV and PET) has also been described in detail. Moreover, the impact of plastics degradation products on soil ecology and ecosystem functions has critically been discussed. The report ends with special focus on future recommendations for the development of sustainable waste management strategies to control pollution due to plastics waste. SIGNIFICANCE AND IMPACT OF THE STUDY: Polyester-based BPs considered as a solution to current plastic waste problem as well as leading polymers in terms of biodegradability and sustainability has been critically discussed. The role of microorganisms and their enzymes involved in the biodegradation of these polymers and ecotoxicological impact of degradation products of BPs on soil microbial community and biogeochemical cycles has also been described. This report will provide an insight on the key research areas to bridge the gap for development of simulated systems as an effective and emerging strategy to divert the overflow of plastic in the environment as well as for the greener solution to the plastic waste management problems.

A method to evaluate factors influencing the microbial reduction in domestic dishwashers

AIMS

To develop a method that is able to determine the microbial reduction in different dishwasher cleaning cycles and differentiate between different program parameters used.

METHODS AND RESULTS

Stainless steel biomonitors were contaminated with Micrococcus luteus or Entereococcus faecium and cleaned in a specially programmed household dishwasher with different cleaning temperatures and durations. No detergent, bleach-free detergent or detergent containing activated oxygen bleach was used. The logarithmic reduction (LR) was determined. The microbial reduction depended on the cleaning temperature, the duration of the cleaning cycles and the detergent type used. LR increased with higher temperatures, longer cleaning cycles and use of detergent.

CONCLUSIONS

The factors cleaning cycle temperature, cleaning cycle duration, final rinsing temperature and the use of detergent all contributed to the reduction of test-strains in dishwasher cycles. A combination of longer dishwashing cycles and increased temperatures resulted in LR_max of the microbial load.

SIGNIFICANCE AND IMPACT OF THE STUDY

Cycles in domestic appliances are very diverse; therefore a standardized method to determine their ability to reduce the microbial load is of great use. The method described here is able to demonstrate the reductions achieved by dishwashing cycles with different parameters and might help to find the necessary balance between energy saving and an acceptable level of hygiene.

Early Host Interactions That Drive the Dysregulated Response in Sepsis

Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. While many individual cells and systems in the body are involved in driving the excessive and sometimes sustained host response, pathogen engagement with endothelial cells and platelets early in sepsis progression, are believed to be key. Significant progress has been made in establishing key molecular interactions between platelets and pathogens and endothelial cells and pathogens. This review will explore the growing number of compensatory connections between bacteria and viruses with platelets and endothelial cells and how a better understanding of these interactions are informing the field of potential novel ways to treat the dysregulated host response during sepsis.

Biosurfactant production by yeasts from different types of soil of the South Shetland Islands (Maritime Antarctica)

AIM

To screen and identify a potential biosurfactant-producing yeast strain isolated from Antarctic soil and to evaluate the fermentation process kinetics of the most promising strain on biosurfactant production using glycerol as carbon source.

METHODS AND RESULTS

From the 68 isolated yeast strains, 11 strains were able to produce biosurfactants after Emulsification Index (E.I.) and Drop Collapse tests, reaching an E.I. higher than 10%. Strain 1_4.0 was the best producer, identified as Candida glaebosa based on molecular analysis. Yeast was cultivated in a medium composed of glycerol supplemented with yeast extract for 120 h to determine the process kinetics. The increased C/N ratio affected yeast growth and biosurfactant production. Biosurfactant release was associated with the end of exponential and beginning of the stationary growth phases. Results indicated an E.I. of 30% at the end of the fermentation.

CONCLUSIONS

The feasiability of C. glaebosa to produce biosurfactant from a low-cost medium cultivation shows a great impact on the development of bioresource in the Antarctica terrestrial environment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Although the diversity of psychrophilic/psychrotolerant micro-organisms from Antarctica has been the preferred subject of study by microbiologists, terrestrial microfungal communities are scarcely investigated and literature about the biotechnological potential of such micro-organisms should cover important biomolecules in addition to cold-adapted enzymes. In the present study, for the first time, the Maritime Antarctica environment was screened as a novel source of biosurfactants produced by micro-organisms.

Clinically applicable irreversible electroporation for eradication of micro-organisms

Irreversible electroporation (IRE) damages cell membranes and is used in medicine for nonthermal ablation of malignant tumours. Our aim was to evaluate the antimicrobial effect of IRE. The pathogenic micro-organisms, Staphylococcus aureus, Streptococcus pyogenes, Escherichia coli, Pseudomonas aeruginosa and Candida albicans were subjected to IRE. Survival was measured as a function of voltage and the number of pulses applied. Combined use of IRE and oxacillin for eradication of Staph. aureus was also tested. Log10 reduction in micro-organisms positively correlated with the number of applied pulses. The colony count of Strep. pyogenes and E. coli declined by 3·38 and 3·05 orders of magnitude, respectively, using an electric field of 2000 V and 100 pulses. Killing of Staph. aureus and P. aeruginosa was achieved with a double cycle of IRE (2000, 1500 V and repeated 1250 V respectively) of 50-100 IRE pulses. The addition of subclinical inhibitory concentrations of oxacillin to the Staph. aureus suspension prior to IRE led to total bacterial death, demonstrating synergism between oxacillin and IRE. Our results demonstrate that using IRE with clinically established parameters has a marked in vitro effect on pathogenic micro-organisms and highlights the potential of IRE as a treatment modality for deep-seated infections, particularly when combined with low doses of antibiotics.

SIGNIFICANCE AND IMPACT OF THE STUDY

Irreversible electroporation (IRE) is utilized in interventional radiology to treat cancer patients. In this study we evaluated in vitro the antimicrobial effect of IRE. We demonstrated that using IRE with clinically established parameters has a marked effect on pathogenic micro-organisms and is synergistic to antimicrobials when both are combined. Our results point to the potential of IRE as a treatment modality for deep-seated infections.

Micro-organisms growing on rapeseed during storage affect the profile of volatile compounds of virgin rapeseed oil

BACKGROUND

Micro-organisms populate on rapeseed after harvest during storage depending on the growing conditions. The composition of the bacterial colonization is unknown, although its contribution to the profile of volatile aroma-active compounds determines the sensory quality of virgin cold-pressed rapeseed oil.

RESULTS

From four rapeseed samples, 46 bacterial strains were isolated. By DNA-sequencing, the identification of four bacteria species and 17 bacteria genera was possible. In total, 22 strains were selected, based on their typical off-flavors resembling those of virgin sensory bad cold-pressed rapeseed oils. The cultivation of these strains on rapeseed meal agar and examination of volatile compounds by solid phase microextraction-gas chromatography-mass spectrometry allowed the identification of 29 different compounds, mainly degradation products of fatty acids such as alkanes, alkenes, aldehydes, ketones and alcohols and, in addition, sulfur-containing compounds, including one terpene and three pyrazines. From these compounds, 19 are described as aroma-active in the literature.

CONCLUSION

Micro-organisms populating on rapeseed during storage may strongly influence the sensory quality of virgin rapeseed oil as a result of the development of volatile aroma-active metabolic products. It can be assumed that occurrence of off-flavor of virgin rapeseed oils on the market are the result of metabolic degradation products produced by micro-organisms populating on rapeseed during storage. © 2017 Society of Chemical Industry.

Contact killing and antimicrobial properties of copper

With the emergence of antibiotic resistance, the interest for antimicrobial agents has recently increased again in public health. Copper was recognized in 2008 by the United States Environmental Protection Agency (EPA) as the first metallic antimicrobial agent. This led to many investigations of the various properties of copper as an antibacterial, antifungal and antiviral agent. This review summarizes the latest findings about 'contact killing', the mechanism of action of copper nanoparticles and the different ways micro-organisms develop resistance to copper.

Dynamics of a vertical-flow windrow vermicomposting system

Large-scale vermicomposting under outdoor conditions may differ from small-scale procedures in the laboratory. The present study evaluated changes in selected properties of a large-scale vertical-flow windrow vermicomposting system with continuous feeding with household biowaste. The windrow profile was divided into five layers of differing thickness and age after more than 12 months of vermicomposting. The top layer (0-30 cm, age <3 months) was characterised by partially decomposed organic matter with a high pH value and an elevated carbon/nitrogen (C/N) ratio. The earthworm biomass was 15 g kg^-1 with a population density of 125 earthworms per kilogram predominantly found in clusters. The greatest amount of fungi (3.5 µg g^-1 dw) and bacteria (62 µg g^-1 dw) (expressed as phospholipid fatty acid analysis) was found in this layer. Thus, the top layer could be used for an additional cycle of windrow vermicomposting and for the preparation of aqueous extracts to protect plants against diseases. The lower layers (graduated by 30 cm and by 3 months of age) were mature as reflected by the low content of ammonia nitrogen, ratio of ammonia to nitrate nitrogen and dissolved organic carbon, and high ion-exchange capacity and its ratio to carbon. These layers were characterised by elevated values for electrical conductivity, total content of nutrients, available magnesium content, and a relatively large bacterial/fungal ratio. On the basis of the observed properties, the bottom layers were predetermined as effective fertilisers.

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms

Biological treatment represents a key step in nutrient removal from wastewater. Until now these process has mainly been considered prokaryotic, with the interactions between prokaryotes and eukaryotes not being properly explored. We therefore investigated the co-occurrence of eukaryotes and prokaryotes in biological nitrogen removal biofilms. We found that biofilms in the nitrifying reactor contained the highest diversity and abundance of both prokaryotes and eukaryotes, with nearly three times higher prokaryote species richness than for the denitrifying reactor. The positive associations between eukaryote abundance and prokaryote diversity could potentially be explained by mutualism - and/or predator/prey interactions. Further mechanistic insight, however, is needed to determine the main diversifying mechanisms. In summary, eukaryote and prokaryote interactions seem to play a fundamental yet underexplored role in biological wastewater treatment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Eukaryote and prokaryote interactions may play an important role in wastewater treatment. This study found that prokaryote species richness was nearly three times higher in the aerobe nitrification than in an anaerobe denitrification reactor, coinciding with the highest level of eukaryotes. This knowledge can be important in process control, and potentially in the development of novel approaches based on nitrate accumulating denitrifying eukaryotes.

Incidence and Antimicrobial Sensitivity Profiles of Normal Conjunctiva Bacterial Flora in the Central Area of China: A Hospital-Based Study

Objective: To study the distribution and patterns of resistance to antimicrobial agents of normal conjunctival bacteria. Materials and Methods: Conjunctival specimens were collected from 8,224 patients and then cultured, which underwent antimicrobial susceptibility test following standard methods. Patients with infectious symptoms such as erythema or oedema and those using systemic or topical antibiotics within 1 month were excluded. Results: In this study, the incidence of isolated bacteria was 24.2%. The middle aged group of 41-65 years presented the lowest rate of bacterial isolation which was 19.4%, while the highest isolation rate (83.1%) was found in patients in the age range of 0-6 years. In every age group, the incidence of bacterial isolation in men was higher than that in women. The top 3 most commonly isolated micro-organisms were Staphylococcus epidermidis (39.7%), Streptococcus pneumoniae (4.5%), and Staphylococcus aureus (2.7%), of which about 83.1% S. aureus were isolated in the group of 0-6 years. We found that coagulase-negative Staphylococcus (CONS) were more resistant to penicillin, macrolides, clindamycin and sulfonamides with the rate ranging from 57.9 to 90.8%, which were highly susceptible to vancomycin, linezolid, rifampin, tetracyclines, and aminoglycosides. Contrasting to CONS, the general resistance rate of S. aureus was significantly lower. Additionally, Streptococcus was susceptible well to the majority of antimicrobial agents, while highly resistant to macrolides and tetracyclines with the rate >80%. Conclusions: In conclusion, our study revealed the incidence and antimicrobial sensitivity profiles of normal conjunctiva bacterial flora in the central area of China, which could be useful in the prevention of ocular infections. Importantly, our data could be used to guide the selection of appropriate prophylactic agents.

Biotic and environmental dynamics through the Late Jurassic-Early Cretaceous transition: evidence for protracted faunal and ecological turnover

The Late Jurassic to Early Cretaceous interval represents a time of environmental upheaval and cataclysmic events, combined with disruptions to terrestrial and marine ecosystems. Historically, the Jurassic/Cretaceous (J/K) boundary was classified as one of eight mass extinctions. However, more recent research has largely overturned this view, revealing a much more complex pattern of biotic and abiotic dynamics than has previously been appreciated. Here, we present a synthesis of our current knowledge of Late Jurassic-Early Cretaceous events, focusing particularly on events closest to the J/K boundary. We find evidence for a combination of short-term catastrophic events, large-scale tectonic processes and environmental perturbations, and major clade interactions that led to a seemingly dramatic faunal and ecological turnover in both the marine and terrestrial realms. This is coupled with a great reduction in global biodiversity which might in part be explained by poor sampling. Very few groups appear to have been entirely resilient to this J/K boundary 'event', which hints at a 'cascade model' of ecosystem changes driving faunal dynamics. Within terrestrial ecosystems, larger, more-specialised organisms, such as saurischian dinosaurs, appear to have suffered the most. Medium-sized tetanuran theropods declined, and were replaced by larger-bodied groups, and basal eusauropods were replaced by neosauropod faunas. The ascent of paravian theropods is emphasised by escalated competition with contemporary pterosaur groups, culminating in the explosive radiation of birds, although the timing of this is obfuscated by biases in sampling. Smaller, more ecologically diverse terrestrial non-archosaurs, such as lissamphibians and mammaliaforms, were comparatively resilient to extinctions, instead documenting the origination of many extant groups around the J/K boundary. In the marine realm, extinctions were focused on low-latitude, shallow marine shelf-dwelling faunas, corresponding to a significant eustatic sea-level fall in the latest Jurassic. More mobile and ecologically plastic marine groups, such as ichthyosaurs, survived the boundary relatively unscathed. High rates of extinction and turnover in other macropredaceous marine groups, including plesiosaurs, are accompanied by the origin of most major lineages of extant sharks. Groups which occupied both marine and terrestrial ecosystems, including crocodylomorphs, document a selective extinction in shallow marine forms, whereas turtles appear to have diversified. These patterns suggest that different extinction selectivity and ecological processes were operating between marine and terrestrial ecosystems, which were ultimately important in determining the fates of many key groups, as well as the origins of many major extant lineages. We identify a series of potential abiotic candidates for driving these patterns, including multiple bolide impacts, several episodes of flood basalt eruptions, dramatic climate change, and major disruptions to oceanic systems. The J/K transition therefore, although not a mass extinction, represents an important transitional period in the co-evolutionary history of life on Earth.

The effects of food web structure on ecosystem function exceeds those of precipitation

Ecosystems are being stressed by climate change, but few studies have tested food web responses to changes in precipitation patterns and the consequences to ecosystem function. Fewer still have considered whether results from one geographic region can be applied to other regions, given the degree of community change over large biogeographic gradients. We assembled, in one field site, three types of macroinvertebrate communities within water-filled bromeliads. Two represented food webs containing both a fast filter feeder-microbial and slow detritivore energy channels found in Costa Rica and Puerto Rico, and one represented the structurally simpler food webs in French Guiana, which only contained the fast filter feeder-microbial channel. We manipulated the amount and distribution of rain entering bromeliads and examined how food web structure mediated ecosystem responses to changes in the quantity and temporal distribution of precipitation. Food web structure affected the survival of functional groups in general and ecosystem functions such as decomposition and the production of fine particulate organic matter. Ecosystem processes were more affected by decreased precipitation than were the abundance of micro-organisms and metazoans. In our experiments, the sensitivity of the ecosystem to precipitation change was primarily revealed in the food web dominated by the single filter feeder-microbial channel because other top-down and bottom-up processes were weak or absent. Our results show stronger effects of food web structure than precipitation change per se on the functioning of bromeliad ecosystems. Consequently, we predict that ecosystem function in bromeliads throughout the Americas will be more sensitive to changes in the distribution of species, rather than to the direct effects caused by changes in precipitation.

Live yeasts enhance fibre degradation in the cow rumen through an increase in plant substrate colonization by fibrolytic bacteria and fungi

AIMS

To monitor the effect of a live yeast additive on feedstuff colonization by targeted fibrolytic micro-organisms and fibre degradation in the cow rumen.

METHODS AND RESULTS

Abundance of adhering fibrolytic bacteria and fungi on feedstuffs incubated in sacco in the cow rumen was quantified by qPCR and neutral detergent fibre (NDF) degradation was measured. Saccharomyces cerevisiae I-1077 (SC) increased the abundance of fibre-associated Fibrobacter succinogenes on wheat bran (WB) and that of Ruminococcus flavefaciens on alfalfa hay (AH) and wheat silage (WS). The greatest effect was observed on the abundance of Butyrivibrio fibrisolvens on AH and soya hulls (SH) (P < 0·001). Fungal biomass increased on AH, SH, WS and WB in the presence of SC. NDF degradation of AH and SH was improved (P < 0·05) with SC supplementation.

CONCLUSIONS

Live yeasts enhanced microbial colonization of fibrous materials, the degree of enhancement depended on their nature and composition. As an effect on rumen pH was not likely to be solely involved, the underlying mechanisms could involve nutrient supply or oxygen scavenging by the live yeast cells.

SIGNIFICANCE AND IMPACT OF THE STUDY

Distribution of this microbial additive could be an interesting tool to increase fibre digestion in the rumen and thereby improve cow feed efficiency.

Pathological evaluation for sterilization of routinely used prosthodontic and endodontic instruments

Background:

In daily practice of dentistry, we use same instruments on many patients. Before use, all instruments must be cleaned, disinfected, and sterilized to prevent any contamination. Pre-cleaning and sterilization of some devices can be difficult because of their small size and complex architecture. Dental burs and endodontic files are such instruments. Dental burs come in a variety of shapes and sizes, all with highly complex and detailed surface features.

Aim:

To determine the effectiveness of various disinfectants and sterilization techniques for disinfection and resterilization of dental burs and endodontic files.

Materials and Methods:

The materials used for the study were dental burs and endodontic files. Disinfectants used were Quitanet plus, glutaraldehyde, glass-bead sterilizer, and autoclave. The sterility of used dental burs and endodontic files was analyzed. Burs and files that had been used were pre-cleaned, resterilized, and then tested for various pathogens. Each item was transferred by sterile technique into Todd-Hewitt broth, incubated at 37°C for 72 h, and observed for bacterial growth.

Results:

The present study shows that the endodontic files and burs sterilized by autoclaving and glutaraldehyde showed complete sterilization. Burs and files immersed in glutaraldehyde (2.4%) for 12 h showed complete sterilization, whereas Quitanet plus solution and glass-bead sterilizer showed incomplete sterilization.

Conclusion:

The present study results indicate that autoclaving and glutaraldehyde (2.4%) showed complete sterilization. Other methods cannot be relied upon for sterilization.

Metabolic engineering for isoprenoid-based biofuel production

Sustainable economic and industrial growth is the need of the hour and it requires renewable energy resources having better performance and compatibility with existing fuel infrastructure from biological routes. Isoprenoids (C ≥ 5) can be a potential alternative due to their diverse nature and physiochemical properties similar to that of petroleum based fuels. In the past decade, extensive research has been done to utilize metabolic engineering strategies in micro-organisms primarily, (i) to overcome the limitations associated with their natural and non-natural production and (ii) to develop commercially competent microbial strain for isoprenoid-based biofuel production. This review briefly describes the engineered isoprenoid biosynthetic pathways in well-characterized microbial systems for the production of several isoprenoid-based biofuels and fuel precursors.

In vitro antimicrobial and anti-endotoxin action of Zingiber Officinale as auxiliary chemical and medicament combined to calcium hydroxide and chlorhexidine

OBJECTIVE

This study was conducted in vitro to compare the effectiveness of Zingiber Officinale as an auxiliary chemical substance followed by placement of different intra-canal medication in removing endotoxins and cultivable micro-organisms from infected root canals.

MATERIALS AND METHODS

Seventy-two root canals were contaminated with Enterococcus faecalis, Candida albicans and Escherichia coli for 28 days. After, the teeth were instrumented using Zingiber Officinale and divided into six groups according to the intra-canal medication: chlorhexidine gel; calcium hydroxide + chlorhexidine gel; glycolic ginger extract; calcium hydroxide + glycolic ginger extract; calcium hydroxide + saline solution and saline solution (control). Sample collections were performed after root canal contamination (Baseline; S1), after instrumentation (S2), 7 days after instrumentation (S3), after 14 days with intra-canal medication (S4) and 7 days after removal of intra-canal medication (S5). The results were analyzed by the Kruskal-Wallis and Dunn tests.

RESULTS

It was observed that in S2 and S3 there was significant reduction of the micro-organisms and the quantity of endotoxins after instrumentation. In samples S4 and S5 there was complete elimination of micro-organisms and significant reduction of endotoxins.

CONCLUSION

It was concluded that Zingiber Officinale as an auxiliary chemical substance was effective on the micro-organisms tested, yet was unable to eliminate the endotoxins. Similarly, the intra-canal medication were effective on micro-organisms, yet did not completely eliminate the endotoxins.

Influence of Ni2+ on urease activity produced by biofilms of Arthrobacter oxydans 1388

New TiO₂-based hybrid materials composed of an organic polymer, cellulose acetate butyrate and copolymer of acrylonitrile acrylamide (AN + AA) were prepared. The effectiveness of immobilization of microbial strain Arthrobacter oxydans 1388 on the newly synthesized hybrid membranes was investigated by biochemical methods. The obtained results revealed that the matrix more suitable for biofilm formation was composed of organic polymers without a metal component in the membrane composition. The influence of Ni²⁺ on urease activity produced by biofilms was investigated. The experimental results demonstrated that 2 mg L^-1 concentration of Ni²⁺ in the nutrient medium is more appropriate for biofilm proliferation.

Diversity of cultivable β-glycosidase-producing micro-organisms isolated from the soil of a ginseng field and their ginsenosides-hydrolysing activity

This research aimed to explore the diversity of cultivable β-glycosidase-producing micro-organisms in ginseng field soil. Fifty-three strains showing β-glucosidase activity were isolated from a ginseng field, using a newly designed Esculin-R2A agar. All the isolated strains belonged to the genus Agrobacterium, Arthrobacter, Burkholderia, Dyella, Edaphobacter, Luteibacter, Mucilaginibacter, Paenibacillus, Phenylobacterium, Pseudomonas, Sphingomonas and Streptomyces. The main β-glucosidase-producing micro-organisms in the ginseng field soil were Sphingomonas, Burkholderia, Luteibacter and Streptomyces, while concentrations of Agrobacterium, Arthrobacter, Paenibacillus and Pseudomonas were relatively low. Of these micro-organisms, the strain GS 09 could hydrolyse major ginsenosides Rb1, Rb2 and Rc to the active metabolite compound K. The strain GS 09 belonged to the genus Sphingomonas, and its 16S rRNA gene sequence showed 100% similarities with that of Sphingomonas asaccharolytica.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to provide information of cultivable β-glycosidase-producing micro-organisms in ginseng field soil. The strain GS 09 has potential to be applied on the preparation for minor ginsenoside C-K in pharmaceutical industry.

Profile of micro-organisms in intensive care unit of a level-1 trauma centre: A retrospective study

Background:

Patients with trauma usually require highly specialized care in ICU and many times their recovery is complicated by infections. Aim of this study was to determine the profile of pathogens and their impact on outcome among these patients.

Materials and Methods:

The clinical records of 101 consecutive patients who were admitted for more than 48-hrs in ICU during Jun-Dec 2007 were analyzed.

Results:

Total of 953 samples from blood, urine, BAL or pus/collection were subjected to cultures. From 276 samples, 299 organisms were isolated. Among pathogens Candida Spp. [89 (29%)] were the most common, followed by Acinetobacter Spp. [69 (23%)], Pseudomonas Spp. [63 (21%)], Klebsiella Spp. [31 (10%)], coagulase negative Staphylococcus aureus [16 (5%)], E coli [12 (4%)], Enterobacter Spp. [7 (2%)], S aureus [6 (2%)], Enterococcus Spp. [5 (2%)], Citrobacter Spp. [2 (0.6%)], S maltophila [1 (0.3%)] and Providentia Spp. [1 (0.3%)]. For gram negative pathogens drug-resistance rates were as follows: Fluoroquinolones, 76%; 3^rd generation cephalosporins, 74%; aminoglycosides, 66%; β-lactams/β-lactamase inhibitors combinations, 64%; and carbapenems, 50%. Among these 27% of pathogens were resistant to all 5 classes of drugs. 58% of Staphylococcus aureus were methicillin-resistant whereas 85% of coagulase negative Staphylococcus were methicillin resistant. The mortality was higher among patients in whom pathogens were isolated [Odd's Ratio (OR) 0.185; 95% confidence interval (CI) 0.049-0.640; P = 0.002].

Conclusions:

Isolation of multi-drug resistant pathogens is common among trauma patients admitted in ICU and is associated with increased mortality and could impact on the consumption of hospital resources. The importance of high rate of fungal isolation needs to be studied among these patients.

Treponema denticola associates with increased levels of MMP-8 and MMP-9 in gingival crevicular fluid

OBJECTIVES

The aim was to assess the association between the presence of site-specific subgingival micro-organisms and the levels of matrix metalloproteinases-8 and matrix metalloproteinases-9 (MMP-8 and MMP-9) in gingival crevicular fluid (GCF).

MATERIALS AND METHODS

The patient group consisted of 56 subjects with periodontitis and the control group of 43 subjects without periodontitis. GCF samples from four test sites for each subject were collected. Polymerase chain reaction was used to detect the presence of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia, and Treponema denticola. MMP-8 concentrations were analyzed by a time-resolved immunofluorometric assay, and MMP-9 levels were determined by enzyme-linked immunosorbent assay. Student's unpaired t-test, chi-square test, and Fisher's exact P-value were calculated.

RESULTS

The presence of T. denticola in the test sites was significantly higher in the patient group than in the control group. The presence of T. forsythia and T. denticola was associated with increased levels of MMP-8 in the test sites. Respectively, site-specific presence of T. denticola was associated with an increase in MMP-9 levels in three of the four test sites.

CONCLUSIONS

The presence of subgingival micro-organisms in GCF, particularly T. denticola, appeared to induce a host response with an increased release of MMP-8 and MMP-9 in the test sites.

Probiotics in dentistry: A boon or sham

Probiotics are dietary supplements, which have been advocated for the prevention and the treatment of a wide range of diseases. These products consist of beneficial micro-organisms, which stimulate health promoting flora thus, suppressing the pathologic colonization and disease spread. Since, probiotics are now widely used in both medical (such as cancer risk reduction, gastrointestinal tract health, and urinary tract health) and dental specialties (reduction in caries development, in achieving periodontal health, reducing oral malodor, etc.), a thorough understanding of their risks and benefits are essential. This review focuses on the recent trends in use of probiotics in dentistry as well as the potential risks associated with them.

The frequency and clinical significance of intra-amniotic inflammation in women with preterm uterine contractility but without cervical change: do the diagnostic criteria for preterm labor need to be changed?

OBJECTIVE

The objective of this study was to determine the frequency and clinical significance of intra-amniotic inflammation in patients with preterm increased uterine contractility with intact membranes but without cervical change.

METHODS

Amniocentesis was performed in 132 patients with regular uterine contractions and intact membranes without cervical change. Amniotic fluid was cultured for bacteria and mycoplasmas and assayed for matrix metalloproteinase-8 (MMP-8). Intra-amniotic inflammation was defined as an elevated amniotic fluid MMP-8 concentration (>23 ng/mL).

RESULTS

(1) Intra-amniotic inflammation was present in 12.1% (16/132); (2) Culture-proven intra-amniotic infection was diagnosed in 3% (4/132) of patients without demonstrable cervical change on admission or during the period of observation; and (3) Patients with intra-amniotic inflammation had significantly higher rates of preterm delivery and adverse outcomes, and shorter amniocentesis-to-delivery intervals than those without intra-amniotic inflammation (P < 0.05 for each). Adverse outcomes included chorioamnionitis, funisitis, and neonatal death.

CONCLUSION

Intra-amniotic inflammation was present in 12% of patients with regular uterine contractions without cervical change, while culture-proven intra-amniotic infection was present in 3%. The presence of intra-amniotic inflammation was a significant risk factor for adverse neonatal outcomes. These observations question whether cervical changes should be required for the diagnosis of preterm labor, because patients without modifications in cervical status on admission or during a period of observation are at risk for adverse pregnancy outcomes.

Cancer chemopreventive and anticancer evaluation of extracts and fractions from marine macro- and microorganisms collected from Twilight Zone waters around Guam

The cancer chemopreventive and cytotoxic properties of 50 extracts derived from Twilight Zone (50-150 m) sponges, gorgonians and associated bacteria, together with 15 extracts from shallow water hard corals, as well as 16 fractions derived from the methanol solubles of the Twilight Zone sponge Suberea sp, were assessed in a series of bioassays. These assays included: Induction of quinone reductase (QR), inhibition of TNF-alpha activated nuclear factor kappa B (NFkappaB), inhibition of aromatase, interaction with retinoid X receptor (RXR), inhibition of nitric oxide (NO) synthase, inhibition 2,2-diphenyl-1-picrylhydrazyl radical scavenging (DPPH), and inhibition of HL-60 and MCF-7 cell proliferation. The results of these assays showed that at least 10 extracts and five fractions inhibited NFkappaB by greater than 60%, two extracts and two fractions inhibited DPPH by more than 50%, nine extracts and two fractions affected the survival of HL-60 cells, no extracts or fractions affected RXR, three extracts and six fractions affected quinone reductase (QR), three extracts and 12 fractions significantly inhibited aromatase, four extracts and five fractions inhibited nitric oxide synthase, and one extract and no fractions inhibited the growth of MCF-7 cells by more than 95%. These data revealed the tested samples to have many and varied activities, making them, as shown with the extract of the Suberea species, useful starting points for further fractionation and purification. Moreover, the large number of samples demonstrating activity in only one or sometimes two assays accentuates the potential of the Twilight Zone, as a largely unexplored habitat, for the discovery of selectively bioactive compounds. The overall high hit rate in many of the employed assays is considered to be a significant finding in terms of "normal" hit rates associated with similar samples from shallower depths.

Allopatric origins of microbial species

Although allopatric divergence is a well-accepted mechanism of speciation for eukaryotic macro-organisms, the importance of geographical barriers to divergence in microbial populations is a subject of great debate. Do geographically separated populations of micro-organisms diverge independently, or does their structure fit the often quoted Bass-Becking description 'everything is everywhere; the environment selects'? Aided by high-resolution genetic and genomic tools, the search for 'microbial marsupials' has revealed that in fact both are true; some species of micro-organisms demonstrate allopatric divergence, while others do not. This discovery opens the door for comparative analyses, where questions about the differences in evolutionary and ecological mechanisms that drive divergence and speciation in different microbial species can begin to be explored. Investigating these differences in evolutionary mechanisms will greatly enhance interest in, and understanding of, the dynamic processes that create and maintain the vast diversity of the microbial world.

Consequences of detritus type in an aquatic microsystem: effects on water quality, micro-organisms and performance of the dominant consumer

1. Variation in detritus quality and quantity can have significant effects on aquatic invertebrate food webs. Allochthonous inputs of detritus are the principal energy source for organisms in aquatic tree hole microsystems. We compared the effects of two major detritus types found in tree holes, senescent leaves (Sugar Maple and White Oak) and invertebrate carcasses (dead adult fruit flies and crickets), on several water quality characteristics of laboratory microcosms as well as on mass, survival and population performance of the dominant tree hole consumer, Ochlerotatus triseriatus (Diptera: Culicidae). To date, no study has documented the effects of animal detritus in tree hole microsystems or on resident consumers.2. Aquatic environments receiving invertebrate carcasses had significantly greater total nitrogen, total reactive phosphorus and higher pH, than leaf-based environments. Decay rate of invertebrate carcasses was greater compared to leaf material. Consumption of O(2) by micro-organisms increased with increasing detritus amounts, but we detected no difference between detritus types.3. Ochlerotatus triseriatus larvae grew faster in animal-based treatments, and mean mass of larvae was significantly greater when more animal detritus was used. The effect of animal-based treatments on larvae translated into higher performance for adults, which were three times heavier than counterparts from plant-based containers. Survivorship and estimated population growth rates were significantly greater for O. triseriatus reared on animal-based versus plant-based detritus.4. We hypothesise two mechanisms for the pronounced effect of invertebrate carcasses on mosquito performance relative to that associated with leaf detritus: (i) invertebrate carcasses decompose more quickly and release nutrients more effectively into the aquatic environment; or (ii) O. triseriatus larvae may directly ingest nutrient-rich components of invertebrate carcasses. Because even relatively small animal detritus additions can have strong effects on O. triseriatus populations, studies need to be conducted to explore the overall role of animal detritus in tree holes in nature.

Competition between micro-organisms and roots of barley and sorghum for iron accumulated in the root apoplasm

Graminaceous plant species respond to iron (Fe)-deficiency stress by enhancing the release of phytosiderophores from the roots and the uptake of Fe-phytosiderophores. For studying the mobilization and uptake of apoplasmic root Fe by barley (inherently high phytosiderophore release) and sorghum (inherently low phytosiderophore release) in axenic and nonaxenic (inoculated) nutrient solution, Fe pools in the root apoplasm were loaded during plant preculture with 10^-4 M Fe(III)-EDTA. After 27 d growth in Fe-deficient nutrient solution, inoculated barley plants developed moderate Fe-deficiency chlorosis compared with the less chlorotic axenic plants. In inoculated plants, recovery of phytosiderophores and mobilization of apoplasmic root Fe tended to be slightly lower than in axenic plants, and in both treatments apoplasmic root Fe was completely depleted at harvest. As determined by the nonsoluble Fe fraction (> 0·2 μm) in the nutrient solution and at the rhizoplane, the microbial uptake and immobilization of apoplasmic root Fe was estimated at about 3% of the total amount of apoplasmic root Fe after preculture and at less than 10% of plant Fe uptake. Under axenic conditions, Fe-deficient sorghum also depleted apoplasmic root Fe and developed moderate Fe-deficiency chlorosis, although phytosiderophore recovery was 5-10-fold lower than in barley. By contrast, in inoculated sorghum plants, phytosiderophore recovery and Fe mobilization were extremely low. At harvest, in inoculated sorghum plants apoplasmic Fe pools were still considerably loaded and plant Fe uptake was c. 60% lower than that of axenic plants, resulting in severe Fe-deficiency chlorosis. Thus, in Fe-deficient sorghum plants, the lower rate of phytosiderophore release and its degradation restricted an efficient mobilization of apoplasmic root Fe in the presence of micro-organisms. In barley, however, the higher rate of phytosiderophore release allowed a complete mobilization of apoplasmic root Fe even in inoculated nutrient solution. Furthermore, the results show that the dominating effect of micro-organisms in their competition with barley and sorghum for apoplasmic root Fe is the degradation of phytosiderophores rather than the immobilization or uptake of Fe.