16S rRNA Sequence Analysis Research Articles

Identification and molecular characterization of mycobacteria isolated from animal sources in a developing country

The essential role of animals in the transmission of infectious diseases has long been recognized. Apart from zoonosis due to Mycobacterium bovis in domestic cattle, acquired mycobacterial zoonosis from animals are vastly under-reported worldwide. This is partly the result of not recognizing that animals can be the source of zoonotic nontuberculous mycobacteria (NTM) infection. The present study intended to be a contribution to the knowledge of somewhat neglected role of animals in harboring, maintenance and dissemination of NTM in the environment. A total of 326 samples from 250 animals were collected and analyzed for the presence of mycobacteria using standard protocols. The preliminary identification and Runyon's classification of isolates were performed by conventional tests. The PCR amplification of a 228 bp fragment of 65-kDa heat shock protein (hsp) gene was applied for the genus identification and the partial sequence analysis of 16S rRNA was applied for the species identification. In total 32 isolates including 26 rapidly growing and 6 slowly growing mycobacteria were recovered from 250 animal samples (12.8%). The isolates recovered from 21 (65.60%) fish, 8 (25%) insects and 3 (9.4%) house cats, dogs and mice. M. fortuitum was the most frequent Mycobacterium spp (13 isolates; 40.6% of all isolates), followed by M. abscessus-chelonae-M. saopaulense group, (5 isolates; 15.6% of all isolates), M. iranicum (3 isolates; 9.4% of all isolates),and M. marinum, M. terrae complex and M. chlorophenolicum (2 isolates each; 18.8% of all isolates), and the single isolates of M. mucogenicum, M. neoaurum, M. conceptionense, M. virginiense, and M. gordonae (5 isolates; 15.6% of all isolates). The current study indicates that a variety of animals can be a permanent or transient source of mycobacterial agents. This ensures the life cycle of the bacteria and the chance of their survival in the environment, which may pose a potential threat to human health.

Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain.

A highly chitinolytic facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive, rod-shaped bacterial strain N10T was isolated from the feces of a river otter in the Castril Natural Park (Granada, Spain). It is a slightly halophilic, motile, catalase-, oxidase-, ACC deaminase- and C4 and C8 lipase-positive strain. It is aerobic, respiratory and has a fermentative metabolism using oxygen as an electron acceptor, produces acids from glucose and can fix nitrogen. Phylogenetic analysis of the 16S rRNA gene sequence, multilocus sequence analysis (MLSA) of 16S rRNA, gyrB, recA and rpoB, as well as phylogenomic analyses indicate that strain N10T is a novel species of the genus Paenibacillus, with the highest 16S rRNA sequence similarity (95.4%) to P. chitinolyticus LMG 18047T and <95% similarity to other species of the genus Paenibacillus. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANIb) were 21.1% and <75%, respectively. Its major cellular fatty acids were anteiso-C15:0, C16:0, and iso-C15:0. G + C content ranged between 45%–50%. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with chemotaxonomic and phenotypic data, we demonstrate that type strain N10T (= CECT 9541T =LMG 30535T) is a novel species of genus Paenibacillus and the name Paenibacillus lutrae sp. nov. is proposed.

Isolation and selection of highly effective phosphate solubilizing bacterial strains to promote wheat growth in Egyptian calcareous soils

BackgroundForty phosphate solubilizing bacterial (PSB) isolates were isolated from the root zone of wheat plants cultivated in the Delta and the Northwestern coast regions of Egypt. All isolates proofed their ability to dissolve tricalcium phosphate on the National Botanical Research Institute's phosphate growth medium (NBRIP) by producing clear zone and increasing the available phosphorus that ranged between 40 and 707 mg l−1. They were designated as Egyptian native phosphate solubilizing bacteria (ENPSB).ResultsAll strains proofed their ability to dissolve tricalcium phosphate on (NBRIP) medium by producing clear zone and increasing the available phosphorus that ranged between 40 and 707 mg l−1. The ENPSB 1, 2, and 3 strains were highly efficient as they gave 707, 653, and 693 mg l−1 soluble phosphorus respectively. Intriguingly, the two highly efficient strains for phosphate solubilization were isolated from the Northwestern coast alkaline soils. Moreover, 75% of strains were also produced profitable amounts of indole acetic acid (IAA) ranged from 0.79 to 50.5 mg l−1. Amazingly, the most efficient strain ENPSB 1 in solubilizing phosphorus (707 mg l−1soluble P) was the best one for producing IAA (50.5 mg l−1). The three efficient strains were identified using the sequencing of 16S rRNA. Sequence analysis of 16S rRNA for selected strains confirmed that the strains ENPSB 1, 2, and 3 were genetically closed to Enterobacter aerogenes; Pantoea sp. and Enteriobacter sp. respectively.ConclusionThe inoculation by mix cultures of strains (ENPSB 1, 2, and 3) contributed to raising the dry weight and P content of wheat plants by 76% and 12% over the full fertilized plants. Inoculation of soil PSB can be used to solve the deficiency of phosphorus and promote plant growth effectively in calcareous soils.

Prevalence and molecular characterization of non-tuberculous mycobacteria in hospital soil and dust of a developing country, Iran.

The presence and diversity of mycobacteria that are capable of survival in a harsh and adverse condition, such as hospital environments, have not been comprehensively studied. This study aimed to assess the frequency and diversity of mycobacteria in hospital soil and dust of a developing country using a combination of molecular and conventional methods. A total of 318 hospital dust and soil samples collected from 38 hospitals were analysed using standard protocols for characterization of mycobacteria. The conventional tests were used for preliminary identification and Runyon's classification, the PCR amplification of the hsp65 gene and sequence analyses of 16SrRNA were applied for genus and species identification. In total, 28 samples (8.8 %) were positive for mycobacteria. The isolates included 33 mycobacteria species including 19 rapidly growing and 14 slowly growing organisms. The most prevalent species were M. setense and M. lentiflavum, five isolates (15.1 %) each, M. fortuitum, four isolates (12.12 %) and M. kumamotonense and M. massiliense/abscessus complex three isolates (9.1 %) each, M. arupense and M. frederiksbergense, two isolates (6 %) each. The remaining isolates consisted the single strains of eight various mycobacterium species, the results of our study revealed that soil and dust in hospitals can be the reservoir of mycobacteria. This reaffirms the fact that these organisms due to intrinsic resistance can persist in hospitals and create a threat to patient's health, in particular to those who suffer from weakness of immunity.

Lysobacter terrigena sp. nov., isolated from a Korean soil sample.

A bacterial strain isolated from a soil collected in Jeju Island, designated as 17J7-1T, was Gram-negative, rod-shaped, yellow colored, and motile by gliding. This strain was able to grow at temperature range from 10 to 42°C, pH 7-9, and tolerated up to 1% NaCl. Analysis of 16S rRNA sequence identified strain 17J7-1T as a member of the genus Lysobacter with close sequence similarity with Lysobacter mobilis 9NM-14T (97.4%), Lysobacter xinjiangensis RCML-52T (97.0%), and Lysobacter humi FJY8T (96.9%). The genomic DNA G + C content of the isolate was 67.9mol%. DNA-DNA relatedness between strain 17J7-1T and L. mobilis, L. humi, and L. xinjiangensis were 42.3%, 39.5%, and 35.8%, respectively, clearly showing that the isolate is distinct from its closest phylogenetic neighbors in the genus Lysobacter. Average nucleotide identity (ANI) and digital DNA-DNAhybridization (dDDH) values between strain 17J7-1T and L. enzymogenes ATCC 29487T, the type species of this genus, and several other close Lysobacter species were less than 77% and 22%, respectively. Major fatty acids were C16:0 iso (29.8%), summed feature 9 (C17:1 iso ω9c/C16:0 10-methyl; 20.1%), and C15:0 iso (17.7%). The predominant respiratory quinone was ubiquinone Q-8 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. In the light of the polyphasic evidence accumulated in this study, strain 17J7-1T is considered to represent a novel species in the genus Lysobacter, for which name Lysobacter terrigena sp. nov. is proposed. The type strain is 17J7-1T (= KCTC 62217T = JCM 33057T).

Variations of soil microbial communities accompanied by different vegetation restoration in an open-cut iron mining area

Overexploitation of iron mining in China has caused serious environmental pollution. Therefore, establishing a stable ecological restoration with vegetation in mining areas has gradually aroused people's awareness and obtained extensive concerns. This study aimed to evaluate vegetation restoration with Robinia pseudoacacia (RP), Acer mono (AM) and Pinus koraiensis (PK) in iron mining compared with unrestored area, to investigate the soil environment factors and microbial communities, and to better understand the correlations between soil environment factors and soil microbial communities. Vegetation restoration could reduce soil pH and alleviate soil alkaline, and remarkably increase soil nutrients, especially in RP site. Analysis of 16S rRNA and ITS rRNA gene sequences provided a total of 645,004 and 906, 276 valid sequences clustered into 7091 OTUs and 1689 OTUs at a 0.03 genetic distance for bacteria and fungi, respectively. The predominant bacterial and fungal phyla were Actinobacteria and Ascomycota in studied sites, respectively. Additionally, revegetation significantly increased the relative abundances of Proteobacteria, Gemmatimonadetes, Bacteroidetes and Patescibacteria, and decreased the relative abundance of Actinobacteria. Robinia pseudoacacia harbored the highest soil fungal community diversity, and bacterial Simpson index and Shannon index. Vegetation restoration with RP could clearly shifted soil communities compared to AM and PK. Along with the restoration of vegetation, the remarkable abiotic changes were the accumulation of total C, total N, total P, available P, available N and available K and the decreasing of soil pH, which were the most important factors affecting soil microbial communities. Our results addressed that Robinia pseudoacacia was the best preferable species than AM and PK in improving soil nutrients, soil community diversity and structure in Fe mining, providing a helpful guideline for selection of tree species.

Arbuscular mycorrhizal fungal community differentiation along a post-coal mining reclamation chronosequence in South Africa: A potential indicator of ecosystem recovery

Arbuscular mycorrhizal (AM) fungi contribute to the restoration of soil ecological functions and processes during ecosystem development. Here, diversity and differentiation of AM fungi in rhizosphere soils and roots of the dominant vegetation along a post-coal mining reclamation soil chronosequence of 3, 11, 15, 19 and 24 years after reclamation were investigated. High-throughput sequence analysis of partial Glomeromycotan 18S rRNA in soils and roots revealed a high number of core operational taxonomic units (OTUs) across chronosequence. Arbuscular mycorrhizal fungal (AMF) OTU richness, Shannon-Weiner index and species dominance were not significantly different across soil and root but were significantly (P < 0.05) correlated with ammonium, nitrate, silt fraction, litter, pH, foliar and/or basal covers. AMF community structure was significantly different (P < 0.05) across unmined and reclamation chronosequence soils, with differentiation between younger reclaimed areas (3 and 11 years) and older reclamation ages (19 and 24 years) in multivariate space. In contrast, structural differentiation in the AMF community colonising the single plant-host across the chronosequence was not significant (PERMANOVA, P > 0.05), although community composition and structure were heterogeneous within 3–11 years but similar within 15–24 years. Seven Glomeromycotan genera were detected in soil and roots, including the relatively dominant Glomus genus, and the differentially abundant Acaulospora, Diversispora, Paraglomus and Scutellospora in either earlier or later years since post-mining reclamation. Canonical correspondence analysis revealed that nitrates (NO3-N), clay content and bulk density significantly influenced (P < 0.05) the AMF community structure in soil, whereas, the AMF community in root was not significantly influenced (P > 0.05) by environmental variables. Overall, the study suggests that AMF community differentiation reflect ecosystem development over chronological space-time. Thus, AMF species differentiation may be included as part of a minimum dataset for monitoring ecosystem restoration following post-mining reclamation.

Long-Term Potable Effects of Alkalescent Mineral Water on Intestinal Microbiota Shift and Physical Conditioning.

Background An alkalescent (pH 8.3) mineral water (AMW) of Hita basin, located in the northwestern part of Kyushu island in Japan, has been recognized for the unique quality of ingredients including highly concentrated silicic acid, sodium, potassium, and hydrogen carbonate. The biological effects of AMW intake were evaluated with a particular focus on its “antiobesity” properties through its modulation of the gut microbiota population. Methods Two groups of C57BL6/J mice (8-week-old male) were maintained with a standard diet and tap water (control: TWC group) or AMW (AMW group) for 6 months and the following outputs were quantitated: (1) food and water intake, (2) body weight (weekly), (3) body fat measurements by CT scan (monthly), (4) sera biochemical values (TG, ALT, AST, and ALP), and (5) UCP-1 mRNA in fat tissues (terminal point). Two groups of ICR mice (7-week-old male) were maintained with the same method and their feces were collected at the 0, 1st, 3rd, and 6th month at which time the population rates of gut microbiota were quantitated using metagenomic sequencing analysis of 16S-rRNA. Results Among all antiobesity testing items, even though a weekly dietary consumption was increased (p=0.012), both ratios of weight gain (p=1.21E − 10) and visceral fat accumulation (p=0.029) were significantly reduced in the AMW group. Other criteria including water intake (p=0.727), the amounts of total (p=0.1602), and subcutaneous fat accumulation (p=0.052) were within the margin of error and UCP-1 gene expression level (p=0.171) in the AMW group was 3.89-fold higher than that of TWC. Among 8 major gut bacteria families, Lactobacillaceae (increased, p=0.029) and Clostridiaceae (decreased, p=0.029) showed significant shift in the whole population. Conclusion We observed significantly reduced (1) weight gaining ratio (average −1.86%, up to −3.3%), (2) visceral fat accumulation ratio (average −4.30%, up to −9.1%), and (3) changes in gut microbiota population. All these consequences could support the “health benefit” functionality of AMW.

Metagenomic insights unveil the dominance of undescribed Actinobacteria in pond ecosystem of an Indian shrine

Actinobacteria have been an excellent source of novel antibiotics for several decades. However, their community remains unexplored in the pond sediments. The metagenomic analysis holds immense potential for identifying rare and uncharacterized microorganisms from many ecological habitats. The present study was designed to delineate and understand the bacterial diversity with special focus on Actinobacteria in pond sediment collected from Sanjeeviraya Hanuman Temple, Tamil Nadu, India. The sediment had an average temperature (25.32%), pH (7.13), salinity (0.960 Mmhos/cm) and high organic content (10.7%) posing minimal stress on growth condition of the microbial community. Subsequent molecular manipulations, sequencing and metagenomics analysis of 16S rRNA confirmed the presence of 40 phyla, 100 classes, 223 orders, 319 families and 308 genera in the sediment sample dominated by Acidobacteria (18.14%), Proteobacteria (15.13%), Chloroflexi (12.34), Actinobacteria (10.84%), and, Cyanobacteria (5.58%). Within the Actinobacteria phylum, Acidothermus (29.68%) was the predominant genus followed by Actinospica (17.65%), Streptomyces (14.64%), Nocardia (4.55%) and Sinomonas (2.9%). At the species level, only 15.2% within the Actinobacterial phylum were assigned to cultured species. This study reveals the huge unexplored diversity of Actinobacterial community indicating that the microbial ecology of pond sediment is a neglected field which needs attention and also illustrates the highly enriched bioactivity with potential pharmaceutical and industrial significance.

Acinetobacter Strain KUO11TH, a Unique Organism Related to Acinetobacter pittii and Isolated from the Skin Mucus of Healthy Bighead Catfish and Its Efficacy Against Several Fish Pathogens.

The bacterial strain KU011TH was isolated from the skin mucus of healthy bighead catfish. The strain is a Gram-negative coccobacillus that is nonmotile, aerobic, catalase positive, oxidase negative, and nonhemolytic. Sequence analyses of the housekeeping genes 16S rRNA, gyrB and rpoB indicate that this strain is a new member of the Acb complex of the genus Acinetobacter and is closely related to Acinetobacter pittii and Acinetobacter lactucae. In addition, the genome relatedness-associated ANIb (<95–96%) and in silico DDH (<70%) values clearly supported the new member of the genus Acinetobacter and the Acb complex. The genome of the strain KU011TH was approximately 3.79 Mbp in size, comprising 3619 predicted genes, and the DNA G+C content was 38.56 mol%. The major cellular fatty acids were C18:1ω9c, C16:0, C16:1, C20:2, C18:2ω6c and C18:1ω9t. The whole-genome sequences and phenotypic, phylogenetic, and chemotaxonomic data clearly support the classification of the strain KU011TH as a new member in the genus Acinetobacter which is closest to A. pittii. Additionally, the new bacterial strain exhibited strong activity against a broad range of freshwater fish pathogens in vitro.

Karakterisasi Protease Ekstraseluler Clostridium spp. T11-3

Protease is one of the leather commercial enzymes which is widely used such in food processing, medicine and leather industry. Clostridium sp T11-3 was isolated from Tiu Jeruk River in Nusa Tenggara Barat. Sequence analysis of 16S rRNA indicated that Clostridium spp T11-3 was closely related to C. bifermentans. This isolate produced maximum protease activity after 18 hours of cultivation in liquid media. Protease of Clostridium spp 11-3 displayed maximum activity at pH 5 and 60oC with casein as substrate. In the presence of 1 mM divalent ion Mg2+ the enzym activity increased to 141 %, while others ion divalent (Ca2+, Zn2+, Cu2+, Fe2+, and Co2+) inhibited protease activity.

Tabrizicola alkalilacus sp. nov., isolated from alkaline Lake Dajiaco on the Tibetan Plateau.

A novel Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium was isolated from Lake Dajiaco on the Tibetan Plateau. Strain DJCT grew without NaCl and tolerated up to 3 % (w/v) NaCl. Growth occurred at pH 6.0-10.0 (optimum, pH 7.0-8.0) and 15-37 °C (optimum, 25-30 °C). Vitamins were not required for growth. The main polar lipids of strain DJCT were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-10. The major fatty acid was C18 : 1ω7c. Genome sequencing revealed a genome size of 4.61 Mbp and a G+C content of 62.9 mol%. Analysis of 16S rRNA sequences showed that strain DJCT belonged to the genus Tabrizicola, with the closest neighbour Tabrizicola aquatica RCRI19T (97.5 %). DNA-DNA relatedness between strain DJCT and the closest phylogenetically related strain T. aquatica RCRI19T was 40.8 %. Stain DJCT was clearly distinguished from the type strain mentioned above through phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristic comparisons. Based on its phenotypic and chemotaxonomic characteristics, strain DJCT could be classified as a representative of a novel species of the genus for which the name Tabrizicola alkalilacus sp. nov. is proposed. The type strain is DJCT (=CICC 24242T=KCTC 62173T).

Diversity of Nocardia species isolated from transplantation and cancer centers of Tehran hospitals.

Objective: To identify the biodiversity of Nocardia species isolated from the environments of Tehran hospitals via phenotypic and PCR molecular methods. Methods: A total of 236 samples were collected from the transplantation and cancer centers of five Tehran hospitals, and the presence of Nocardia was identified by using standard protocols. Conventional tests were used for preliminary identification, and PCR amplification of the 598 bp amplicon of the 16S rRNA and sequence analysis of 16S rRNA were performed for genus and species identification. Results: From the 236 soil samples, 16 samples were identified as positive based on the culture tests, while 8 samples showed positive results based on the molecular method. The phylogenetic tree showed that the most frequent genus of Nocardia was related to Nocardia cyriacigeorgica. Conclusion: The hospital environment is a potential reservoir of a diverse range of Nocardia species. Due to the strong capability of survival, these bacteria bring a threat to the health of patients. Its identification can help physicians to implement treatments and is important for healthcare centers.

Niche partitioning of methane-oxidizing bacteria along the oxygen-methane counter gradient of stratified lakes.

Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen-methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen-methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and pmoA genes, and 16S rRNA and pmoA transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen-methane interface. The interface sometimes harbored additional taxa. Within the dominant Methylococcales, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions. Candidatus Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen-methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.

Isolation and characterization of bioactive compounds with antibacterial, antioxidant and enzyme inhibitory activities from marine-derived rare actinobacteria, Nocardiopsis sp. SCA21

A rare actinobacteria strain designated SCA21, producing bioactive metabolites was isolated from marine sediment of Havelock Island, Andaman and Nicobar Islands, India. Analysis of 16S rRNA sequences suggested that the strain SCA21 belonged to the genus Nocardiopsis. Chemical investigation of the fermentation broth led to the isolation of two pure bioactive compounds (1-2). Compound 1: 4-bromophenol, a bromophenol derivative; Compound 2: Bis (2-ethylhexyl) phthalate, a phthalate ester. The structure of compound 1 and 2 were elucidated by the detailed analysis of FT-IR, HR-ESI-MS, 1D and 2D NMR, along with literature data analysis. The isolated metabolites were evaluated for enzyme inhibition activity against α-glucosidase and α-amylase, free radical scavenging activity against DPPH and ABTS radicals, metal chelating and antibacterial activity against clinical pathogens. 1 and 2 exhibited remarkable enzyme inhibitory activities against α-glucosidase. However, Compound 2 was found less active against α-amylase. They showed significant free radical scavenging activity against DPPH and ABTS radicals. In addition, except the strain Salmonella typhi ATCC 25241 and Listeria cytogens ATCC 13932, 1 and 2 showed broad spectrum inhibitory activity against MRSA ATCC NR-46171, MRSA ATCC-46071, Klebsiella pneumonia ATCC 13883, Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 12600. In conclusion, to best of our knowledge these findings are the first report of isolation of 4-bromophenol and Bis (2-ethylhexyl) phthalate from genus Nocardiopsis, thus suggesting that rare actinomycetes are promising source of therapeutically important bioactive metabolites.

ISOLATION, CHARACTERIZATION AND FORMULATION OF ANTAGONISTIC BACTERIA AGAINST FUNGAL PLANT PATHOGENS

Concerns regarding food safety and the environment have led to reduced use ofagrochemicals and the development of sustainable agriculture. In this context,biological control of fungal plant pathogens can improve global food availability,one of the three pillars of food security, by reducing crop losses, particularly forlow-income farmers. Antagonistic bacteria are common soil inhabitants withpotential to be developed into biofungicides for the management of fungal plantpathogens. In this study, antagonistic bacterium was isolated from the commercialcompost from a Resen factory for compost and screened for its growth inhibition offungal pathogens in laboratory tests. The zone of inhibition (mm) was recorded bymeasuring the distance between the edges of the growing mycelium and theantagonistic bacterium. Five replications were maintained for each isolate. Basedon phenotypic characteristics, biochemical tests, and sequence analysis of 16SrRNA, the antagonistic bacterium was identified as Paenibacillus alvei (strain DZ-3). The bacterium suppressed the growth of all five tested fungal plant pathogens(Fusarium oxysporum, Rhizoctonia solani, Alternaria alternata, Botrytis cinereaand Plasmopara viticola) in in vitro conditions over. The survival of antagonisticbacterium in peat and talc formulations decreased time at room temperature, butthe populations remained above 108 CFU/g during the 180-day storage period. Thisstudy suggests that this bacterium can be developed and formulated asbiofungicides for minimizing the crop losses caused by fungal plant pathogens anddiseases caused by them.

Occurrence, Genetic Diversities And Antibiotic Resistance Profiles Of Salmonella Serovars Isolated From Chickens.

PurposeContamination with Salmonella on food products and poultry in particular has been linked to foodborne infections and/or death in humans. This study investigated the occurrence, genetic diversities and antibiotic resistance profiles of Salmonella strains isolated from chickens.Patients and methodsTwenty each duplicate faecal swab samples were collected from five different poultry pens of broilers, layers and indigenous chickens in the North-West Province, South Africa. Isolates identities were confirmed through amplification and sequence analysis of 16S rRNA and the invA gene fragments after which phylogenetic tree was constructed. Salmonella enteritidis (ATCC:13076TM), Salmonella Typhimurium (ATCC:14028TM) and E. coli (ATCC:259622TM) were used as positive and negative controls, respectively. The serotypes of Salmonella isolates were determined. Antibiotic-resistant profiles of the isolates against eleven antimicrobial agents were determined.ResultsEighty-four (84%) of representative isolates possessed the invA genes. The percent occurrence and diversity of Salmonella subspecies in chickens were 1.81–30.9% and was highest in Salmonella enterica subsp. enterica. Notably, the following serotypes Salmonella bongori (10.09%), Salmonella Pullorum (1.81%), Salmonella Typhimurium (12.72%), Salmonella Weltevreden, Salmonella Chingola, Salmonella Houten and Salmonella Bareily (1.81%). Isolates (96.6%) displayed multidrug resistance profiles and the identification of isolates with more than nine antibiotic resistance was a cause for concern.ConclusionThis study indicates that isolates had pre-exposure histories to the antibiotics tested and may pose severe threats to food security and public health.

Molecular, serological, and parasitological detection of Babesia vogeli in dogs in the state of Piauí, Brazil

Studies on canine babesiosis in northeastern Brazil are scarce, although the weather conditions in this region are favorable for the development of the tick vector. This study determined the prevalence of Babesia vogeli in dogs sampled in Teresina, state of Piauí, northeast Brazil, using direct and indirect diagnostic methods and performed a phylogenetic analysis of 18S rRNA sequences. A total of 315 dogs were screened during routine care regardless of clinical suspicion. Blood was collected by jugular venipuncture to perform indirect immunofluorescence assay (IFA) and polymerase chain reaction (PCR) and for parasite screening in peripheral blood smears. Positivity was 2.2% (7/315) by microscopy, 4.8% (15/315) by PCR, and 48.6% (153/315) by IFA. PCR amplified a 602-bp fragment of the piroplasmid 18S rRNA gene, and sequence alignment and analysis revealed 99% homology with B. vogeli isolates from other regions of Brazil and other countries. In addition, there was high variability among sequences from other northeast states of Brazil. This study is the first to perform the molecular analysis of B. vogeli in Piauí. The results demonstrate that canine babesiosis is endemic in dogs sampled in Teresina and that PCR may be the method of choice to perform parasite screening in this region.

Detoxification of Deoxynivalenol by a Mixed Culture of Soil Bacteria With 3-epi-Deoxynivalenol as the Main Intermediate.

Deoxynivalenol (DON) is a widely distributed mycotoxin that frequently occurs in various agricultural raw materials and feeds. DON acts as a virulence factor that accelerates the spread of plant diseases; moreover, its accumulation in grains causes yield loss and serious health problems to humans and livestock. Biodegradation of DON into less- or non-toxic substances using naturally existing microorganisms is considered the best approach for DON detoxification. Although various single isolates and mixed cultures capable of detoxifying DON have been reported, details of the metabolic pathways and the degrading enzymes/coding genes involved are scarce. In this study, we aimed to isolate DON-degrading bacteria from soil samples and explore the mechanisms. Toward this end, 85 soil samples collected from different provinces in China were enriched under aerobic conditions with mineral media containing 50 μg/ml of DON as the sole carbon source. The bacterial consortium LZ-N1 exhibited highly efficient and steady DON-transforming activity. High-throughput sequencing was used to characterize the composition of the involved microflora, and analysis of 16S rRNA sequences indicated that LZ-N1 was composed of at least 11 bacterial genera, with Pseudomonas accounting for nearly half the relative abundance. Coincubation of a mixed culture of two novel strains from the LZ-N1 consortium, namely Pseudomonas sp. Y1 and Lysobacter sp. S1, showed sustained transformation of DON into the metabolite 3-epi-deoxynivalenol, with no degradation products detected after 72 h. The cell-free supernatant, lysate, and cell debris of the mixed culture possessed DON-degrading ability, with the supernatant reaching a DON degradation rate of 100% within 48 h with 50 μg/ml of DON. This is the first report of two-step enzymatic epimerization of DON by a mixed culture, which may provide a new insight into this pathway for future applications in detoxification of DON-contaminated cereals and feed.

Isolation, identification and characterisation of an emerging fish pathogen, Acinetobacter pittii, from diseased loach (Misgurnus anguillicaudatus) in China.

Although members of the genus Acinetobacter have emerged as important nosocomial pathogens causing severe human infections, there are few reports about their occurrence as fish pathogens. In this study, five bacterial strains were isolated from diseased loach (Misgurnus anguillicaudatus) cultured in a farm in China. The diseased loach displayed shedding of skin mucus and many petechial haemorrhages all over the body. Based on sequence analyses of 16S rRNA and rpoB genes, the isolates were identified as Acinetobacter pittii. An experimental infection assay confirmed their pathogenicity to loach. The results of artificial infection in zebrafish (Barchydanio rerio) and nematode (Caenorhabditis elegans) suggested that, as well as loach, these A. pittii isolates are pathogenic and highly virulent to these organisms. Multilocus sequence typing analysis revealed that all the isolates belong to sequence type (ST) 839, which may be the dominant clone causing fish disease and exhibits a close phylogenetic relationship with ST396 from human clinical samples in Korea or Taiwan China. This is the first report demonstrating that A. pittii is an emerging causal agent of mass mortality in loach and poses significant risks to fish culturing besides causing human clinical infection worldwide.