Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms

Diversity of Gut Bacteria of Field-Collected Aedes aegypti Larvae and Females, Resistant to Temephos and Deltamethrin

The Aedes aegypti mosquito serves as a vector for several diseases, including dengue, Zika, chikungunya, and yellow fever. This species is well adapted to urban environments and poses a significant threat to public health. Some studies suggest that the gut bacteria of insect vectors may play a crucial role in developing resistance to insecticides. This study assessed the resistance of Ae. aegypti from Florencia, Caquetá, to temephos and deltamethrin and analyzed the diversity of gut bacteria in resistant larvae and adult females. Larvae exhibited resistance to temephos at a lethal concentration 50 (LC50) of 0.034 µg/mL, while females showed resistance to deltamethrin at a discriminant concentration of 10 µg/mL. The bacterial load in the guts of deltamethrin-treated females (3.42 × 106 CFU/mL) was significantly higher compared to temephos-treated larvae (9.4 × 105 CFU/mL) and untreated females (8 × 104 CFU/mL). A total of sixty-eight bacterial strains were isolated from the guts of both larval and resistant females Ae. aegypti, with 31 strains identified through 16S rRNA gene analysis and 11 confirmed by gyrB gene sequencing. In untreated females, Bacillus comprised 12.55% of the gut bacteria and was identified as an exclusive genus. In resistant larvae, Serratia was the most abundant and exclusive genus, accounting for 35.29%, while in resistant females, Cedecea was the predominant genus, representing 66.67%. These findings suggest that gut bacteria may influence the resistance of Ae. aegypti to temephos and deltamethrin. Furthermore, this research provides valuable information that can be considered for the design of local vector control strategies. The results highlight new research focused on the study of insecticide tolerance and degradation within the gut microbiota of insect vectors of arboviruses.

Development and validation of a LAMP-based method for rapid and reliable detection of Xanthomonas albilineans, the causal agent of sugarcane leaf scald

Introduction

Xanthomonas albilineans (Xalb)-induced leaf scald (LS) is a significant bacterial disease affecting sugarcane and posing a global threat to the sugarcane industry. The presence of irregular symptoms makes traditional phenotypic detection difficult, and molecular methods necessitate costly equipment, labor, and extended sample-to-answer processing times.

Methods

This study introduces an innovative rapid DNA isolation method requiring no reagents, combined with an isothermal amplification-based assay for efficient detection of Xalb DNA in sugarcane xylem sap, leaf tissue, and meristematic tissue samples. Sugarcane samples from infected plants were subjected to heat lysis, followed by loop-mediated isothermal amplification (LAMP)-based fluorescence and colorimetric quantification within a single microcentrifuge tube.

Results

The method exhibited exceptional detection sensitivity (detecting as low as 1 cell/μL), reproducibility [with a standard deviation (SD) of <5% for n = 3], and a broad linear dynamic range (10 pM to 1 aM or 107-100 copies/μL, r = 0.99). Quantification of Xalb was accurately correlated with sugarcane cultivar disease ratings. Validation using qPCR showed 91-98% agreement. This assay also effectively determined optimal sampling times and plant parts by monitoring the progression of the disease over time.

Discussion

This diagnostic assay holds significant potential as a commercial opportunity for a kit-based DNA extraction/purification-free molecular detection alternative. It can be adapted into a handheld device, enabling on-farm detection and quantification of the pathogen responsible for LS disease.

Insights on the virulence and genomic features of Lactococcus garvieae isolated from giant freshwater prawn Macrobrachium rosenbergii (de Man 1879)

Giant freshwater prawn (Macrobrachium rosenbergii (MR)) is a significant aquafarm species commercially cultured in Taiwan. Intensive farming practices have led to the outbreak of Lactococcus garvieae (LG), which causes Lactococcosis in MR. Recently, LG has re-emerged and the number of mortalities in prawn farms has increased in Taiwan. However, there is no preventative strategy described and a lack of knowledge on virulence factors and pathogenesis from LG in MR. The most virulent strain of L. garvieae from M. rosenbergii was screened in vivo among seven isolates selected for infectivity testing injecting 0.1 mL of 108 CFU/mL bacterial concentration. Among the seven isolates screened, L. garvieae 109-6 resulted in 100% mortality within 3 days post-infection. Furthermore, 109-6 L. garvieae LD50 dosage from in MR was found to be 106 CFU/mL. Subsequently, the most virulent strain 109-6 was sequenced using MinIon Nanopore sequencing. Results indicated that the LG genome yielded a protein-coding of 3857 with 59 tRNA and 16 rRNA and no plasmid. Interestingly, the distribution of subsystems in the annotated genome revealed genes related to virulence, defence, and disease among LG 50 genes. Altogether, the virulent strain and its genome data revealed distinctive features of LG, which hinted toward its pathogenicity and could facilitate for better preventive strategies.

Comparative analysis of Spodoptera frugiperda (J. E. Smith) (Lepidoptera, Noctuidae) corn and rice strains microbiota revealed minor changes across life cycle and strain endosymbiont association

Background

Spodoptera frugiperda (FAW) is a pest that poses a significant threat to corn production worldwide, causing millions of dollars in losses. The species has evolved into two strains (corn and rice) that differ in their genetics, reproductive isolation, and resistance to insecticides and Bacillus thuringiensis endotoxins. The microbiota plays an important role in insects' physiology, nutrient acquisition, and response to chemical and biological controls. Several studies have been carried out on FAW microbiota from larvae guts using laboratory or field samples and a couple of studies have analyzed the corn strain microbiota across its life cycle. This investigation reveals the first comparison between corn strain (CS) and rice strain (RS) of FAW during different developmental insect stages and, more importantly, endosymbiont detection in both strains, highlighting the importance of studying both FAW populations and samples from different stages.

Methods

The composition of microbiota during the life cycle of the FAW corn and rice strains was analyzed through high-throughput sequencing of the bacterial 16S rRNA gene using the MiSeq system. Additionally, culture-dependent techniques were used to isolate gut bacteria and the Transcribed Internal Spacer-ITS, 16S rRNA, and gyrB genes were examined to enhance bacterial identification.

Results

Richness, diversity, and bacterial composition changed significantly across the life cycle of FAW. Most diversity was observed in eggs and males. Differences in gut microbiota diversity between CS and RS were minor. However, Leuconostoc, A2, Klebsiella, Lachnoclostridium, Spiroplasma, and Mucispirilum were mainly associated with RS and Colidextribacter, Pelomonas, Weissella, and Arsenophonus to CS, suggesting that FAW strains differ in several genera according to the host plant. Firmicutes and Proteobacteria were the dominant phyla during FAW metamorphosis. Illeobacterium, Ralstonia, and Burkholderia exhibited similar abundancies in both strains. Enterococcus was identified as a conserved taxon across the entire FAW life cycle. Microbiota core communities mainly consisted of Enterococcus and Illeobacterium. A positive correlation was found between Spiroplasma with RS (sampled from eggs, larvae, pupae, and adults) and Arsenophonus (sampled from eggs, larvae, and adults) with CS. Enterococcus mundtii was predominant in all developmental stages. Previous studies have suggested its importance in FAW response to B. thuringensis. Our results are relevant for the characterization of FAW corn and rice strains microbiota to develop new strategies for their control. Detection of Arsenophonus in CS and Spiroplasma in RS are promising for the improvement of this pest management, as these bacteria induce male killing and larvae fitness reduction in other Lepidoptera species.

Nocardiosis and other common diseases of cultured golden pompano (Trachinotus blochii) in Taiwan

Golden pompano (Trachinotus blochii) is a carnivorous teleost cultured in the Asia-Pacific region. Fish culture in high densities and numbers results in disease outbreaks, causing huge economic losses. Here, we collected cultured golden pompanos from 2021 to 2022 and identified the pathogens isolated from the diseased fish. Out of a total of 64 clinical cases observed in both sea cages and fish ponds, it was found that Nocardia seriolae was the predominant pathogen (26%), followed by Lactococcus garvieae (13%). Trichodina spp. was the most prevalent parasite in sea cages and earthen ponds (21%), while Neobenedenia spp. was the primary parasitic pathogen (16%) in sea cages. Given these findings, further investigations were conducted, including antibiotic susceptibility and pathogenicity tests specific to N. seriolae in golden pompanos. Antibiotic susceptibility tests of N. seriolae revealed that all strains were susceptible to doxycycline, oxytetracycline, florfenicol and erythromycin but resistant to amoxicillin and ampicillin. Additionally, a pathogenicity assessment was carried out by administering an intraperitoneal injection of 0.1 mL containing 107  CFU of N. seriolae per fish. The mortality rates observed varied between 40% and 90%, with the P2 strain exhibiting the highest level of virulence, resulting in a cumulative mortality of 90%. Therefore, disease outbreaks in fish can be minimized by developing effective treatments and prevention methods.

Application of Advanced Molecular Methods to Study Early-Onset Neonatal Sepsis

Early-onset sepsis (EOS) is a global health issue, considered one of the primary causes of neonatal mortality. Diagnosis of EOS is challenging because its clinical signs are nonspecific, and blood culture, which is the current gold-standard diagnostic tool, has low sensitivity. Commonly used biomarkers for sepsis diagnosis, including C-reactive protein, procalcitonin, and interleukin-6, lack specificity for infection. Due to the disadvantages of blood culture and other common biomarkers, ongoing efforts are directed towards identifying innovative molecular approaches to diagnose neonates at risk of sepsis. This review aims to gather knowledge and recent research on these emerging molecular methods. PCR-based techniques and unrestricted techniques based on 16S rRNA sequencing and 16S-23S rRNA gene interspace region sequencing offer several advantages. Despite their potential, these approaches are not able to replace blood cultures due to several limitations; however, they may prove valuable as complementary tests in neonatal sepsis diagnosis. Several microRNAs have been evaluated and have been proposed as diagnostic biomarkers in EOS. T2 magnetic resonance and bioinformatic analysis have proposed potential biomarkers of neonatal sepsis, though further studies are essential to validate these findings.

Comparison of genotyping methods and toxin gene profiles of Staphylococcus aureus isolates from clinical specimens

Staphylococcus aureus is a frequent cause of infections worldwide. Methicillin-resistant S. aureus (MRSA) is one of the main causes of Gram-positive infections, and methicillin-susceptible strains (MSSA) primarily colonize and infect community hosts. Multiple virulence factors are involved, with toxins playing a significant role in several diseases. In this study, we assess the prevalence of toxin genes in 89 S. aureus clinical isolates (31 MRSA and 58 MSSA). We evaluated the discriminatory power of the association of internal transcribed spacer-PCR (ITS-PCR) and 3'- end coa gene ( coa-PCR) when compared with other more commonly used and costly techniques. The isolates showed a high level of genetic diversity, and toxins were found in all the isolates. While most toxin classes displayed no statistically significant correlations and were equally distributed in isolates regardless of their resistance status, classic enterotoxins ( sea-see) showed a positive correlation with MSSA isolates. The combination of coa-PCR with ITS-PCR showed a discriminatory index of 0.84, discriminating 22 genotypes that agree with previously determined data by PFGE and MLST. This association between the two PCR-based methods suggests that they can be useful for an initial molecular epidemiological investigation of S. aureus in hospitals, providing significant information while requiring fewer resources.

First identification, molecular characterization, and pathogenicity assessment of Lactococcus garvieae isolated from cultured pompano in Taiwan

Lactococcosis, caused by Lactococcus garvieae, is an acute hemorrhagic septicemia in fish recorded in marine and freshwater aquaculture during the summer months. In 2020-2021, several sea cage Pompano farms recorded sudden fish mortality events. Based on the results of phenotypic and biochemical tests, L. garvieae was predicted to be the cause. PCR with L. garvieae specific primers (pLG1 and pLG2) targeting the 16S rRNA region further confirmed the etiological agent as L. garvieae after amplifying an 1100 base pairs (bp) product. Furthermore, the 16S rRNA sequences of the two representative strains (AOD109-196-2B and AOD110-215-2B) shared 99.81% identity with L. garvieae (GenBank accession number: MT597707.1). The genetic profiles of the strains were classified using pulsed-field gel electrophoresis after digestion with SmaI and ApaI, which clustered our strains under the same pulsotype. Multiplex PCR targeting the capsule gene cluster and serotype-specific PCR collectively showed that the strains were non-capsulated; thus, they belonged to serotype I. An experimental infection was designed to fulfil Koch's postulates by infecting healthy Pompano with case-driven L. garvieae strains (AOD109-196-2B and AOD110-215-2B) with a cumulative mortality of 70%. Overall, L. garvieae infection in Pompano emphasizes the need for better monitoring and control procedures in aquaculture settings.

Genotypes and virulence factors in Staphylococcus aureus isolated from dairy cows with subclinical mastitis in Serbia

This study aimed to determine the prevalence of Staphylococcus aureus subclinical mastitis and to genotype the S. aureus isolates using the 16S-23S rRNA intergenic spacer (RS-PCR) method. In addition, the genes responsible for adherence, biofilm formation, host evasion, tissue necrosis, methicillin resistance, and enterotoxin production of S. aureus were investigated. The overall prevalence of S. aureus subclinical mastitis in lactating cows was 5.4% (95% confidence interval, CI=4.7-6.1%). An increased risk of S. aureus intramammary infection was observed on small family farms (odds ratio, OR=4.2, 95% CI=2.6-6.6, P < 0.001) and medium-sized farms (OR=3.5, 95% CI=2.2-5.7, P < 0.001). The RS-PCR analysis revealed 44 genotypes and genotype variants, of which 15 new genotypes and five new variants were detected within small and medium-sized farms. S. aureus isolates of new genotypes and genotype variants carried the clfA gene responsible for adherence at a lower frequency (64.8%) and enterotoxin-producing genes sea (20.4%), seb (14.8%) and sec (14.8%) at a higher frequency than the other known genotypes (P < 0.001), and were confirmed to carry the sej and sep genes. The spa gene was detected in all S. aureus isolates, whereas none harbored bap, ser, or tsst-1 genes. Methicillin-resistant strains of S. aureus (MRSA) were also detected, with a higher prevalence (19.2%) on large farms with more than 50 cows (P < 0.001). Using molecular techniques as diagnostic tools provides a better understanding of intramammary staphylococcal infections' occurrence, spread, and eradication.

Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins

Background

Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.

Methods

The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.

Results

Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.

Bacterial culture and susceptibility of samples taken from septic foot lesions of adult beef cattle

BACKGROUND

Lameness is an economically important and common disease of cattle, and foot disease is the most common cause of lameness in cattle. Limited data is available regarding lameness in cow-calf operations.

OBJECTIVES

Describe the bacteria most commonly isolated from septic lesions of the feet of adult beef cattle and the antimicrobial susceptibility patterns of the isolated bacteria.

ANIMALS

Fifty-four adult cattle from cow-calf operations and diagnosed with a sole abscess or distal interphalangeal joint sepsis were enrolled.

METHODS

Prospective observational study. Abscess fluid from a convenience sample of clinical cases was cultured. Isolated bacteria were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry or 16s rRNA gene sequencing. Antimicrobial susceptibility profiling was performed on isolates when a bacterial species was identified from ≥5 samples.

RESULTS

Fifty of the 54 samples were polymicrobial. Trueperella pyogenes (22/54), Streptococcus uberis (16/54), and Bacteroides pyogenes (14/54) were the most commonly isolated bacteria. Eighty-one of 96 tested isolates were resistant to at least 1 antimicrobial; multidrug resistance was identified in 37/96 isolates. Oxytetracycline (50/96), tylosin (40/96), and florfenicol (37/96) resistance was commonly identified. Resistance to ceftiofur (5/96) was rare.

CONCLUSIONS AND CLINICAL IMPORTANCE

Septic processes of the foot in these adult beef cattle frequently were polymicrobial. Most of the isolated bacteria were resistant to at least 1 antimicrobial with over one-third being multidrug resistant. Although simple sole abscesses do not require antimicrobial treatment, deep septic processes of the foot often are treated with antimicrobials. Culture and susceptibility of deep septic lesions may guide judicious antimicrobial usage.

Enterococcus faecium 129 BIO 3B is classified as Enterococcus lactis 129 BIO 3B

Enterococcus faecium 129 BIO 3B is a lactic acid bacterium that has been safely used as a probiotic product for over 100 years. Recently, concerns about its safety have arisen because some species of E. faecium belong to the vancomycin-resistant enterococci. The groups of E. faecium with less pathogenic potential have been split into a separate species (Enterococcus lactis). In this study, I investigated the phylogenetic classification and safety of E. faecium 129 BIO 3B as well as E. faecium 129 BIO 3B-R, which is naturally resistant to ampicillin. Mass spectrometry and basic local alignment search tool analysis using specific gene regions failed to differentiate 3B and 3B-R into E. faecium or E. lactis. However, multilocus sequence typing successfully identified 3B and 3B-R as the same sequence types as E. lactis. Overall genome relatedness indices showed that 3B and 3B-R have high degrees of homology with E. lactis. Gene amplification was confirmed for 3B and 3B-R with E. lactis species-specific primers. The minimum inhibitory concentration of ampicillin was confirmed to be 2 µg/mL for 3B, which is within the safety standard for E. faecium set by the European Food Safety Authority. Based on the above results, E. faecium 129 BIO 3B and E. faecium 129 BIO 3B-R were classified as E. lactis. The absence of pathogenic genes except for fms21 in this study demonstrates that these bacteria are safe for use as probiotics.

Development of a Real-Time Quantitative PCR Assay for the Specific Detection of Bacillus velezensis and Its Application in the Study of Colonization Ability

Bacillus velezensis is a widely used biocontrol agent closely related to B. amyloliquefaciens, and the two species cannot be distinguished by universal primers that are currently available. The study aimed to establish a rapid, specific detection approach for B. velezensis. Many unique gene sequences of B. velezensis were selected through whole genome sequence alignment of B. velezensis strains and were used to design a series of forward and reverse primers, which were then screened by PCR and qPCR using different Bacillus samples as templates. The colonization ability of B. velezensis ZF2 in different soils and different soil environmental conditions was measured by qPCR and a 10-fold dilution plating assay. A specific primer pair targeting the sequence of the D3N19_RS13500 gene of B. velezensis ZF2 was screened and could successfully distinguish B. velezensis from B. amyloliquefaciens. A rapid specific real-time qPCR detection system for B. velezensis was established. B. velezensis ZF2 had a very strong colonization ability in desert soil, and the optimal soil pH was 7-8. Moreover, the colonization ability of strain ZF2 was significantly enhanced when organic matter from different nitrogen sources was added to the substrate. This study will provide assistance for rapid specificity detection and biocontrol application of B. velezensis strains.

Detection of pathogenic bacteria in milk and whey samples using a fluorescence resonance energy transfer aptasensor based on cerium oxide nanoparticles

Herein, we present a facile and sensitive fluorescence resonance energy transfer (FRET) aptasensor for the detection of pathogenic bacteria, where antibiotic-functionalized cerium oxide nanoparticles were served as an energy donor and aptamer-modified gold nanoparticles (aptamer-AuNPs) were employed as an energy acceptor. To illustrate the feasibility of this strategy, Escherichia coli (E. coli) was examined. The strategy for the detection of E. coli bacteria as a target molecule is described using the FRET pair of azithromycin-functionalized CeO₂ nanoparticles (Azm-CeO₂NPs) and aptamer-AuNPs. The spectral overlap between these two nanoparticles and Azm and the aptamer binding on the surface of E. coli specifically provides the condition, which leads to the occurrence of the FRET phenomenon. In this way, a good linear correlation between the fluorescence intensity of Azm-CeO₂NPs and E. coli concentration was obtained in the range of 10-1.5 × 10⁵ cfu mL^-1. The detection limit of the proposed method at a signal to noise ratio of 3 (3σ) was estimated to be 1.04 cfu mL^-1. Further, the proposed method was applied to detect E. coli in real samples within 30 min, which indicates the applicability of the proposed method. This method could be used for other pathogenic bacterium recognition or synchronous detection by employing molecules that are particular to the desired bacteria.

Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations

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This study report statistically significant differences in beta-diversity correlated with soil properties, including Cd concentrations.

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Culture-dependent techniques allowed the isolation of bacterial strains tolerating high Cd concentrations up to 120 mgL⁻¹ for potencial Cd biosorption or intracellular sequestration.

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The combination of different approaches provides a baseline about the bacterial composition and Cd tolerant strains found in these soils influence for lower Cd accumulation in cocoa crops.

Heavy metals can be found in soil as natural components or as product of contaminations events; plants growing in soils are prone to bioaccumulate heavy metals on their biomass. Theobroma cacao L. can bioaccumulate cadmium (Cd) in the seed and could be in derived food products, it considered a human health risk; therefore, removal of Cd is desirable but not vet technically and economically feasible; only to avoid Cd in cocoa is by selecting lands plots exhibiting lower Cd concentrations in soils, imposing a serious limitation to farmers and regulators. The study of bacterial communities and isolation bacteria with tolerance and mechanisms to counteract the translocation of Cd to the parts of cocoa plant exhibits high relevance in Colombia economy and especially to companies producing chocolate and derivatives. Here, we explore bacterial communities associated with soils having relatively high natural Cd concentrations in a large agricultural cocoa plot located in the Santander region. We characterized the bacterial communities’ compositions by amplicon 16S rRNA sequencing from metagenomics soil DNA and by culturing-based enumeration and isolation approaches.

Culture-dependent techniques allowed the isolation of bacteria tolerant to Cd concentration, complement the information for Colombia, and expand the number of strains characterized with adaptive capacity against Cd with tolerance in a concentration of 120 mg/L, which represents the first capacity for Exiguobacterium sp., Ralstonia sp., Serratia sp., Dermacoccus sp., Klebsiella sp., Lactococcus sp. and Staphylococcus sp. In addition to confirming that there is a greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa in Colombia. As for the results of new generation sequencing, they revealed that, the alpha-diversity in bacterial composition, according to the ANOVA, there are statistically significant differences of the bacterial communities present in the samples. Regarding Pearson correlation analysis, it was found the Shannon Simpson indices, have a positive correlation against OM, C, pH, Mn, C.E.C.I., Ca, P and negatively correlated with S; respect to bacterial community structure, a principal component analysis, which revealed that independent of the concentration of Cd present in soil samples, separates them according to pH value. Phyla to high abundance relative in all samples were Proteobacteria, Acidobacteriota, Actinobacteriota, Verrucomicrobiota, Myxococcota, Chloroflexi, Plactomycetota, Bacteroidota, Gemmatimonadota, Nitrospirota, Firmicutes and NB1_J; the bacteria genera with higher relative abundance (>0.5%) Nitrospira, candidatus Udaeobacter, Haliangium, Cupriavidus, MND1, Bacillus, Kitasatospora, Niveibacterium, Acidothermus, Burkholderia, Acidibacter, Terrimonas, Gaiella, candidatus Solibacter, Kitasatospora, Sphingomonas, Streptomyces, this genus with a relationship with the Cd tolerance process. After it, redundancy analysis was performed between the variation of the bacterial communities identified by dependent and independent techniques and edaphic soil variables, where their positive correlation was found against K, OM, C, Ca, pH (p<0.01) and P, C.E.C.I (p<0.05). For soil samples, the bacterial genera that make up the core community were identified, which are present in all samples as Nitrospira sp., Cupriavidus sp., Burkholderia sp., Haliangium sp., candidatus Udaeobacter, MND1, Kitasatospora, Acidothermus, Acidibacter, Streptomyces, Gaiella, candidatus Solibacter and Terramonas; the genera identified has a different and fundamental role in ecosystem functioning. The combination of different approaches offers new clues regarding the assessment of bacterial communities in soils cultivated with cocoa in soils with elevated Cd content in Colombia, and the ecological role and interplay of soil components and bacterial communities that contribute to modulate the effect of bioaccumulation in products.

Study of the diversity of 16S-23S rDNA internal transcribed spacer (ITS) typing of Escherichia coli strains isolated from various biotopes in Tunisia

We investigated the 16S-23S rRNA intergenic spacer region (ISR)-PCR and the phylogenetic PCR analyses of 150 Escherichia coli isolates as tools to explore their diversity, according to their sampling origins, and their relative dominance in these sampling sources. These genetic markers are used to explore phylogenetic and genetic relationships of these 150 E. coli isolates recovered from different environmental sources (water, food, animal, human and vegetables). These isolates are tested for their biochemical pattern and later genotyped through the 16S-23S rRNA intergenic spacer PCR amplification and their polymorphism investigation of PCR-amplified 16S-23S rDNA ITS. The main results of the pattern band profile revealed one to four DNA fragments. Distributing 150 E. coli isolates according to their ITS and using RS-PCR, revealed four genotypes and four subtypes. The DNA fragment size ranged from 450 to 550 bp. DNA band patterns analysis revealed considerable genetic diversity in interspecies. Thus, the 450 and 550 bp sizes of the common bands in all E. coli isolates are highly diversified. Genotype I appeared as the most frequent with 77.3% (116 isolates), genotype II with 12% (18 isolates); genotype III with 9.7% (14 isolates), and the IV rarely occurred with 4% (2 isolates). Distributing the E. coli phylogroups showed 84 isolates (56%) of group A, 35 isolates (23.3%) of group B1, 28 isolates (18.7%) of group B2 and only three isolates (2%) of group D.

Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia

Spodoptera frugiperda is a polyphagous pest of several crops of economic importance. Nowadays, the insect is broadly distributed in America and, recently, in Africa, Asia, and Australia. The species has diverged into corn and rice strains. The role of the gut microbiota in insect physiology is relevant due to its participation in crucial functions. However, knowledge of seasonal variations that alter the gut microbiome in pests is limited. Gut microbiome composition between the dry and rainy seasons was analyzed with cultured and uncultured approaches in S. frugiperda corn strain larvae collected at Northwest Colombia, as seasonal microbiome changes might fluctuate due to environmental changes. On the basis of culture-dependent methods, results show well-defined microbiota with bacterial isolates belonging to Enterococcus, Klebsiella (Enterobacteriales: Enterobacteriaceae), Enterobacter (Enterobacterales: Enterobacteriaceae), and Bacillus (Bacillales: Bacillaceae) genera. The community composition displayed a low bacterial diversity across all samples. The core community detected with uncultured methods was composed of Enterococcus, Erysipelatoclostridium (Erysipelotrichales: Erysipelotrichaceae), Rasltonia (Burkholderiales: Burkholderiaceae), and Rhizobium (Hyphomicrobiales: Rhizobiaceae) genera, and Enterobacteriaceae family members. Significant differences in microbiome diversity were observed between the two seasons. The relative abundance of Erysipelatoclostridium was high in the dry season, while in the phylotype ZOR0006 (Erysipelotrichales: Erysipelotrichaceae) and Tyzzerella (Lachnospirales: Lachnospiraceae) genus, the relative abundance was high in the rainy season. The overall low gut bacterial diversity observed in the S. frugiperda corn strain suggests a strong presence of antagonist activity as a selection factor possibly arising from the host, the dominant bacterial types, or the material ingested. Targeting the stability and predominance of this core microbiome could be an additional alternative to pest control strategies, particularly in this moth.

Biodiversity and Phylogenetic Relationships of Novel Bacteriocinogenic Strains Isolated from Animal's Droppings at the Zoological Garden of Lille, France

This study aimed at exploring droppings of animals living in captivity in the zoological garden (Zoo) of Lille (France), as novel sources of bacteriocinogenic strains. A collection of 295 bacterial isolates was constituted from droppings of capybara, alpaca, muntjac, zebra, tapir, rhinoceros, binturong, armadillo, saki monkey and cockatoo. Of 295 isolates, 51 exhibited antagonism against a panel of pathogenic target bacteria like Escherichia coli MC4100, Clostridium perfringens DSM 756 and Salmonella enterica subsp. enterica Newport ATCC6962. Remarkably, within this collection, only 2 Gram-negative bacilli exhibited activity against E. coli MC4100 strain used as target organism. Then, the 16S rDNA sequencing revealed these thereafter cited species, Pediococcus pentosaceus, Weissella cibaria, E. coli, Lactobacillus reuteri, Enterococcus hirae and Enterococcus faecalis. Characterization of this antagonism has revealed 11 strains able producing extracellular protease-sensitive inhibitory compounds. These strains included E. coli ICVB442 and ICVB443, Ent. faecalis ICVB472, ICVB474, ICVB477 ICVB479, ICVB481, ICVB497 and ICVB501 and Ped. pentosaceus ICVB491 and ICVB492. The genomes of the 5 most promising bacteriocinogenic strains were sequenced and analysed with Bagel4 software. Afterwards, this bioinformatics analysis permitted to locate genes encoding bacteriocins like colicin Y (E. coli), enterocin 1071A, enterocin 107 B (Ent. faecalis) and penocin A (Ped. pentosaceus), associating the above-mentioned antibacterial activity of proteinaceous nature to possible production of bacteriocins. All these results enabled us to select different bacteriocinogenic strains for a further characterization in terms of beneficial traits.

Isolation and Characterization of a Plant Growth-Promoting Bacterium Acinetobacter sp. SuKIC24 From in vitro-Grown Basilicum polystachyon (L.) Moench

In the present study, a plant growth-promoting bacterium isolated from contaminated in vitro-grown Basilicum polystachyon (L.) Moench, an herbaceous plant, was studied and identified as Acinetobacter strain SuKIC24 based on the 16S rRNA gene sequence analysis. The results revealed that the identified strain exhibited a strong ability to solubilize the phosphate with phosphate solubilization index of 4.0 and produced 387 µg/ml of soluble phosphate in Pikovskaya media after 7 days of incubation, whereas zinc solubilization efficacy was determined to be 175%. Reversed-phase high-performance liquid chromatography (RP-HPLC) analysis revealed that the bacterium strain produced 77.36 µg/ml of indole-3-acetic acid. Plant inoculated with the bacterium strain was found to demonstrate a significant increase in height of B. polystachyon as compared to the control plant. The present findings indicated that the identified bacterium strain might act as plant growth-promoting bacterium (PGPB).

First report on genetic characterization, cell-surface properties and pathogenicity of Lactococcus garvieae, emerging pathogen isolated from cage-cultured cobia (Rachycentron canadum)

The diseased cage-cultured cobia (Rachycentron canadum) displayed clinical signs, haemorrhagic eyes, dorsal darkness and gross pathological lesions, enlargement of spleen and liver. Haemorrhages were found in brain, heart and liver with cumulative mortality rates ranging from 20% to 50%. Extensive congestion in the heart, liver, spleen, kidney and brain was observed histopathologically. Epicarditis and meningitis were also revealed in diseased cobia. All isolates recovered from the organs (liver, spleen, head kidney, posterior kidney, brain and muscle) of cobia were found to be gram-positive, non-motile, ovoid cocci, short-chain-forming (diplococci) and α-haemolytic. The API 32 strep system together with the polymerase chain reaction assay for species-specific primers (pLG1 and pLG2) and the internal transcribed spacer (ITS) region (G1 and L1 primers) confirmed all four selected isolates as Lactococcus garvieae. Partial 16S rDNA nucleotide sequence (~1,100 bp) of one representative L. garvieae isolate AOD109191 (GenBank accession number, MW328528.1) shared 99.9% identities with the 16S rDNA nucleotide sequence of L. garvieae (GenBank accession numbers: MT604790.1). Transmission electron microscopy (TEM) evaluation of one representative L. garvieae isolate (AOD109191) and the results of multiplex PCR did not reveal the presence of the capsular gene cluster (CGC), thus categorizing the isolate as the KG+ phenotype. Capsule staining and TEM observations confirmed the presence of a hyaluronic acid-like capsule, a possible virulence factor in KG+ phenotype L. garvieae isolates. The pathogenic potential of the representative isolate (AOD109191) was assessed through intraperitoneal injection challenges in cobia. The gross lesions and histopathological changes found in experimentally infected cobia were similar to those seen in naturally infected fish. This is the first report that confirms L. garvieae-induced 'warm water lactococcsis' can cause outbreaks of diseases in cage-cultured cobia.

Complete Genome Sequence Resource of a Strain of Curtobacterium flaccumfaciens pv. flaccumfaciens, the Causal Agent of Bacterial Wilt of Common Bean, from Turkey

Curtobacterium flaccumfaciens pv. flaccumfaciens is the causal agent of bacterial wilt of common bean (Phaseolus vulgaris), a disease that can reduce yields of this economically important crop worldwide. Current genomics resources for this bacterial pathogen are limited. Therefore, long-read sequencing was used to determine the complete genome sequence of a pathogenic C. flaccumfaciens pv. flaccumfaciens strain isolated from common bean leaves showing irregular necrotic lesions with yellow borders collected in a commercial field in Turkey in 2015.

Differentiation Among Rodentibacter Species Based on 16S-23S rRNA Internal Transcribed Spacer Analysis

The internal transcribed spacer (ITS) regions of Rodentibacter pneumotropicus, R. heylii, R. rarus, R. ratti, and R. heidelbergensis and of a Rodentibacter- related β-hemolytic Pasteurellaceae taxon isolated from laboratory rodents were studied for their feasibility to discriminate among these species. The 6 species analyzed showed species-specific ITS patterns that were shared by the type strains and clinical isolates and that allowed their identification. Nevertheless, differentiating between the ITS band patterns of R. pneumotropicus and R. ratti is visually challenging. In all species tested, sequence analysis of the ITS fragments revealed a larger ITS^ile+ala, which contained the genes for tRNA^Ile(GAU) and tRNA ^Ala(UGC), and a smaller ITS^glu with the tRNA^Glu(UUC) gene. The ITS sequences varied among the 6 species evaluated, displaying identity levels ranging from 62% to 86% for ITS^ile+ala and 68% to 90% for ITS^glu. Overall, ITS amplification proved to be a reliable method to differentiate among these important Pasteurellaceae species of laboratory rodents. Moreover, the ITS sequence variations recorded here might facilitate the design of probes for specific identification of these species. The ability to diagnose these organisms to the species level could increase our understanding of their clinical significance.

Analysis of Streptococcal Infection and Correlation with Climatic Factors in Cultured Tilapia Oreochromis spp. in Taiwan

Tilapia (Oreochromis spp.), a prominent warm water food fish, is one of the major fish species grown in the aquaculture industry in south-east Asia. Tilapia can tolerate adverse water quality and other stressors, like diverse salinity and fluctuation of pH value, better than most other commercial aquaculture species. Environmental fluctuations are one of the main factors that affect the outbreak of infectious diseases in cultured tilapia. Cultured tilapia in Taiwan appears to be more susceptible to infections caused by Streptococci during the summer season. The present study emphasizes the Streptococcus spp. infection in tilapia in Taiwan and is the first study on the analysis of the potential impact of climate change on streptococcal infection in cultured tilapia in Asia. The data collected from the treatment and diagnosis system (TDS) of the aquatic animal diseases database from 2006 to 2015 were used to analyze the endemic streptococcal infection and the effect of climatic factors. Based on the results, the factor, average atmospheric pressure, is negatively correlated to streptococcal infection, while the other three, including average temperature, ultraviolet (UV) index, and rainfall, are positively correlated to streptococcal infection. A multivariate logistic regression model with these four factors was also built. When the average temperature is above 27.0 °C, the average atmospheric pressure is lower than 1005.1 hPa, or the UV index is above 7.2, the percentage of cumulated positive farms from all submitted tilapia cases was more than 50%. In addition, within 3 days of rain, rainfall is relevant to the occurrence of Streptococcus in tilapia. Using TDS to alert the occurrence of streptococcal infection in tilapia can be a very useful tool for veterinary aquatic animal inspection stations, and reducing economic losses and labour costs in aquatic agriculture.

Novel insights into the enterotoxigenic potential and genomic background of Staphylococcus aureus isolated from raw milk

In this study, 53 Staphylococcus (S.) aureus strains were typed by 16S-23S rDNA intergenic spacer region (ISR) typing and staphylococcal enterotoxin gene (SEg) typing for all the staphylococcal enterotoxin (se) and staphylococcal enterotoxin-like toxin (sel) genes known to date, revealing a higher discriminatory power than that of multi locus sequence typing. Six strains, one of each ISR- and SEg-type, were genome sequenced and the ability to produce some classical and new SEs when growing in milk was investigated. The manual analysis of the six genomes allowed us to confirm, correct and expand the results of common available genomic data pipelines such as VirulenceFinder. Moreover, it enabled us to (i) investigate the actual location of se and sel genes, even for genes such as selY, whose location (in the core genome) was so far unknown, (ii) find novel allelic variants of se and sel genes and pseudogenes, (iii) correctly annotate se and sel genes and pseudogenes, and (iv) discover a novel type of enterotoxin gene cluster (egc), i.e. the egc type 5 in strains 356P and 364P, while S. argenteus MSHR1132 harbored the egc type 6. Four of the six S. aureus strains produced sufficient amounts of SEA, SEC, SED and SEH in milk to cause staphylococcal food poisoning (SFP), with S. aureus 372 P being the highest producer of SED in milk found to date, producing as much as ca. 47,300 ng/mL and 49,200 ng/mL of SED, after 24 and 48 h of incubation in milk at 37 °C, respectively. S. aureus 372 P released a low amount of SER in milk, most likely because the seR gene was present as a pseudogene, putatively encoding only 51 amino acids. These findings confirm that not only the classical SEs, but also the new ones can represent a potential hazard for the consumers' health if produced in foods in sufficient amounts. Therefore, the detection of SEs in foods, especially if involved in SFP cases, should focus not only on classical, but also on all the new SEs and SEls known to date. Where reference methods are unavailable, the presence of the relevant genes, by using the conventional and real time PCR protocols we exhaustively provided herein, and their nucleotide sequences, should be investigated.

Evaluation of the QuantaMatrix Multiplexed Assay Platform for Molecular Diagnosis of Multidrug- and Extensively Drug-Resistant Tuberculosis Using Clinical Strains Isolated in Myanmar

Background

Although the incidence of tuberculosis (TB) is decreasing, cases of multidrug-resistant (MDR) TB and extensively drug-resistant (XDR) TB continue to increase. As conventional phenotype drug susceptibility testing (pDST) takes six to eight weeks, molecular assays are widely used to determine drug resistance. we developed QuantaMatrix Multiplexed Assay Platform (QMAP) MDR/XDR assay (QuantaMatrix Inc., Seoul, Korea) that can simultaneously detect mutations related to both first- and second-line drug resistance (rifampin, isoniazid, ethambutol, fluoroquinolones, second-line injectable drugs, and streptomycin).

Methods

We used 190 clinical Mycobacterium tuberculosis (MTB) strains isolated from Myanmar, compared QMAP and pDST results, and determined concordance rates. Additionally, we performed sequence analyses for discordant results.

Results

QMAP results were 87.9% (167/190) concordant with pDST results. In the 23 isolates with discordant results, the QMAP and DNA sequencing results completely matched.

Conclusions

The QMAP MDR/XDR assay can detect all known DNA mutations associated with drug resistance for both MDR- and XDR-MTB strains. It can be used for molecular diagnosis of MDR- and XDR-TB to rapidly initiate appropriate anti-TB drug therapy.

Autochthonous and Probiotic Lactic Acid Bacteria Employed for Production of "Advanced Traditional Cheeses"

Microbial characterization of two Italian traditional cheeses, Giuncata and Caciotta Leccese, was carried out, with the aim to isolate autochthonous bacterial strains to be used as starters to improve and standardize the quality of these cheeses. More than 400 bacterial isolates were found, using PCR-based identification, to belong to 12 species of the Streptococcus, Lactococcus, Lactobacillus, and Leuconostoc genera. The dominant strains were screened for antagonistic activity against pathogenic and spoilage bacteria and exopolysaccharide production, acidification, and proteolytic activity. Since Streptococcus macedonicus was found to be the most prevalent lactic acid bacteria species present in milk and in both types of cheese, the best performing strain of this species was successfully used, alone or in combination with a selected autochthonous Lactococcus lactis strain, in pilot-scale productions of Giuncata and Caciotta Leccese cheeses, respectively. The combined inoculums of selected autochthonous strains positively influenced the sensory characteristics of both Giuncata and Caciotta cheeses. Finally, the selected autochthonous cultures were enriched with a potentially probiotic Lactobacillus rhamnosus strain and successfully used in pilot-scale productions of these traditional cheeses. To the best of our knowledge, this is the first study reporting the use of an autochthonous S. macedonicus strain as a starter for the production of cheeses with added probiotics. In addition, the identification of the probiotic strain in the feces of healthy volunteers fed with the advanced traditional cheese proved its effectiveness as a carrier for the delivery of probiotics to the human body.

Marinitenerispora sediminis gen. nov., sp. nov., a member of the family Nocardiopsaceae isolated from marine sediment

Three novel actinobacterial strains, designated as TPS16^T, TPS81 and TPS83, were isolated from a sample of marine sediment collected from Tioman Island, Malaysia. The strains formed abundant branched substrate mycelia without fragmentation along with production of blue spores and blue diffusible pigment on soybean meal agar. The strains could grow at pH ranging from pH 6 to 12 and in 0-8 % (w/v) NaCl. Cell-wall hydrolysis showed the presence of meso-diaminopimelic acid. The strains were closely related to Marinactinospora thermotolerans SCSIO 00652^T (97.60 %) and Marinactinospora endophytica YIM 690053^T (96.87 %) based on phylogenetic analysis of 16S rRNA gene sequences. Multilocus sequence analysis including gyrB, recA and rpoB genes further confirmed that strain TPS16^T represented a distinct branch within the family Nocardiopsaceae. The predominant menaquinones were MK-11(H₂), MK-10(H₂), MK-11(H₄) and MK-10(H₄), while the major fatty acids were found to be iso-C_16 : 0, anteiso-C_17 : 0, iso-C_15 : 0 and C_18 : 1ω9c. Genome sequencing revealed genome sizes of approximately 6 Mb and G+C contents of 73.8 mol%. A new genus, Marinitenerispora gen. nov., is proposed within the family Nocardiopsaceae based on polyphasic data and the type species is Marinitenerispora sediminis gen. nov., sp. nov. The type strain is TPS16^T (=DSM 46825^T=TBRC 5138^T).

Molecular typing of cytotoxin-producing Klebsiella oxytoca isolates by 16S-23S internal transcribed spacer PCR

Cytotoxin is one of the important pathogenic factors, which plays a role in the virulence of Klebsiella oxytoca. The aim of this study was to investigate molecular typing of clinical isolates of the cytotoxin-producing K. oxytoca using internal transcribed spacer (ITS) PCR. A total of 75 isolates of K. oxytoca were isolated from clinical samples; they were verified as K. oxytoca by standard microbiological tests and PCR. Production of toxin determines the cytotoxic effects on HEp-2 cells. The genetic diversity of isolates of the cytotoxin-producing K. oxytoca were defined by ITS-PCR. Of all the isolates investigated, five K. oxytoca strains isolated from stool cultures, two strains from blood samples, one strain from a wound and one strain isolated from urine had cytotoxic effects on HEp-2 cells. The ITS-PCR patterns showed genetic diversity among cytotoxin-producing isolates. The ITS-PCR method had good discriminatory power; performance of this method and interpretation of the results were easy and repeatable. Five genetic diversity patterns were identified by ITS-PCR.

Characterization of Anti-Listeria monocytogenes Properties of two Bacteriocin-Producing Enterococcus mundtii Isolated from Fresh Fish and Seafood

This study addressed the bacteriocin production in 116 lactic acid bacteria isolated from 143 fish and seafood samples. The screening for the production of antibacterial substances allowed for the selection of 16 LAB isolates endowed with inhibitory capability. Bacteriocins (bacLP17 and bacLP18) of two strains, Enterococcus mundtii LP17 and Enterococcus mundtii LP18, respectively, isolated from red mullet and sardine samples, determined large inhibition zones against all the Listeria species. Virulence traits and antibiotic resistances of all producers were verified, and no isolates presented dangerous characteristics, including the two best bacteriocin producers E. mundtii LP17 and E. mundtii LP18, which were subsequently investigated for their potential use in fish and seafood products biopreservation. For both strains, the highest level of bacteriocin production (1280 AU/ml) was recorded when cells were grown at 30 °C in MRS broth at pH ranging from 6.0 to 9.0, and high levels of adsorption of bacteriocins, bacLP17 and bacLP18, to the target cells Listeria monocytogenes were also observed. The results obtained in this study revealed that two strains of E. mundtii originating from seafood exhibited a strong inhibitory activity against L. monocytogenes and may be useful in controlling the growth of this pathogen in the same food products.

Structural and mechanistic insights into EchAMP: A antimicrobial protein from the Echidna milk

BACKGROUND

Antibiotic resistance is a problem that necessitates the identification of new antimicrobial molecules. Milk is known to have molecules with antimicrobial properties (AMPs). Echidna Antimicrobial Protein (EchAMP) is one such lactation specific AMP exclusively found in the milk of Echidna, an egg-laying mammal geographically restricted to Australia and New Guinea. Previous studies established that EchAMP exhibits substantial bacteriostatic activity against multiple bacterial genera. However, the subsequent structural and functional studies were hindered due to the unavailability of pure protein.

RESULTS

In this study, we expressed EchAMP protein using a heterologous expression system and successfully purified it to >95% homogeneity. The purified recombinant protein exhibits bacteriolytic activity against both Gram-positive and Gram-negative bacteria as confirmed by live-dead staining and scanning electron microscopy. Structurally, this AMP belongs to the family of intrinsically disordered proteins (IDPs) as deciphered by the circular-dichroism, tryptophan fluorescence, and NMR spectroscopy. Nonetheless, EchAMP has the propensity to acquire structure with amphipathic molecules, or membrane mimics like SDS, lipopolysaccharides, and liposomes as again observed through multiple spectroscopic techniques.

CONCLUSIONS

Recombinant EchAMP exhibits broad-spectrum bacteriolytic activity by compromising the bacterial cell membrane integrity. Hence, we propose that this intrinsically disordered antimicrobial protein interact with the bacterial cell membrane and undergoes conformational changes to form channels in the membrane resulting in cell lysis.

GENERAL SIGNIFICANCE

EchAMP, the evolutionarily conserved, lactation specific AMP from an oviparous mammal may find application as a broad-spectrum antimicrobial against pathogens that affect mammary gland or otherwise cause routine infections in humans and livestock.

A Piscibacillus sp. Isolated from A Soda Lake Exhibits Anticancer Activity Against Breast Cancer MDA-MB-231 Cells

Microorganisms thrive in extreme environments and are known for synthesizing valuable metabolites. Salt-loving microorganisms can flourish in saline environments which inhibit the growth of other microbial life, and they possess the potential to produce stable and novel biomolecules for the use in biotechnological applications, including anticancer compounds. Sambhar Lake is the largest inland soda lake in India and is an appropriate habitat for halophilic bacterial and archaeal strains in terms of diversity and potential production of bioactive compounds. In the present study, a moderately halo-alkaliphilic bacterial strain C12A1 was isolated from Sambhar Lake, located in Rajasthan, India. C12A1 was gram-positive, motile, rod-shaped, formed oval endospores, produced carotenoids, and exhibited optimal growth at 37 °C in 10–15% NaCl (pH 8). C12A1 was found to be able to hydrolyze skimmed milk, gelatin, and Tween 80 but unable to hydrolyze starch and carboxymethylcellulose. C12A1 showed 98.87% and 98.50% identity in 16S rRNA gene sequence to P. halophilus and P. salipiscarius, respectively. Nevertheless, C12A1 was clustered within the clade consisting of P. salipiscarius strains, but it showed a distinct lineage. Thus, C12A1 was designated as Piscibacillus sp. Cell proliferation assay results showed that C12A1 broth extract (BEP) decreased cell viability in breast cancer MDA-MB-231 cells, which was confirmed by the MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. Induction of cell toxicity was visualized by microscopy. Reverse Transcriptase PCR (RT-PCR) analysis demonstrated that BEP inhibited the expression of proliferative B-cell lymphoma-extra large (Bcl-xL) and cell cycle marker Cyclin-dependent kinase 2 (CDK2) at transcript levels. Similarly, cell migration and colony formation along with mesenchymal marker vimentin and stem cell marker BMI transcripts were found to be inhibited when cells were treated with the BEP. The anti-breast cancer potential of C12A1 indicates that microorganisms inhabiting saline-alkaline habitats, with Piscibacillus sp. in particular, are a promising source for discovery of novel bioactive substances.

Isolation and evaluation of endophytic Bacillus tequilensis GYLH001 with potential application for biological control of Magnaporthe oryzae

Biological control is a promising measure in the control of plant disease. In the present study, we isolated 13 endophytic strains from Angelica dahurica. Among them, an endophytic strain which was named GYLH001 exhibited remarkable activity against Magnaporthe oryzae. 16S rRNA sequence analysis, biochemical and physiological proved that it is Bacillus tequilensis. The sterilized culture filtrate of GYLH001 can inhibit the growth of M.oryzae, which suggests the presence of secondary metabolites. Proved by experiment, GYLH001 can produce cellulase, protease, gelatinase, indole-3-acetic acid and 1-amino-cyclopropane-1-carboxylate deaminase. In addition, the temperature experiment showed that secondary metabolites produced by GYLH001 had good thermal stability. They can remain activity even heated at 100°C for 30 min. They also had good acid-resistance in heavily acidic condition. But under alkaline condition, the antifungal effect decreased significantly. By simulative field tests, the spraying of GYLH001 spore solution could prevent and treat rice blast. Through continuous separation and purification of sterilized culture filtrate and identification by mass spectrometry, the molecular weight of an active substance is 364.26. In the control of rice blast, B. tequilensis GYLH001 has potential as a biological control agent in agriculture.

Evaluating Established Methods for Rumen 16S rRNA Amplicon Sequencing With Mock Microbial Populations

The rumen microbiome scientific community has utilized amplicon sequencing as an aid in identifying potential community compositional trends that could be used as an estimation of various production and performance traits including methane emission, animal protein production efficiency, and ruminant health status. In order to translate rumen microbiome studies into executable application, there is a need for experimental and analytical concordance within the community. The objective of this study was to assess these factors in relation to selected currently established methods for 16S phylogenetic community analysis on a microbial community standard (MC) and a DNA standard (DS; ZymoBIOMICS^TM). DNA was extracted from MC using the RBBC method commonly used for microbial DNA extraction from rumen digesta samples. 16S rRNA amplicon libraries were generated for the MC and DS using primers routinely used for rumen bacterial and archaeal community analysis. The primers targeted the V4 and V3–V4 region of the 16S rRNA gene and samples were subjected to both 20 and 28 polymerase chain reaction (PCR) cycles under identical cycle conditions. Sequencing was conducted using the Illumina MiSeq platform. As the bacteria contained in the microbial mock community were well-classified species, and for ease of explanation, we used the results of the Basic Local Alignment Search Tool classification to assess the DNA, PCR cycle number, and primer type. Sequence classification methodology was assessed independently. Spearman’s correlation analysis indicated that utilizing the repeated bead beating and column method for DNA extraction in combination with primers targeting the 16S rRNA gene using 20 first-round PCR cycles was sufficient for amplicon sequencing to generate a relatively accurate depiction of the bacterial communities present in rumen samples. These results also emphasize the requirement to develop and utilize positive mock community controls for all rumen microbiomic studies in order to discern errors which may arise at any step during a next-generation sequencing protocol.

Rapid and Efficient FISH using Pre-Labeled Oligomer Probes

Fluorescence in situ hybridization (FISH) is used to visualize the distribution of DNA elements within a genome. Conventional methods for FISH take 1-2 days. Here, we developed a simplified, rapid FISH technique using pre-labeled oligonucleotide probes (PLOPs) and tested the procedure using 18 PLOPs from 45S and 5S rDNA, Arabidopsis-type telomere, and newly-identified Panax ginseng-specific tandem repeats. The 16 developed rDNA PLOPs can be universally applied to plants and animals. The telomere PLOPs can be utilized in most plants with Arabidopsis-type telomeres. The ginseng-specific PLOP can be used to distinguish P. ginseng from related Panax species. Differential labeling of PLOPs allowed us to simultaneously visualize different target loci while reducing the FISH hybridization time from ~16 h to 5 min. PLOP-FISH is efficient, reliable, and rapid, making it ideal for routine analysis, especially of newly sequenced genomes using either universal or specific targets, such as novel tandem repeats identified from whole-genome sequencing data.

Epizootics of Pseudomonas anguilliseptica among cultured seabream (Sparus aurata) populations: Control and treatment strategies

The present study was investigating the clinical pictures, prevalence, as well as the ecological conditions associated with Pseudomonas anguilliseptica outbreaks in four cultured seabream, Sparus aurata farms at different localities in Egypt during winter of 2016. The phenotypic and genotypic patterns of Pseudomonas isolates were investigated. The existence of intraspecific heterogeneity among different isolates was analyzed using Restriction Fragment Length Polymorphism (RFLP) technique. Attempts on disease control using antibiogram or dietary supplement were also considered. To achieve these goals, various commercial antibiotic discs were analyzed against Ps. anguilliseptica isolates using the disc diffusion method. Additionally, the impact of one-month dietary incorporation with 3% garlic extract or 0.5% potassium diformate on S. aurata viability and response for prolonged bathing treatment with florfenicol was evaluated following challenge with the virulent strain of Ps. anguilliseptica. Most of the naturally infected fish displayed spiral-swimming behavior with no obvious external lesions. The prevalence of infections in the four investigated farms (F1, F2, F3, and F4) were 44.9, 69.04, 67.72, and 83.4%, respectively. Water analysis revealed a significant variation in total hardness, pH, dissolved oxygen (D.O), ammonia and salinity among different localities. All isolates were rather uniform in most of the biochemical characteristics and were identical on the basis of RFLP analysis. The analyses of PAF-PAR gene pointed out specific amplification bands of 439 bp length. The antibiogram revealed a potential activity of florfenicol, ciprofloxacin, nitrofurantoin, and oxytetracycline against all isolates. Experimentally challenged fish fed on garlic extract or potassium diformate presented lower mortality and better therapeutic response to florfenicol than those fed on a normal basal diet. In conclusion, Ps. anguilliseptica is a prevalent pathogen among cultured seabream where dietary inclusion of 3% garlic extract or 0.5% potassium diformate seemed to improve seabream health status and subsequently, increase the efficacy of the treatment with the selective antibiotic.

Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique

Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLAST_n sequence analysis of 16S rRNA and four housekeeping genes (glnII, gyrB, recA, and rpoB) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, Bradyrhizobium yuanmingense, and a novel Bradyrhizobium sp., as well as Rhizobium tropici, Rhizobium pusense, and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes.

IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea nodulation in Mozambique was found in this study. Future studies could prove useful in evaluating these bacterial isolates for symbiotic efficiency and strain competitiveness in Mozambican soils.

Detection Methodologies for Pathogen and Toxins: A Review

Pathogen and toxin-contaminated foods and beverages are a major source of illnesses, even death, and have a significant economic impact worldwide. Human health is always under a potential threat, including from biological warfare, due to these dangerous pathogens. The agricultural and food production chain consists of many steps such as harvesting, handling, processing, packaging, storage, distribution, preparation, and consumption. Each step is susceptible to threats of environmental contamination or failure to safeguard the processes. The production process can be controlled in the food and agricultural sector, where smart sensors can play a major role, ensuring greater food quality and safety by low cost, fast, reliable, and profitable methods of detection. Techniques for the detection of pathogens and toxins may vary in cost, size, and specificity, speed of response, sensitivity, and precision. Smart sensors can detect, analyse and quantify at molecular levels contents of different biological origin and ensure quality of foods against spiking with pesticides, fertilizers, dioxin, modified organisms, anti-nutrients, allergens, drugs and so on. This paper reviews different methodologies to detect pathogens and toxins in foods and beverages.

Development of a new real-time quantitative PCR assay for the detection of Staphylococcus aureus genotype B in cow milk, targeting the new gene adlb

The specific and reliable diagnosis of mastitis pathogens is essential for successful sanitation programs. The aim of the present study was to develop and evaluate a new real-time quantitative PCR (qPCR) assay for the very sensitive and specific detection of Staphylococcus aureus genotype B in cow milk samples. This mastitis pathogen is contagious and particularly prevalent in Switzerland and other central European countries. The new test is based on a rapid preparation of bacteria, followed by DNA isolation and qPCR for a unique target gene coding for the adhesion-like bovine protein (adlb). The inclusivity of the new target gene was 97% and the exclusivity 98%, meaning that other genotypes and bacterial species could be excluded with high reliability. The limit of detection of the new assay was 235 staphylococcal cell equivalents/mL of culture. The new test shows high intra- and interassay repeatability. Results are available within 2 d after sampling, allowing farmers and veterinarians to apply sanitation measures immediately. Based on the results of a preliminary field study, the diagnostic sensitivity and specificity of the new qPCR assay are 99 and 100%, respectively. The new analytical procedure is straightforward and can be applied for routine diagnostics.

Phylogenetically diverse group of native bacterial symbionts isolated from root nodules of groundnut (Arachis hypogaea L.) in South Africa

Groundnut is an economically important N_​2-fixing legume that can contribute about 100–190 kg N ha⁻¹ to cropping systems. In this study, groundnut-nodulating native rhizobia in South African soils were isolated from root nodules. Genetic analysis of isolates was done using restriction fragment length polymorphism (RFLP)-PCR of the intergenic spacer (IGS) region of 16S-23S rDNA. A total of 26 IGS types were detected with band sizes ranging from 471 to 1415 bp. The rhizobial isolates were grouped into five main clusters with Jaccard's similarity coefficient of 0.00–1.00, and 35 restriction types in a UPGMA dendrogram. Partial sequence analysis of the 16S rDNA, IGS of 16S rDNA-23S rDNA, atpD, gyrB, gltA, glnII and symbiotic nifH and nodC genes obtained for representative isolates of each RFLP-cluster showed that these native groundnut-nodulating rhizobia were phylogenetically diverse, thus confirming the extent of promiscuity of this legume. Concatenated gene sequence analysis showed that most isolates did not align with known type strains, and may represent new species from South Africa. This underscored the high genetic variability associated with groundnut Rhizobium and Bradyrhizobium in South African soils, and the possible presence of a reservoir of novel groundnut-nodulating Bradyrhizobium and Rhizobium in the country.

Microbial Typing by Machine Learned DNA Melt Signatures

There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.

Distribution of resistance genetic determinants among Vibrio cholerae isolates of 2012 and 2013 outbreaks in IR Iran

The objective of this study was to characterize antimicrobial resistance determinants in relation to antimicrobial susceptibility and genotyping profile in 20 clinical isolates of Vibrio cholerae. All of the isolates were resistant to streptomycin. The second most prevalent resistance was observed to trimethoprim (75%), co-trimoxazole (60%), tetracycline (50%), and minocycline (45%). About 50% of the isolates fulfilled the criteria of Multi Drug Resistance (MDR) phenotype. None of the isolates carried tet A, B, C, and, D determinants. This finding shows that tetracycline resistance determinants recognized so far, does not satisfactorily describe the 50% tetracycline resistance phenotype in this study, suggesting the possible contribution of other not yet characterized resistance mechanisms involved. Class 1 integron, widely distributed among enteric bacteria, was not detected among V. cholerae strains under study. Conversely, 100% of the isolates harbored SXT constin_(int), among which 70% were positive for dfrA1, strA, and strB genes. The sul1gene was present in 60% of the isolates while none of them contained floR gene. All the isolates uniformly appeared to be identical in fingerprinting profiles expected from outbreak strains. In conclusion, SXT element with its mosaic structure was the exclusive antimicrobial resistance determinant of clonal V. cholerae isolates taken from outbreaks of 2012 and 2013 in Iran.