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Frontiers in Microbiology 2024, a wild plant in southern Africa, is utilized in traditional medicine for various ailments, leading to its endangerment and listing on the Red List of South African...
, a wild plant in southern Africa, is utilized in traditional medicine for various ailments, leading to its endangerment and listing on the Red List of South African Plants. To date, there have been no reports on bacterial endophytes from this plant, their classes of secondary metabolites, and potential medicinal properties. This study presents (i) taxonomic characterization of bacterial endophytes in leaf and root tissues using 16S rRNA, (ii) bacterial isolation, morphological, and phylogenetic characterization, (iii) bacterial growth, metabolite extraction, and LC-MS-based metabolite fingerprinting, and (iv) antimicrobial testing of bacterial crude extracts. Next-generation sequencing yielded 693 and 2,459 DNA read counts for the rhizomes and leaves, respectively, detecting phyla including Proteobacteria, Bacteroidota, Gemmatimonadota, Actinobacteriota, Verrucomicrobiota, Dependentiae, Firmicutes, and Armatimonodata. At the genus level, , , , and Ralstonia were the most dominant in both leaves and rhizomes. From root tissues, four bacterial isolates were selected, and 16S rRNA-based phylogenetic characterization identified two closely related sp. (strain BNWU4 and 5), BNWU2, and BNWU1. The ethyl acetate:chloroform (1:1 v/v) organic extract from each isolate exhibited antimicrobial activity against all selected bacterial pathogens. Strain BNWU5 displayed the highest activity, with minimum inhibitory concentrations ranging from 62.5 μg/mL to 250 μg/mL against diarrhoeagenic , , , antibiotic-resistant , , , and . LC-MS analysis of the crude extract revealed common antimicrobial metabolites produced by all isolates, including Phenoxomethylpenicilloyl (penicilloyl V), cis-11-Eicosenamide, 3-Hydroxy-3-phenacyloxindole, and 9-Octadecenamide.
PubMed: 38855763
DOI: 10.3389/fmicb.2024.1383854 -
Frontiers in Cellular and Infection... 2024Lower respiratory tract infections represent prevalent ailments. Nonetheless, current comprehension of the microbial ecosystems within the lower respiratory tract...
BACKGROUND
Lower respiratory tract infections represent prevalent ailments. Nonetheless, current comprehension of the microbial ecosystems within the lower respiratory tract remains incomplete and necessitates further comprehensive assessment. Leveraging the advancements in metagenomic next-generation sequencing (mNGS) technology alongside the emergence of machine learning, it is now viable to compare the attributes of lower respiratory tract microbial communities among patients across diverse age groups, diseases, and infection types.
METHOD
We collected bronchoalveolar lavage fluid samples from 138 patients diagnosed with lower respiratory tract infections and conducted mNGS to characterize the lung microbiota. Employing various machine learning algorithms, we investigated the correlation of key bacteria in patients with concurrent bronchiectasis and developed a predictive model for hospitalization duration based on these identified key bacteria.
RESULT
We observed variations in microbial communities across different age groups, diseases, and infection types. In the elderly group, exhibited the highest relative abundance, followed by and . and emerged as the dominant genera at the genus level in the younger group, while and were prevalent species. Within the bronchiectasis group, dominant bacteria included , , and . Significant differences in the presence of were noted between the bronchiectasis group and the control group. In the group with concomitant fungal infections, the most abundant genera were and , with and as the predominant species. Notable differences were observed in the presence of , , , , and between the group with concomitant fungal infections and the bacterial group. Machine learning algorithms were utilized to select bacteria and clinical indicators associated with hospitalization duration, confirming the excellent performance of bacteria in predicting hospitalization time.
CONCLUSION
Our study provided a comprehensive description of the microbial characteristics among patients with lower respiratory tract infections, offering insights from various perspectives. Additionally, we investigated the advanced predictive capability of microbial community features in determining the hospitalization duration of these patients.
Topics: Humans; Machine Learning; Metagenomics; Middle Aged; Respiratory Tract Infections; Aged; Male; Female; Adult; Bacteria; Bronchoalveolar Lavage Fluid; Microbiota; High-Throughput Nucleotide Sequencing; Young Adult; Bronchiectasis; Aged, 80 and over; Metagenome; Adolescent; Lung; Hospitalization
PubMed: 38846353
DOI: 10.3389/fcimb.2024.1385562 -
Microbiology Resource Announcements Jun 2024In this study, we report the draft genome sequence data of sp. 37f, isolated from soil beneath Roxb. in Thailand. The genome consists of 5,305,449 base pairs, with a...
In this study, we report the draft genome sequence data of sp. 37f, isolated from soil beneath Roxb. in Thailand. The genome consists of 5,305,449 base pairs, with a GC content of 67.5%.
PubMed: 38767399
DOI: 10.1128/mra.00324-24 -
Data in Brief Jun 2024A ubiquitous and pink-pigmented facultatively methylotrophic bacterium, designated LRY1-08 (=JCM 33120), was isolated from a lichen in Thailand. Strain LRY1-08 and NBRC...
A ubiquitous and pink-pigmented facultatively methylotrophic bacterium, designated LRY1-08 (=JCM 33120), was isolated from a lichen in Thailand. Strain LRY1-08 and NBRC 112876 shared 99.92 % similarity based on the 16S rRNA gene sequence. The draft genome of LRY1-08 was 5.26 Mbp with 4,952 protein-coding sequences and an average G + C content of 70.0 mol%. Comparing strain LRY1-08 to NBRC 112876, the ANIb, ANIm, AAI, and digital DNA-DNA hybridization values were 96.29 %, 97.10 %, 96.7 %, and 82.29 %, respectively. Based on the phenotypic characteristics and genome analysis, it was identified as . Its genomic sequence data revealed the PHB and CoQ10 biosynthesis genes. Therefore, the results offer suggestions for further investigation into possible applications of this bacterium in biotechnology. The draft genome was deposited at DDBJ/EMBL/GenBank (DNA Databank of Japan/European Molecular Biology Laboratory/Genbank) (JAYEEX000000000).
PubMed: 38764453
DOI: 10.1016/j.dib.2024.110485 -
MedRxiv : the Preprint Server For... Apr 2024The microbiome likely plays a role in tuberculosis (TB) pathogenesis. We evaluated the site-of-disease microbiome and predicted metagenome in people with presumptive...
BACKGROUND
The microbiome likely plays a role in tuberculosis (TB) pathogenesis. We evaluated the site-of-disease microbiome and predicted metagenome in people with presumptive tuberculous pericarditis, a major cause of mortality, and explored for the first time, the interaction between its association with C-reactive protein (CRP), a potential diagnostic biomarker and the site-of-disease microbiome in extrapulmonary TB.
METHODS
People with effusions requiring diagnostic pericardiocentesis (n=139) provided background sampling controls and pericardial fluid (PF) for 16S rRNA gene sequencing analysed using QIIME2 and PICRUSt2. Blood was collected to measure CRP.
RESULTS
PF from people with definite (dTB, n=91), probable (pTB, n=25), and non- (nTB, n=23) tuberculous pericarditis differed in β-diversity. dTBs were, vs. nTBs, and enriched. Within dTBs, HIV-positives were , , and -enriched vs. HIV-negatives and HIV-positive dTBs on ART were - and -depleted vs. those not on ART. Compared to nTBs, dTBs exhibited short-chain fatty acid (SCFA) and mycobacterial metabolism microbial pathway enrichment. People with additional non-pericardial involvement had differentially PF taxa (e.g., -enrichment and -depletion associated with pulmonary infiltrates). reads were in 34% (31/91), 8% (2/25) and 17% (4/23) of dTBs, pTBs, and nTBs, respectively. β-diversity differed between patients with CRP above vs. below the median value ( -depleted). There was no correlation between enriched taxa in dTBs and CRP.
CONCLUSIONS
PF is compositionally distinct based on TB status, HIV (and ART) status and dTBs are enriched in SCFA-associated taxa. The clinical significance of these findings, including mycobacterial reads in nTBs and pTBs, requires evaluation.
PubMed: 38712063
DOI: 10.1101/2024.04.26.24306431 -
MSystems May 2024A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core...
UNLABELLED
A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, lacked serine hydroxymethyltransferase (SHMT), and exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for sp. 4M-Z18 and sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications.
IMPORTANCE
Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for sp. 4M-Z18 and sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.
PubMed: 38695578
DOI: 10.1128/msystems.00248-24 -
Saudi Journal of Biological Sciences Jun 2024This study investigated the impact of a mixture of six endophytic bacterial strains isolated from cucumber plants on the growth and microbiome diversity of six cucumber...
This study investigated the impact of a mixture of six endophytic bacterial strains isolated from cucumber plants on the growth and microbiome diversity of six cucumber traditional varieties and hybrids. Six bacterial species were isolated and identified by 16 s rRNA sequencing. All the bacteria showed plant growth promoting traits. showed 80 % inhibition of the mycelia growth of f.sp. (Foc). Mixed culture of all the bacteria was prepared and applied back to the varieties and hybrids of cucumber plants through seed soaking. Plant growth characteristics indicated that the treated plants showed increased plant growth in terms of plant height, number of leaves, vine length, male:female flower ratio, number of fruits and fruit length. Bacteria treated plants of hybrid HiVeg Chitra recorded 19 cm increase in vine length compared to control plants. The matataxonomic analysis of leaf samples by Illumina sequencing highlighted a diverse bacterial community shift in treated plants, with significant increases in genera like and . The core microbiome analysis identified key genera such as , etc that could be pivotal in plant growth promotion. and showed increased abundance in treated varieties, correlating with the observed in plant growth parameters thus indicating their role in growth promotion of cucumber plants. Endophytic bacterial species identified from cucumber plants when re-applied by seed soaking, they promote the plant growth by modulating the microbiome. The bacterial species identified in the study could be potential candidates as microbial bioinputs for cucumber cultivation.
PubMed: 38646566
DOI: 10.1016/j.sjbs.2024.103997 -
FEMS Microbiology Ecology May 2024Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the...
Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula, and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter, had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents.
Topics: Coffea; Plant Diseases; Plant Leaves; Basidiomycota; Microbiota; Disease Resistance; Bacteria; Fungi
PubMed: 38599638
DOI: 10.1093/femsec/fiae049 -
Plants (Basel, Switzerland) Mar 2024Algae and bacteria have co-occurred and coevolved in common habitats for hundreds of millions of years, fostering specific associations and interactions such as... (Review)
Review
Algae and bacteria have co-occurred and coevolved in common habitats for hundreds of millions of years, fostering specific associations and interactions such as mutualism or antagonism. These interactions are shaped through exchanges of primary and secondary metabolites provided by one of the partners. Metabolites, such as N-sources or vitamins, can be beneficial to the partner and they may be assimilated through chemotaxis towards the partner producing these metabolites. Other metabolites, especially many natural products synthesized by bacteria, can act as toxins and damage or kill the partner. For instance, the green microalga establishes a mutualistic partnership with a , in stark contrast to its antagonistic relationship with the toxin producing . In other cases, as with a coccolithophore haptophyte alga and a bacterium, the same alga and bacterium can even be subject to both processes, depending on the secreted bacterial and algal metabolites. Some bacteria also influence algal morphology by producing specific metabolites and micronutrients, as is observed in some macroalgae. This review focuses on algal-bacterial interactions with micro- and macroalgal models from marine, freshwater, and terrestrial environments and summarizes the advances in the field. It also highlights the effects of temperature on these interactions as it is presently known.
PubMed: 38592793
DOI: 10.3390/plants13060829 -
Frontiers in Microbiology 2024Endophytic and rhizospheric microorganisms associated with plants play a crucial role in plant health, pest and disease defense, and fruit yield by actively...
Endophytic and rhizospheric microorganisms associated with plants play a crucial role in plant health, pest and disease defense, and fruit yield by actively participating in the plant's adaptation to its environment. In this study, high-throughput sequencing technology was employed to analyze the community structure and diversity of endophytic and rhizospheric soil microorganisms in var. . The results revealed significant differences in microbial diversity and community structure between the soil and plant compartments within the same geographic region. Microbial diversity and species composition varied among different geographic locations. The dominant bacteria in plants were Cyanobacteria and Proteobacteria, with dominant genera including , and . In contrast, the dominant bacteria in soil were Proteobacteria, Acidobacteriota, and Actinobacteriota, with dominant genera such as , and , with was considered core groups present in all plant and soil samples. As for fungi, the dominant phyla in both plants and soil were Ascomycota, Basidiomycota, and Mortierellomycota, with different dominant genera between the two compartments, including , , and , totaling 59 genera. Linear discriminant analysis at the genus level identified 102 bacterial and 54 fungal indicator taxa associated with plants and soil. Co-occurrence network analysis indicated close interactions among soil bacterial microorganisms. Functional prediction of the top 10 microbial genes revealed three bacterial metabolic pathways shared between soil and plants, while the predominant fungal metabolic types were similar between the two compartments but with varying abundances. This study elucidates the diversity and interplay of endophytic and rhizospheric microorganisms in var. across diverse geographical regions, providing insights crucial for the plant's conservation and development.
PubMed: 38544861
DOI: 10.3389/fmicb.2024.1338956