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Identification of bacteria species in aquaponics system using RapID system and 16S rRNA sequencing
Abstract
Aquaponics is an integrated production system of aquaculture and hydroponics. Beneficial bacteria convert the ammonia and solid wastes produced by fish in the aquaculture component into essential nutrients for plant growth in hydroponics. The objective of the present study was to identify the bacteria community in the aquaponics system. This study was set by using barb fish and basils as organisms of cultivation. The fish tank (aquaculture) water was pumped into the treatment tank containing bio-ring functions as nitrifying bacteria by converting ammonia to nitrates. The nutrient-rich water from the treatment tank was then pumped into the hydroponics containing lightweight expanded clay aggregate (LECA) and plants. Water samples from the treatment tank and hydroponics were pipetted and transferred onto different agar plates for colony growth. Another set of soil growth plant was used for comparison in bacteria community between aquaponics and conventional land agriculture. RapID system and 16S rRNA gene were used to identify gram-negative and gram-positive bacteria respectively. The identified bacteria species from the hydroponics (LECA) and treatment tank (Bio-ring) were Moellerella wisconsensis, Achromobacter xylosoxidans, Bacillus cereus, Burkholderia pseudomallei and Bacillus sp. respectively whereas the bacteria species isolated from soil were Bacillus sp. and Bacillus pumilus.
Supplementary resource (1)
World is changing and changing for the demand of the civilization. Peoples are used to prefer food from outside due to time constrain. They are used to take food which can be prepared easily and take less time to consume. That’s why, Fried Rice menu is preferable than others menu. Peoples who are used to take Fried Rice in their regular meal, they have more chance to develop Fried Rice Syndrome than others. It is a food borne bacterial in-toxication which is caused by toxin of Bacillus cereus. To increase awareness among the consumer, food handler and food maker is the effective method to control the life-threatening food borne
The omnipresence of filterable bacteria that can pass through 0.22-μm membrane filters demands a change in the sterile filtration practice. In this study, we identified that filterable bacteria enriched from a surface water are members of the Bacteroidetes, Proteobacteria, Spirochaetae, Firmicutes, and Actinobacteria. Filterable bacteria displayed superior filterability during the entire bacterial growth phase, especially at the exponential phase. Maximal passage percentages were comparable at different cell densities, and achieved earlier at high cell density. Furthermore, filter retention for the investigated bacteria is independent of liquid temperature. However, cultivation temperature could affect the growth of some specific filterable bacteria and lead to variability in the passage percentage. Additionally, membrane materials, pore size and filtering flux greatly affected the passage of filterable bacteria. The majority of filterable Hylemonella and SAR324 could pass through 0.1-μm polyvinylidene fluoride and polyethersulfone filters but could not pass through 0.1-μm polycarbonate and mixed cellulose esters filters. Taken together, our results demonstrated that the ultra-small size of filterable bacteria, membrane characteristics and filtration operational conditions could challenge the validity of the 0.22/ 0.1-μm sterilizing grade filters in providing bio-safety barriers.
Along with the intensive development of methods of livestock breeding, breeders’ expectations are growing concerning
feed additives that would guarantee such results as accelerating growth rate, protection of health from pathogenic
infections and improvement of other production parameters such as: absorption of feed and quality of meat,
milk, eggs. The main reason for their application would be a strive to achieve some benefcial efects comparable to
those of antibiotic-based growth stimulators, banned on 01 January 2006. High hopes are being associated with the
use of probiotics, prebiotics and synbiotics. Used mainly for maintenance of the equilibrium of the intestinal microbiota
of livestock, they turn out to be an efective method in fght against pathogens posing a threat for both animals
and consumers. This paper discusses defnitions of probiotics, prebiotics and synbiotics. Criteria that have to be met
by those kinds of formulas are also presented. The paper ofers a list of the most commonly used probiotics and prebiotics
and some examples of their combinations in synbiotic formulas used in animal feeding. Examples of available
study results on the efect of probiotics, prebiotics and synbiotics on animal health are also summarised.
Objective:
The treatment of Achromobacter xylosoxidans bacteremia is challenged by antimicrobial resistance and the paucity of data. We aimed at offering a contemporary description of this uncommon entity.
Methods:
Retrospective case series of 13 episodes of A. xylosoxidans bacteremia diagnosed over a 10-year period (November 2007 to May 2017) in our tertiary care center.
Results:
Solid organ cancer and heart failure were the most common comorbidities (4/13 [30.7%]). All but one episodes were hospital-acquired. Most patients had received previous antibiotic therapy (7/13 [53.8%]) and had a central venous catheter in place (6/13 [46.1%]). Primary and intravascular catheter were the most common sources (4/13 [30.7%] each). Meropenem was the agent with best in vitro activity (92.3% [12/13] of susceptible isolates). All-cause 30-day mortality (overall 23.1%) was higher in patients with primary bacteremia (50.0% vs. 11.1%; P-value=0.203) and prior chemotherapy (66.7% vs. 10.0%; P-value=0.108).
Conclusions:
Bacteremia due to A. xylosoxidans constitutes a serious infection among immunocompromised hosts. Carbapenem-based therapy may be appropriate in most cases.
Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements.
In this preliminary article we present data on plant nutrient concentrations in aquaponic systems, and compare them to nutrient concentrations in " standard " hydroponic solutions. Our data shows that the nutrient concentrations supplied by the fish in aquaponic system are significantly lower for most nutrients, compared to hydroponic systems. Nevertheless, plants do thrive in solutions that have lower nutrient levels than " standard " hydroponic solutions. This is especially true for green leafy vegetables that rarely need additional nutritional supplementation. It is concluded that in the highly complex system of aquaponics, special care has to be taken, via continuous monitoring of the chemical composition of the circulating water, to provide adequate concentrations and ratios of nutrients, and special attention has to be paid to the potentially toxic component, ammonium. If certain plants require nutrient supplementation, we consider that one based on organic substances would be most beneficial. However, protocols for the application of such nutrient amendments still need to be developed.
Burkholderia pseudomallei, a highly pathogenic bacterium that causes melioidosis, is commonly found in soil in Southeast Asia and Northern Australia. Melioidosis can be difficult to diagnose due to its diverse clinical manifestations and the inadequacy of conventional bacterial identification methods. The bacterium is intrinsically resistant to a wide range of antimicrobials, and treatment with ineffective antimicrobials may result in case fatality rates (CFRs) exceeding 70%. The importation of infected animals has, in the past, spread melioidosis to non-endemic areas. The global distribution of B. pseudomallei and the burden of melioidosis, however, remain poorly understood. Here, we map documented human and animal cases and the presence of environmental B. pseudomallei and combine this in a formal modelling framework to estimate the global burden of melioidosis. We estimate there to be 165,000 (95% credible interval 8,000–412,000) human melioidosis cases per year worldwide, from which 89,000 (36,000–227,000) people die. Our estimates suggest that melioidosis is severely underreported in the 45 countries in which it is known to be endemic and that melioidosis is probably endemic in a further 34 countries that have never reported the disease. The large numbers of estimated cases and fatalities emphasize that the disease warrants renewed attention from public health officials and policy makers.
Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “
Omic
” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. “
Omic
” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “
Omic
” tools to characterize the microbial community in aquaponic systems.
Bacillus pumilus SAFR-032 spores isolated from a clean room environment are known to exhibit enhanced resistance to peroxide, desiccation, UV radiation and chemical disinfection than other spore-forming bacteria. The survival of B. pumilus SAFR-032 spores to standard clean room sterilization practices requires development of more stringent disinfection agents. Here, we report the effects of a stabilized chlorine dioxide-based biocidal agent against spores of B. pumilus SAFR-032 and Bacillus subtilis ATCC 6051. Viability was determined via CFU measurement after exposure. Chlorine dioxide demonstrated efficacy towards sterilization of spores of B. pumilus SAFR-032 equivalent or better than exposure to hydrogen peroxide. These results indicate efficacy of chlorine dioxide delivered through a stabilized chlorine dioxide product as a means of sterilization of peroxide- and UV-resistant spores.
Electronic supplementary material
The online version of this article (doi:10.1186/s13568-015-0109-4) contains supplementary material, which is available to authorized users.
Food borne illnesses result from eating food or
drinking beverages that are contaminated with chemical matter,
heavy metals, parasites, fungi, viruses and Bacteria.
Bacillus cereus is one of the food-borne disease causing
Bacteria. Species of Bacillus and related genera have long
been troublesome to food producers on account of their resistant
endospores. Their spores may be present on various types
of raw and cooked foods, and their ability to survive high
cooking temperatures requires that cooked foods be served hot
or cooled rapidly to prevent the growth of this bacteria.
Bacillus cereus is well known as a cause of food poisoning,
and much more is now known about the toxins produced by
various strains of this species, so that its significance in such
episodes are clearer. However, it is still unclear why such
cases are so rarely reported worldwide.
Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.
The physical profile of the growing media is a requirement to measure the efficiency of bio filtration of fish waste in the aquaponics system. Klayton and Light Expanded Clay Aggregate (LECA), both ceramic based growing media, were evaluated based on physical profile. Klayton has higher water absorption per surface area as compared to LECA. High surface area provides more space for the growth of nitrifying bacteria.
Anaerobic digestion is a waste treatment method which is of increasing interest worldwide. At the end of the process, a digestate remains, which can gain added value by being composted. A study was conducted in order to investigate microbial community dynamics during the composting process of a mixture of anaerobic digestate (derived from the anaerobic digestion of municipal food waste), green wastes and a screened compost (green waste/kitchen waste compost), using the COMPOCHIP microarray. The composting process showed a typical temperature development, and the highest degradation rates occurred during the first 14days of composting, as seen from the elevated CO2 content in the exhaust air. With an exception of elevated nitrite and nitrate levels in the day 34 samples, physical-chemical parameters for all compost samples collected during the 63day process indicated typical composting conditions. The microbial communities changed over the 63days of composting. According to principal component analysis of the COMPOCHIP microarray results, compost samples from the start of the experiment were found to cluster most closely with the digestate and screened compost samples. The green waste samples were found to group separately. All starting materials investigated were found to yield fewer and lower signals when compared to the samples collected during the composting experiment.
Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&1492R and 63F&M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample.
The clinical and radiological features of pulmonary melioidosis can mimic tuberculosis. We prospectively evaluated 118 patients with suspected pulmonary tuberculosis who were acid-fast bacilli (AFB) smear negative at Udon Thani Hospital, northeast Thailand. Culture of residual sputum from AFB testing was positive for Burkholderia pseudomallei in three patients (2.5%; 95% confidence interval [CI] 0.5-7.3%). We propose that in melioidosis-endemic areas, residual sputum from AFB testing should be routinely cultured for B. pseudomallei.
Achromobacter xylosoxidans is an aerobic nonfermentative Gram-negative rod considered an important emerging pathogen among cystic fibrosis (CF) patients
worldwide and among immunocompromised patients. This increased prevalence remains unexplained, and to date no environmental
reservoir has been identified. The aim of this study was to identify potential reservoirs of A. xylosoxidans in hospital, domestic, and outdoor environments and to compare the isolates with clinical ones. From 2011 to 2012, 339 samples
were collected in Dijon's university hospital, in healthy volunteers' homes in the Dijon area, and in the outdoor environment
in Burgundy (soil, water, mud, and plants). We designed a protocol to detect A. xylosoxidans in environmental samples based on a selective medium: MCXVAA (MacConkey agar supplemented with xylose, vancomycin, aztreonam,
and amphotericin B). Susceptibility testing, genotypic analysis by pulsed-field gel electrophoresis, and blaOXA-114 sequencing were performed on the isolates. A total of 50 strains of A. xylosoxidans were detected in hospital (33 isolates), domestic (9 isolates), and outdoor (8 isolates) samples, mainly in hand washing
sinks, showers, and water. Most of them were resistant to ciprofloxacin (49 strains). Genotypic analysis and blaOXA-114 sequencing revealed a wide diversity among the isolates, with 35 pulsotypes and 18 variants of oxacillinases. Interestingly,
10 isolates from hospital environment were clonally related to clinical isolates previously recovered from hospitalized patients,
and one domestic isolate was identical to one recovered from a CF patient. These results indicate that A. xylosoxidans is commonly distributed in various environments and therefore that CF patients or immunocompromised patients are surrounded
by these reservoirs.
Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen.
Twitching motility in Acinetobacter baylyi ADP1 is inhibited by moderate intensities of blue light in a temperature-dependent manner (maximally at 20°C. We analyzed the involvement of four predicted blue-light-sensing-using flavin (BLUF) domain-containing proteins encoded in the genome of this strain in the twitching motility phenotype. All four genes were expressed both in light and in darkness. A phylogenetic tree showed that one BLUF domain, ACIAD2110, grouped separately from the other three (ACIAD1499, ACIAD2125 and ACIAD2129). Individual knock-out mutants of the latter, but not of ACIAD2110, fully abolished the light dependency of the twitching motility response. Quantitative analysis of transcripts level of the three genes showed a decreased expression in the light, with dark/light ratios of 1.65 ± 0.28, 1.79 ± 0.21 and 2.69 ± 0.39, for ACIAD2125, ACIAD2129 and ACIAD1499, respectively. Double and triple knock-outs of ACIAD1499, ACIAD2125 and ACIAD2129 confirmed the same phenotype as the corresponding single knock-outs. Complementation of all the single knock-outs and the triple knock-out mutants with any of the three BLUF-domain encoding genes fully restored the inhibition of twitching motility by blue light that is observed in the wild type strain. A. baylyi ADP1 therefore shows a high degree of redundancy in the genes that encode BLUF-containing photoreceptors. Moreover, all plasmid-complemented strains, expressing any of the BLUF- proteins irrespective of the specific set of deleted photoreceptors, displayed increased light-dependent inhibition of twitching motility, as compared to the wild type (p<0.001). We conclude that the three genes ACIAD1499, ACIAD2125 and ACIAD2129 are jointly required to inhibit twitching motility under moderate blue light illumination.
Bacillus species constitute a diverse group of bacteria widely distributed in soil and the aquatic environment. In this study, Bacillus strains isolated from the coastal environment of Cochin, India were identified by detailed conventional biochemical methods, fatty acid methyl ester (FAME) analysis and partial 16S rDNA sequencing. Analysis of the data revealed that Bacillus pumilus was the most predominant species in the region under study followed by B. cereus and B. sphaericus. The B. pumilus isolates were further characterized by arbitrarily primed PCR (AP-PCR), antibiotic sensitivity profiling and PCR screening for known toxin genes associated with Bacillus spp. All B. pumilus isolates were biochemically identical, exhibited high protease and lipase activity and uniformly sensitive to antibiotics tested in this study. One strain of B. pumilus harboured cereulide synthetase gene cesB of B. cereus which was indistinguishable from rest of the isolates biochemically and by AP-PCR. This study reports, for the first time, the presence of the emetic toxin gene cesB in B. pumilus.
Bacillus strains isolated from soil or channel catfish intestine were screened for their antagonism against Edwardsiella ictaluri and Aeromonas hydrophila, the causative agents of enteric septicemia of catfish (ESC) and motile aeromonad septicaemia (MAS), respectively. Twenty one strains were selected and their antagonistic activity against other aquatic pathogens was also tested. Each of the top 21 strains expressed antagonistic activity against multiple aquatic bacterial pathogens including Edwardsiella tarda, Streptococcus iniae, Yersinia ruckeri, Flavobacterium columnare, and/or the oomycete Saprolegnia ferax. Survival of the 21 Bacillus strains in the intestine of catfish was determined as Bacillus CFU/g of intestinal tissue of catfish after feeding Bacillus spore-supplemented feed for seven days followed by normal feed for three days. Five Bacillus strains that showed good antimicrobial activity and intestinal survival were incorporated into feed in spore form at a dose of 8×10(7) CFU/g and fed to channel catfish for 14 days before they were challenged by E. ictaluri in replicate. Two Bacillus subtilis strains conferred significant benefit in reducing catfish mortality (P<0.05). A similar challenge experiment conducted in Vietnam with four of the five Bacillus strains also showed protective effects against E. ictaluri in striped catfish. Safety of the four strains exhibiting the strongest biological control in vivo was also investigated in terms of whether the strains contain plasmids or express resistance to clinically important antibiotics. The Bacillus strains identified from this study have good potential to mediate disease control as probiotic feed additives for catfish aquaculture.
The use of antimicrobials and toxic metals should be considered carefully in aquaculture and surrounding environments. We aimed to evaluate medically relevant bacteria in an aquaculture system and their susceptibility to antimicrobials and toxic metals. Selective cultures for enterobacteria (ENT), non-fermenting Gram-negative rods (NFR) and Gram-positive cocci (GPC) were obtained from water samples collected in two different year seasons. The isolated bacteria were biochemically identified and antimicrobial and toxic metal susceptibility patterns were determined. Overall, 407 representative strains were recovered. In general, bacteria isolated from fish ponds showed higher multiple antibiotic resistance indices when compared to those isolated from a water-fed canal. Resistance to penicillin and azithromycin was observed more frequently in the GPC group, whereas resistance to ampicillin and ampicillin/sulbactam or gentamicin was observed more frequently in the ENT and NFR groups, respectively. All the isolated bacteria were tolerant to nickel, zinc, chromium and copper at high levels (≥1,024 μg mL(-1)), whereas tolerance to cadmium and mercury varied among the isolated bacteria (2-1,024 mg mL-1). Multidrug-resistant bacteria were more frequent and diverse in fish ponds than in the water-fed canal. A positive correlation was observed between antimicrobial resistance and metal tolerance. The data point out the need for water treatment associated with the aquaculture system.
16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation
of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and
phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based on this evaluation a selection
of ‘best available’ primer pairs for Bacteria and Archaea for three amplicon size classes (100–400, 400–1000, ≥1000 bp) is provided. The most promising bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21),
with an amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA amplicons
with 16S rDNA fragments from directly sequenced metagenomes. The results of this study may be used as a guideline for selecting
primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in
PCR-based microbial diversity studies.
In this study, potential probiotic strains were isolated from fermented pickles based on antagonistic activity against two shrimp pathogens (Vibrio harveyi and Vibrio parahaemolyticus). Two strains L10 and G1 were identified by biochemical tests, followed by16S ribosomal RNA gene sequence analysis as Bacillus subtilis, and characterized by PCR amplification of repetitive bacterial DNA elements (Rep-PCR). Subsequently, B. subtilis L10 and G1 strains were tested for antibacterial activity under different physical conditions, including culture medium, salinity, pH and temperature using the agar well diffusion assay. Among the different culture media, LB broth was the most suitable medium for antibacterial production. Both strains showed the highest level of antibacterial activity against two pathogens at 30 °C and 1.0% NaCl. Under the pH conditions, strain G1 showed the greatest activity against V. harveyi at pH 7.3-8.0 and against V. parahaemolyticus at pH 6.0-8.0, whereas strain L10 showed the greatest activity against two pathogens at pH 7.3. The cell-free supernatants of both strains were treated with four different enzymes in order to characterize the antibacterial substances against V. harveyi. The result showed considerable reduction of antibacterial activity for both strains, indicating the proteinaceous nature of the antibacterial substances. A wide range of tolerance to NaCl, pH and temperature was also recorded for both strains. In addition, both strains showed no virulence effect in juvenile shrimp Litopenaeus vannamei. On the basis of these results and safety of strains to L. vannamei, they may be considered for future challenge experiments in shrimp as a very promising alternative to the use of antibiotics.
Achromobacter xylosoxidans is typically isolated from pulmonary sources, presenting as pneumonia in immunosuppressed individuals. We describe a novel
clinical presentation of A. xylosoxidans infection presenting as multiple spiculated, pulmonary nodules mimicking cancer for which the patient underwent a wedge resection
of the lung for diagnosis and staging of presumptive cancer.
Multidrug resistant Acinetobacter baumannii, (MRAB) is an important cause of hospital acquired infection. The purpose of this study is to determine the risk factors for MRAB in a city hospital patient population.
This study is a retrospective review of a city hospital epidemiology data base and includes 247 isolates of Acinetobacter baumannii (AB) from 164 patients. Multidrug resistant Acinetobacter baumannii was defined as resistance to more than three classes of antibiotics. Using the non-MRAB isolates as the control group, the risk factors for the acquisition of MRAB were determined.
Of the 247 AB isolates 72% (177) were multidrug resistant. Fifty-eight percent (143/247) of isolates were highly resistant (resistant to imipenem, amikacin, and ampicillin-sulbactam). Of the 37 patients who died with Acinetobacter colonization/infection, 32 (86%) patients had the organism recovered from the respiratory tract. The factors which were found to be significantly associated (p < or = 0.05) with multidrug resistance include the recovery of AB from multiple sites, mechanical ventilation, previous antibiotic exposure, and the presence of neurologic impairment. Multidrug resistant Acinetobacter was associated with significant mortality when compared with sensitive strains (p < or = 0.01). When surgical patients (N = 75) were considered separately, mechanical ventilation and multiple isolates remained the factors significantly associated with the development of multidrug resistant Acinetobacter. Among surgical patients 46/75 (61%) grew a multidrug resistant strain of AB and 37/75 (40%) were resistant to all commonly used antibiotics including aminoglycosides, cephalosporins, carbepenems, extended spectrum penicillins, and quinolones. Thirty-five percent of the surgical patients had AB cultured from multiple sites and 57% of the Acinetobacter isolates were associated with a co-infecting organism, usually a Staphylococcus or Pseudomonas. As in medical patients, the isolation of Acinetobacter from multiple sites and the need for mechanical ventilation were significantly associated with the development of MRAB.
The factors significantly associated with MRAB in both the general patient population and surgical patients were mechanical ventilation and the recovery of Acinetobacter from multiple anatomic sites. Previous antibiotic use and neurologic impairment were significant factors in medical patients. Colonization or infection with MRAB is associated with increased mortality.
Neil Risch, in a series of seminal papers in 1990 ([1][1], [2][2]), demonstrated the utility of sib-pair linkage analysis in identifying genes for complex genetic traits. In doing so, he defined what is the current paradigm for the genetic dissection of common complex genetic diseases. The recent
The use of cultivation independent methods has revolutionized soil biology in the last decades. Most popular approaches are based on directly extracted DNA from soil and subsequent analysis of PCR-amplified marker genes by next-generation sequencing. While these high-throughput methods offer novel possibilities over cultivation-based approaches, several key points need to be considered to minimize potential biases during library preparation and downstream bioinformatic analysis. This opinion paper highlights crucial steps that should be considered for accurate analysis and data interpretation.
In this research, antagonistic activities of 30 Bacillus species isolated from various fish samples were studied. Isolated Bacillus species were analyzed using the agar diffusion method in terms of their general inhibition effects against some food pathogen/ contaminant bacteria and lactic acid bacteria isolated from the fish intestinal tracts. Some of the strains exhibited antimicrobial activity against Bacillus subtilis, Pseudomonas fluorescens, Lactobacillus coryneformis, Lactobacillus plantarum and Lactobacillus xylosus. Furthermore, the inhibitory effects of the lactic acid bacteria on the Bacillus isolates were analyzed by using the same method. It was determined that the lactic acid bacteria inhibited Bacillus spp. strains at different levels of inhibition zones.
In this work, the antibacterial activity of the lipopeptides produced by Bacillus amyloliquefaciens M1 was examined against multidrug-resistant Vibrio spp. and Shewanella aquimarina isolated from diseased marine animals. A new and cheap medium which contained 1.0 % soybean powder, 1.5 % wheat flour, pH 7.0 was developed. A crude surfactant concentration of 0.28 mg/ml was obtained after 18 h of 10-l fermentation and diameter of the clear zone on the plate seeded with Vibrio anguillarum was 34 mm. A preliminary characterization suggested that the lipopeptide N3 produced by B. amyloliquefaciens M1 was the main product and contained the surfactin isoforms with amino acids (GLLVDLL) and hydroxy fatty acids (of 12-15 carbons in length). The evaluation of the antibacterial activity of the lipopeptide N3 was carried out against S. aquimarina and nine species of Vibrio spp.. It was found that all the Vibrio spp. and S. aquimarina showed resistance to several different antibiotics, suggesting that they were the multidrug resistance. It was also indicated that all the Vibrio spp. strains and S. aquimarina were sensitive to the surfactin N3, in particular V. anguillarum. The results demonstrated that the lipopeptides produced by B. amyloliquefaciens M1 had a broad spectrum of action, including antibacterial activity against the pathogenic Vibrio spp. with multidrug-resistant profiles. After the treatment with the lipopeptide N3, the cell membrane of V. anguillarum was damaged, and the whole cells of the bacterium were disrupted.
A bacterial strain designated Npb-07T was isolated from a freshwater river in Taiwan and characterized using the polyphasic taxonomic approach. Strain Npb-07T was Gram-negative, aerobic, rod-shaped, and motile by means of a single polar flagellum. Growth occurs at 10-37 °C (optimum, 20-30 °C), at pH 6.0-9.0 (optimum, pH 6.0-7.0) and with 0-1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-07T belonged to the genus Vogesella and its most closely related neighbour was Vogesella indigofera ATCC 19706T with sequence similarity of 98.4 %. The major fatty acids were summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c, 44.4 %) and C16:0 (31.9 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and an uncharacterized phospholipid. The DNA-DNA relatedness of strain Npb-07T with respect to Vogesella indigofera ATCC 19706T was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Npb-07T represents a novel species in the genus Vogesella, for which the name Vogesella fluminis sp. nov. is proposed. The type strain is Npb-07T (=LMG 26669T =BCRC 80377T =KCTC 23713T).
Cases of melioidosis (n = 12) and tuberculous pericarditis (n = 33) during 1996–2006 were reviewed. Clinical presentations were similar, but pericardial pathological findings were not.
Nine of 12 patients with melioidosis required pericardectomy. In areas where these diseases are endemic, pericardial fluid
culture and pericardial biopsy can differentiate between melioidosis and tuberculosis.
Over the past decade, the genus Aeromonas has undergone a number of significant changes of practical importance to clinical microbiologists and scientists alike. In parallel with the molecular revolution in microbiology, several new species have been identified on a phylogenetic basis, and the genome of the type species, A. hydrophila ATCC 7966, has been sequenced. In addition to established disease associations, Aeromonas has been shown to be a significant cause of infections associated with natural disasters (hurricanes, tsunamis, and earthquakes) and has been linked to emerging or new illnesses, including near-drowning events, prostatitis, and hemolytic-uremic syndrome. Despite these achievements, issues still remain regarding the role that Aeromonas plays in bacterial gastroenteritis, the extent to which species identification should be attempted in the clinical laboratory, and laboratory reporting of test results from contaminated body sites containing aeromonads. This article provides an extensive review of these topics, in addition to others, such as taxonomic issues, microbial pathogenicity, and antimicrobial resistance markers.
Microbial biofilms developing in aquaculture tanks represent a reservoir for opportunistic bacterial pathogens, and procedures to control formation and bacterial composition of biofilms are important for the development of commercially viable aquaculture industries. This study investigated the effects of seawater ozonation on biofilm development on microscope glass slides placed in small-scale aquaculture tanks containing the live feed organism Artemia. Fluorescence in situ hybridization (FISH) demonstrated that ozonation accelerated the biofilm formation cycle, while it delayed the establishment of filamentous bacteria. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial groups in the biofilm for both water types, but ozonation influenced their dynamics. With ozonation, the bacterial community structure was relatively stable and dominated by Gammaproteobacteria throughout the experiment (21-66% of total bacteria). Without ozonation, the community showed larger fluctuations, and Alphaproteobacteria emerged as dominant after 18 days (up to 54% of total bacteria). Ozonation of seawater also affected the dynamics of less abundant populations in the biofilm such as Betaproteobacteria, Planctomycetales and the Cytophaga/Flavobacterium branch of phylum Bacteroidetes. The abundance of Thiothrix, a bacterial genus capable of filamentous growth and fouling of larvae, increased with time for both water types, while no temporal trend could be detected for the genus Vibrio. Denaturing gradient gel electrophoresis (DGGE) demonstrated temporal changes in the dominant bacterial populations for both water types. Sequencing of DGGE bands confirmed the FISH data, and sequences were related to bacterial groups commonly found in biofilms of aquaculture systems. Several populations were closely related to organisms involved in sulfur cycling. Improved Artemia survival rates in tanks receiving ozonated water suggested a positive effect of ozonation on animal health. Although the used ozonation protocol did not hinder biofilm formation, the results suggest ozonation as a promising approach for manipulation of bacterial populations in aquaculture systems, which can prove beneficial for cultured animals.
Eleven strains of Achromobacter xylosoxidans have been received from among 1106 strains of Gram-negative, non-fermentative bacteria submitted to the National Collection of Type Cultures for computer-assisted identification since 1 January 1972. The strains showed resistance to a wide range of antimicrobial agents and five of the isolates possibly played a pathogenic role. The biochemical characteristics of these 11 strains were compared with those of three culture collection strains.
The name Moellerella wisconsensis is proposed for a group of the family Enterobacteriaceae previously called enteric group 46. The species name, wisconsensis, was coined because six of the nine strains were isolated in Wisconsin. M. wisconsensis strains were negative for indole production, Voges-Proskauer, H2S production, urea, phenylalanine deaminase, lysine and ornithine decarboxylases, arginine dihydrolase, gas production from D-glucose, acid production from trehalose, and motility; the strains were positive for methyl red, citrate (Simmons), and acid production from lactose and raffinose and resistant to colistin. DNAs from five strains of M. wisconsensis were highly related (80 to 93% in reactions assayed on hydroxyapatite at 60 degrees C and 78 to 97% at 75 degrees C) to 32P-labeled DNA of the proposed type strain (CDC 2896-78, ATCC 35017). Labeled DNA from this type strain was only 2 to 32% related (at 60 degrees C) to DNA from 49 strains of named and unnamed species of Enterobacteriaceae. Eight of nine M. wisconsensis strains were isolated from human stool samples. Clinical information on one strain was available, and it was found to be associated with a case of diarrhea. On MacConkey agar, colonies of M. wisconsensis were bright red with precipitated bile around them and thus were indistinguishable from Escherichia coli colonies. Future studies should focus on the isolation of this new organism and its relationship to human disease.
Achromobacter xylosoxidans was isolated from six patients. The organism causes opportunistic infections in patients who are compromised. A. xylosoxidans is a catalase- and oxidase-positive, motile, gram-negative rod that oxidizes xylose and glucose. The organism exists in a water environment and may be confused with Pseudomonas species. Unlike pseudomonas, achromobacter has peritrichous flagella. The clinical and laboratory characteristics of A. xylosoxidans are presented.
- A Chakravorty
- C Heath
- Melioidosis
Chakravorty A. and Heath C., Melioidosis, Australian Journal
for General Practitioners, 48, 6 (2019)
The Complete Nitrogen Cycle
- Fritz Aquatics
Fritz Aquatics, The Complete Nitrogen Cycle., Fritz Industries,
https://fritzaquatics.com/the-complete-nitrogen-cycle/ (2020)
- P Graumann
Graumann P., Bacillus: Cellular and Molecular Biology, 2 nd
ed., Caister Academic Press, Germany (2012)
Chlorine content far below maximum level, says Syabas
The Star, Chlorine content far below maximum level, says
Syabas, Star Media Group, https://www.thestar.com.my/news/
community/2011/05/20/chlorine-content-far-below-maximumlevel-says-syabas (2011)