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Microbiology Resource Announcements Apr 2024We present the whole-genome sequence of four bacterial endophytes associated with German hardneck garlic cloves ( L.). Among them, and are associated with plant...
We present the whole-genome sequence of four bacterial endophytes associated with German hardneck garlic cloves ( L.). Among them, and are associated with plant protection, while and are pathogens. These data will facilitate the identification of genes to improve garlic.
PubMed: 38470029
DOI: 10.1128/mra.01225-23 -
PloS One 2024Antimicrobial resistance (AMR) is a global threat to human health since infections caused by antimicrobial-resistant bacteria are life-threatening conditions with...
Isolation, whole-genome sequencing, and annotation of two antibiotic-producing and antibiotic-resistant bacteria, Pantoea rodasii RIT 836 and Pseudomonas endophytica RIT 838, collected from the environment.
Antimicrobial resistance (AMR) is a global threat to human health since infections caused by antimicrobial-resistant bacteria are life-threatening conditions with minimal treatment options. Bacteria become resistant when they develop the ability to overcome the compounds that are meant to kill them, i.e., antibiotics. The increasing number of resistant pathogens worldwide is contrasted by the slow progress in the discovery and production of new antibiotics. About 700,000 global deaths per year are estimated as a result of drug-resistant infections, which could escalate to nearly 10 million by 2050 if we fail to address the AMR challenge. In this study, we collected and isolated bacteria from the environment to screen for antibiotic resistance. We identified several bacteria that showed resistance to multiple clinically relevant antibiotics when tested in antibiotic susceptibility disk assays. We also found that two strains, identified as Pantoea rodasii RIT 836 and Pseudomonas endophytica RIT 838 via whole genome sequencing and annotation, produce bactericidal compounds against both Gram-positive and Gram-negative bacteria in disc-diffusion inhibitory assays. We mined the two strains' whole-genome sequences to gain more information and insights into the antibiotic resistance and production by these bacteria. Subsequently, we aim to isolate, identify, and further characterize the novel antibiotic compounds detected in our assays and bioinformatics analysis.
Topics: Humans; Anti-Bacterial Agents; Microbial Sensitivity Tests; Gram-Positive Bacteria; Pseudomonas; Anti-Infective Agents; Whole Genome Sequencing; Pantoea
PubMed: 38412159
DOI: 10.1371/journal.pone.0293943 -
Saudi Journal of Biological Sciences Apr 2024Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in...
Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in rural sites of a developing country. The focus was on microbiological safety assessments and antimicrobial resistance, taking into account the risks linked with the consumption of raw colostrum. Shotgun sequencing was employed to analyze microbiome in raw buffalo and cow colostrum. Alpha and beta diversity analyses revealed increased inter and intra-variability within colostrum samples' microbiome from both livestock species. The colostrum microbiome was mainly comprised of bacteria, with over 90% abundance, whereas fungi and viruses were found in minor abundance. Known probiotic species, such as , , , and , were found in the colostrum samples. A relatively higher number of pathogenic and opportunistic pathogenic bacteria were identified in colostrum from both animals, including clinically significant bacteria like , , , and . Binning retrieved 11 high-quality metagenome-assembled genomes (MAGs), with three MAGs potentially representing novel species from the genera and . Notably, 175 antimicrobial resistance genes (ARGs) and variants were detected, with 55 of them common to both buffalo and cow colostrum metagenomes. These ARGs confer resistance against aminoglycoside, fluoroquinolone, tetracycline, sulfonamide, and peptide antibiotics. In conclusion, this study describes a thorough overview of microbial communities in buffalo and cow colostrum samples. It emphasizes the importance of hygienic processing and pasteurization in minimizing the potential transmission of harmful microorganisms linked to the consumption of colostrum.
PubMed: 38404539
DOI: 10.1016/j.sjbs.2024.103957 -
Viruses Feb 2024Fire blight, caused by , is a devastating bacterial disease that threatens apple and pear production. It is mainly controlled by using antibiotics, such as streptomycin....
Fire blight, caused by , is a devastating bacterial disease that threatens apple and pear production. It is mainly controlled by using antibiotics, such as streptomycin. Due to development of resistant strains and the excessive agricultural use of antibiotics, there is an increased awareness of the possibility of antibiotic resistance gene transfer to other microbes. Urgent development of biocontrol agents (BCAs) is needed that can be incorporated into integrated pest management programs as antibiotic alternatives. A novel phage-carrier system (PCS) that combines an antagonistic bacterium, , with its ability to act as a phage-carrier bacterium for phages has been developed. The low viability of cells following spray-drying (SD) has been a challenge for the industrial-scale production of this PCS. Here, an SD protocol was developed for by modifying the growth medium and bacterial cell formulation using D(+)-trehalose and maltodextrin. The developed protocol is amenable to the industrial-scale production of the BCA/PCS. The viability was greater than 90% after SD and had a shelf life at 4 °C of 4 months, and reconstituted cells showed a 3 log reduction in counts with a pear disc assay.
Topics: Bacteriophages; Pantoea; Anti-Bacterial Agents; Malus; Erwinia amylovora; Plant Diseases
PubMed: 38400033
DOI: 10.3390/v16020257 -
Microorganisms Feb 2024Rich endophytic bacterial communities exist in fescue ( L.) and play an important role in fescue growth, cold tolerance, drought tolerance and antibiotic tolerance. To...
Rich endophytic bacterial communities exist in fescue ( L.) and play an important role in fescue growth, cold tolerance, drought tolerance and antibiotic tolerance. To screen for probiotics carried by fescue seeds, seven varieties were collected from three different regions of China for isolation by the milled seed method and analyzed for diversity and motility, biofilm and antibiotic resistance. A total of 91 bacterial isolates were obtained, and based on morphological characteristics, 36 representative dominant strains were selected for 16S rDNA sequencing analysis. The results showed that the 36 bacterial strains belonged to four phyla and nine genera. The Firmicutes was the dominant phylum, and , and were the dominant genera. Most of the strains had motility (80%) and were biofilm-forming (91.7%). In this study, 15 strains were capable of Indole-3-acetic acid (IAA) production, 24 strains were capable of nitrogen fixation, and some strains possessed amylase and protease activities, suggesting their potential for growth promotion. Determination of the minimum inhibitory concentration (MIC) against the bacteria showed that the strains were not resistant to tetracycline and oxytetracycline. (QY6, LH4, MS2) and (YY4) showed resistance to five antibiotics (ampicillin, kanamycin, erythromycin, sulfadiazine and rifampicin). Using Pearson correlation analysis, a significant correlation was found between motility and biofilm, and between biofilm and sulfadiazine. In this study, we screened two strains of (QY6, LH4) with excellent growth-promoting ability as well as broad-spectrum antibiotic resistance. which provided new perspectives for subsequent studies on the strong ecological adaptations of fescue, and mycorrhizal resources for endophytic bacteria and plant interactions.
PubMed: 38399732
DOI: 10.3390/microorganisms12020329 -
Frontiers in Microbiology 2024This paper brings new information about the genome and phenotypic characteristics of strain DBM 3797, isolated from fresh Czech hop () in the Saaz hop-growing region....
BACKGROUND
This paper brings new information about the genome and phenotypic characteristics of strain DBM 3797, isolated from fresh Czech hop () in the Saaz hop-growing region. Although strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth.
METHODS
DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out.
RESULTS AND DISCUSSION
The typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.
PubMed: 38389535
DOI: 10.3389/fmicb.2024.1305338 -
BMC Infectious Diseases Feb 2024In Kenya, diarrhoeal disease is the third leading cause of child mortality after malaria and pneumonia, accounting for nearly 100 deaths daily. We conducted a...
BACKGROUND
In Kenya, diarrhoeal disease is the third leading cause of child mortality after malaria and pneumonia, accounting for nearly 100 deaths daily. We conducted a cross-sectional study in Mukuru informal settlements to determine the bacteria associated with diarrhea and their ASTs to provide data essential for implementing appropriate intervention measures.
METHODS
Diarrheagenic children (≤ 5 years) were purposively recruited from outpatient clinics of Municipal City Council, Mukuru kwa Reuben, Medical Missionaries of Mary, and Mama Lucy Kibaki Hospital, Nairobi. A total of 219 stool samples were collected between May 2021 and August 2021. Stool culture was done on MacConkey and Salmonella Shigella agar, while the recovered bacteria were identified using VITEK®2GNID and polymerase chain reaction (PCR) used for E. coli pathotyping. Antibiotic Susceptibility Testing was done using VITEK®2AST-GN83.
RESULTS
At least one bacterial organism was recovered from each of the 213 (97%) participants, with 115 (56%) participants having only one bacterial type isolated, 90 (43%) with two types of bacteria, and 2 (1%) with three types of bacteria recovered. The most predominant bacteria recovered was 85% (93/109) non-pathogenic E.coli and 15% (16/109)of pathogenic E.coli, with 2 (1%) were Enterohemorrhagic E.coli (EHEC), 6 (3%) were Enteroaggregative E.coli (EAEC), and 8 (4%) were Enteropathogenic E.coli (EPEC). Other potentially pathogenic bacteria included Enterobacter sp (27.8%), Klebsiella sp 33(11%), and Citrobacter sp 15(4.7%). Pathogenic isolates such as Salmonella 7 (2%), Proteus mirabilis 16 (6%), Providencia alcalifaciens 1 (0.3%), and Shigella 16 (4.7%) were detected. Isolates such as Pantoea spp 2(0.67%), Raoultella planticola 1(0.33%), and Kluyvera 6(2%) rarely reported but implicated with opportunistic diarrhoeal disease were also recovered. Ampicillin, cefazolin, and sulfamethoxazole-trimethoprim were the least effective antimicrobials at 64%, 57%, and 55% resistance, respectively, while meropenem (99%), amikacin (99%), tazobactam piperacillin (96%), and cefepime (95%) were the most effective. Overall, 33(21%) of all enterics recovered were multidrug-resistant.
CONCLUSION
The study documented different bacteria potentially implicated with childhood diarrhea that were not limited to E. coli, Shigella, and Salmonella, as previously observed in Kenya. The strains were resistant to the commonly used antibiotics, thus narrowing the treatment options for diarrheal disease.
Topics: Child; Humans; Child, Preschool; Kenya; Cross-Sectional Studies; Diarrhea; Anti-Infective Agents; Enteropathogenic Escherichia coli; Bacteria; Salmonella; Shigella
PubMed: 38388369
DOI: 10.1186/s12879-024-09114-5 -
MBio Mar 2024Flowers are colonized by a diverse community of microorganisms that can alter plant health and interact with floral pathogens. is a flower-inhabiting bacterium and a...
UNLABELLED
Flowers are colonized by a diverse community of microorganisms that can alter plant health and interact with floral pathogens. is a flower-inhabiting bacterium and a pathogen that infects different plant species, including (apple). Previously, we showed that the co-inoculation of two bacterial strains, members of the genera and isolated from apple flowers, reduced disease incidence caused by this floral pathogen. Here, we decipher the ecological interactions between the two flower-associated bacteria and in field experimentation and co-cultures. The two flower commensal strains did not competitively exclude from the stigma habitat, as both bacteria and the pathogen co-existed on the stigma of apple flowers and . This suggests that plant protection might be mediated by other mechanisms than competitive niche exclusion. Using a synthetic stigma exudation medium, ternary co-culture of the bacterial strains led to a substantial alteration of gene expression in both the pathogen and the two microbiota members. Importantly, the gene expression profiles for the ternary co-culture were not just additive from binary co-cultures, suggesting that some functions only emerged in multipartite co-culture. Additionally, the ternary co-culture of the strains resulted in a stronger acidification of the growth milieu than mono- or binary co-cultures, pointing to another emergent property of co-inoculation. Our study emphasizes the critical role of emergent properties mediated by inter-species interactions within the plant holobiont and their potential impact on plant health and pathogen behavior.
IMPORTANCE
Fire blight, caused by , is one of the most important plant diseases of pome fruits. Previous work largely suggested plant microbiota commensals suppressed disease by antagonizing pathogen growth. However, inter-species interactions of multiple flower commensals and their influence on pathogen activity and behavior have not been well studied. Here, we show that co-inoculating two bacterial strains that naturally colonize the apple flowers reduces disease incidence. We further demonstrate that the interactions between these two microbiota commensals and the floral pathogen led to the emergence of new gene expression patterns and a strong alteration of the external pH, factors that may modify the pathogen's behavior. Our findings emphasize the critical role of emergent properties mediated by inter-species interactions between plant microbiota and plant pathogens and their impact on plant health.
Topics: Incidence; Flowers; Malus; Erwinia amylovora; Plant Diseases
PubMed: 38376185
DOI: 10.1128/mbio.00213-24 -
AMB Express Feb 2024Plants have diverse and vast niches colonized by endophytic microorganisms that promote the wellbeing of host plant. These microbes inhabit internal plant tissues with...
Plants have diverse and vast niches colonized by endophytic microorganisms that promote the wellbeing of host plant. These microbes inhabit internal plant tissues with no signs of ill health. Bacterial endophytes from many plants have been isolated and characterized due to their beneficial roles however their diversity in leguminous plants still remain unexploited. Diversity of bacterial endophytes isolated from Sesbania sesban, Leucaena diversifolia and Calliandra calothyrsus was assessed using morphological and molecular characteristics. A total of 27 pure isolates were recovered from C. Calothyrsus, L. diversifolia and S. sesban constituting 44.4%, 33.3% and 22.2% from the leaves, stems and roots respectively. The isolates differentiated into Gram positive and negative with rods and spherical shapes. Analysis of 16S rRNA gene sequences revealed 8 closely related bacterial genera that consisted of Bacillus (33.3%), Staphylococcus (22.2%), Alcaligens (11.1%), Pantoea (11.1%), Xanthomonas,and Sphingomonas (7.4%) each. Others included Acinetobacter, and Pseudomonas at 3.7% each. Bacterial endophytes of genus bacillus were isolated from all the three plants. These results indicate the presence of high diversity of endophytic bacteria associated with the different parts of L. diversifolia, S. sesban and C. salothyrsus growing in western Kenya.
PubMed: 38329624
DOI: 10.1186/s13568-024-01676-6 -
Scientific Reports Feb 2024A novel bacterium, designated strain MMK2, was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were...
A novel bacterium, designated strain MMK2, was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2 and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2 strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2 and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2 (= DSM 115063 = LMG 33049).
Topics: Sequence Analysis, DNA; Pantoea; Trifolium; RNA, Ribosomal, 16S; DNA; Phylogeny; DNA, Bacterial; Fatty Acids; Bacterial Typing Techniques; Nucleic Acid Hybridization
PubMed: 38302681
DOI: 10.1038/s41598-024-53200-2