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MicrobiologyOpen Feb 2020Fermentation, also known as aging, is vital for enhancing the quality of flue-cured tobacco leaves (FTLs). Aged FTLs demonstrate high-quality sensory characteristics,...
Fermentation, also known as aging, is vital for enhancing the quality of flue-cured tobacco leaves (FTLs). Aged FTLs demonstrate high-quality sensory characteristics, while unaged FTLs do not. Microbes play important roles in the FTL fermentation process. However, the eukaryotic microbial community diversity is poorly understood, as are microbial associations within FTLs. We aimed to characterize and compare the microbiota associated with two important categories, fresh and strong flavor style FTLs, and to reveal correlations between the microbial taxa within them. Based on 16S and 18S rRNA Illumina MiSeq sequencing, the community richness and diversity of prokaryotes were almost as high as that of eukaryotes. The dominant microbes of FTLs belonged to seven genera, including Pseudomonas, Bacillus, Methylobacterium, Acinetobacter, Sphingomonas, Neophaeosphaeria, and Cladosporium, of the Proteobacteria, Firmicutes, and Ascomycota phyla. According to partial least square discriminant analysis (PLS-DA), Xanthomonas, Franconibacter, Massilia, Quadrisphaera, Staphylococcus, Cladosporium, Lodderomyces, Symmetrospora, Golovinomyces, and Dioszegia were significantly positively correlated with fresh flavor style FTLs, while Xenophilus, Fusarium, unclassified Ustilaginaceae, Tilletiopsis, Cryphonectria, Colletotrichum, and Cyanodermella were significantly positively correlated with strong flavor style FTLs. Network analysis identified seven hubs, Aureimonas, Kocuria, Massilia, Brachybacterium, Clostridium, Dietzia, and Vishniacozyma, that may play important roles in FTL ecosystem stability, which may be destroyed by Myrmecridium. FTL microbiota was found to be correlated with flavor style. Species present in lower numbers than the dominant microbes might be used as microbial markers to discriminate different flavor style samples and to stabilize FTL microbial communities. This research advances our understanding of FTL microbiota and describes a means of discriminating between fresh and strong flavor FTLs based on their respective stable microbiota.
Topics: Biodiversity; Eukaryotic Cells; Fermentation; High-Throughput Nucleotide Sequencing; Metagenomics; Microbiota; Neural Networks, Computer; Phylogeny; Plant Leaves; Prokaryotic Cells; RNA, Ribosomal, 16S; RNA, Ribosomal, 18S; Sequence Analysis, DNA; Nicotiana
PubMed: 31808296
DOI: 10.1002/mbo3.965 -
Ecology and Evolution May 2018Most spiders are natural enemies of pests, and it is beneficial for the biological control of pests to learn the relationships between symbionts and their spider hosts....
Most spiders are natural enemies of pests, and it is beneficial for the biological control of pests to learn the relationships between symbionts and their spider hosts. Research on the bacterial communities of insects has been conducted recently, but only a few studies have addressed the bacterial communities of spiders. To obtain a complete overview of the microbial communities of spiders, we examined eight species of spider (, , , , , , and ) with high-throughput sequencing based on the V3 and V4 regions of the 16S rRNA gene. The bacterial communities of the spider samples were dominated by five types of endosymbionts, , , , and . The dominant OTUs (operational taxonomic units) from each of the five endosymbionts were analyzed, and the results showed that different spider species were usually dominated by special OTUs. In addition to endosymbionts, , , , , , , , , , , , , , and were detected in spider samples in our study. Moreover, the abundance of , , and in the spider was significantly higher (<.05) than the bacterial abundance of these species in seven other spider species. These findings suggest that same as in insects, co-infection of multiple types of endosymbionts is common in the hosts of the Araneae order, and other bacterial taxa also exist in spiders besides the endosymbionts.
PubMed: 29876068
DOI: 10.1002/ece3.4051 -
Frontiers in Microbiology 2021In the myrmecophytic mutualistic relationship between a ants and plants both species receive protection and exchange nutrients. The presence of microorganisms in this...
In the myrmecophytic mutualistic relationship between a ants and plants both species receive protection and exchange nutrients. The presence of microorganisms in this symbiotic system has been reported, and the symbiotic role of some fungi involved in the myrmecophytic interactions has been described. In this work we focus on bacteria within this mutualism, conducting isolations and screening for antimicrobial activities, genome sequencing, and biochemical characterization. We show that , , , and are the most common cultivable genera of bacteria. Interestingly, spp. isolates showed potent activity against 83% of the pathogens tested in our antimicrobial activity assays, including a phytopathogenic fungus isolated from samples. Given the predicted nitrogen limitations associated with the fungal patches within this myrmecophyte, we performed nitrogen fixation analyses on the bacterial isolates within the Proteobacteria and show the potential for nitrogen fixation in strains. The genome of one strain was sequenced and analyzed. The gene cluster involved in the biosynthesis of cyclic lipodepsipeptides (CLPs) was identified, and we found mutations that may be related to the loss of function in the dual epimerization/condensation domains. The compound was isolated, and its structure was determined, corresponding to the antifungal viscosinamide. Our findings of diazotrophy and production of viscosinamide in multiple isolates suggests that this bacterial genus may play an important role in the symbiosis.
PubMed: 33597940
DOI: 10.3389/fmicb.2021.621274 -
Frontiers in Microbiology 2021Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during...
BACKGROUND
Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied.
RESULTS
To evaluate the microbial colonization of spacesuits, NASA used an Extravehicular Activity swab kit to examine viable microbial populations of 48 samples from spacesuits using both traditional microbiological methods and molecular sequencing methods. The cultivable microbial population ranged from below the detection limit to 9 × 10 colony forming units per 25 cm of sample and also significantly varied by the location. The cultivable microbial diversity was dominated by members of , and However, 16S rRNA-based viable bacterial burden ranged from 10 to 10 copies per 25 cm of sample. Shotgun metagenome sequencing revealed the presence of a diverse microbial population on the spacesuit surfaces, including and from across all sets of spacesuits in high abundance. Among bacterial species identified, higher abundance of , , and reads were documented.
CONCLUSION
The results of this study provide evidence that identical microbial strains may live on the wrist joint, inner gauntlet, and outer gauntlet of spacesuits. This raises the possibility, but does not confirm that microbial contaminants on the outside of the suits could contaminate planetary science operations unless additional measures are taken. Overall, these data provide the first estimate of microbial distribution associated with spacesuit surfaces, which will help future mission planners develop effective planetary protection strategies.
PubMed: 34394013
DOI: 10.3389/fmicb.2021.608478 -
Ticks and Tick-borne Diseases May 2018Our objective of this study was to explore the bacterial microbiome in fresh or fresh-frozen adult Amblyomma maculatum (Gulf Coast ticks) using extracts enriched for...
Our objective of this study was to explore the bacterial microbiome in fresh or fresh-frozen adult Amblyomma maculatum (Gulf Coast ticks) using extracts enriched for microbial DNA. We collected 100 questing adult A. maculatum, surface disinfected them, and extracted DNA from individual ticks collected the same day or after storage at -80 °C. Because only extracts with microbial DNA concentrations above 2 ng/μL were considered suitable for individual analysis, we expected fewer samples to meet these requirements. Of individual ticks extracted, 48 extracts met this minimum concentration. We pooled 20 additional extracts that had lower concentrations to obtain seven additional pools that met the minimum DNA concentration. Libraries created from these 55 samples were sequenced using an Illumina MiSeq platform, and data sets were analyzed using QIIME to identify relative abundance of microorganisms by phylum down to genus levels. Proteobacteria were in greatest abundance, followed by Actinobacteria, Firmicutes, and Bacteroidetes, at levels between 1.9% and 6.4% average relative abundance. Consistent with the Francisella-like endosymbiont known to be present in A. maculatum, the genus Francisella was detected at highest relative abundance (72.9%; SE 0.02%) for all samples. Among the top ten genera identified (relative abundance ≥ 0.5%) were potential extraction kit contaminants, Sphingomonas and Methylobacterium, the soil bacterium Actinomycetospora, and the known A. maculatum-associated genus, Rickettsia. Four samples had Rickettsia at greater than 1% relative abundance, while nine additional samples had Rickettsia at low (0.01-0.04%) relative abundance. In this study, we used the entire microbe-enriched DNA extract for whole ticks for microbiome analysis. A direct comparison of the microbiome in microbe-enriched DNA and total genomic DNA extracts from halves of the same tick would be useful to determine the utility of this extraction method in this system. We anticipate that future tick microbiome studies will be valuable to explore the influence of microbial diversity on pathogen maintenance and transmission, and to evaluate niche-specific microbiomes within individual tick tissues.
Topics: Actinobacteria; Animals; DNA, Bacterial; Francisella; High-Throughput Nucleotide Sequencing; Ixodidae; Microbiota; Mississippi; Phylogeny; Proteobacteria; Rickettsia; Tick Infestations; Tissue Extracts
PubMed: 29530467
DOI: 10.1016/j.ttbdis.2018.02.022 -
Microorganisms Jul 2021Plant-associated microbes can shape plant phenotype, performance, and productivity. Cultivation methods can influence the plant microbiome structure and differences...
Plant-associated microbes can shape plant phenotype, performance, and productivity. Cultivation methods can influence the plant microbiome structure and differences observed in the nutritional quality of differently grown fruits might be due to variations in the microbiome taxonomic and functional composition. Here, the influence of organic and integrated pest management (IPM) cultivation on quality, aroma and microbiome of raspberry ( L.) fruits was evaluated. Differences in the fruit microbiome of organic and IPM raspberry were examined by next-generation sequencing and bacterial isolates characterization to highlight the potential contribution of the resident-microflora to fruit characteristics and aroma. The cultivation method strongly influenced fruit nutraceutical traits, aroma and epiphytic bacterial biocoenosis. Organic cultivation resulted in smaller fruits with a higher anthocyanidins content and lower titratable acidity content in comparison to IPM berries. Management practices also influenced the amounts of acids, ketones, aldehydes and monoterpenes, emitted by fruits. Our results suggest that the effects on fruit quality could be related to differences in the population of , , , and on fruit. Finally, changes in fruit aroma can be partly explained by volatile organic compounds (VOCs) emitted by key bacterial genera characterizing organic and IPM raspberry fruits.
PubMed: 34442697
DOI: 10.3390/microorganisms9081617 -
Brazilian Journal of Microbiology :... Sep 2022Plant microbiota is usually enriched with bacteria producers of secondary metabolites and represents a valuable source of novel species and compounds. Here, we analyzed...
Plant microbiota is usually enriched with bacteria producers of secondary metabolites and represents a valuable source of novel species and compounds. Here, we analyzed the diversity of culturable root-associated bacteria of the medicinal native plant Baccharis trimera (Carqueja) and screened promising isolates for their antimicrobial properties. The rhizobacteria were isolated from the endosphere and rhizosphere of B. trimera from Ponta Grossa and Ortigueira localities and identified by sequencing and restriction analysis of the 16S rDNA. The most promising isolates were screened for antifungal activities and the production of siderophores and biosurfactants. B. trimera presented a diverse community of rhizobacteria, constituted of 26 families and 41 genera, with a predominance of Streptomyces and Bacillus genera, followed by Paenibacillus, Staphylococcus, Methylobacterium, Rhizobium, Tardiphaga, Paraburkholderia, Burkholderia, and Pseudomonas. The more abundant genera were represented by different species, showing a high diversity of the microbiota associated to B. trimera. Some of these isolates potentially represent novel species and deserve further examination. The communities were influenced by both the edaphic properties of the sampling locations and the plant niches. Approximately one-third of the rhizobacteria exhibited antifungal activity against Sclerotinia sclerotiorum and Colletotrichum gloeosporioides, and a high proportion of isolates produced siderophores (25%) and biosurfactants (42%). The most promising isolates were members of the Streptomyces genus. The survey of B. trimera returned a diverse community of culturable rhizobacteria and identified potential candidates for the development of plant growth-promoting and protection products, reinforcing the need for more comprehensive investigations of the microbiota of Brazilian native plants and habitats.
Topics: Anti-Bacterial Agents; Antifungal Agents; Baccharis; Bacteria; Humans; Plant Roots; Plants, Medicinal; Rhizosphere; Siderophores
PubMed: 35499750
DOI: 10.1007/s42770-022-00759-5 -
Frontiers in Microbiology 2024Cervical cancer ranks among the most prevalent cancers globally with high-risk human papillomaviruses implicated in nearly 99% of cases. However, hidden players such as... (Review)
Review
Cervical cancer ranks among the most prevalent cancers globally with high-risk human papillomaviruses implicated in nearly 99% of cases. However, hidden players such as changes in the microbiota are now being examined as potential markers in the progression of this disease. Researchers suggest that changes in the vaginal microbiota might correlate with cervical cancer. This review provides a comprehensive look at the microbiota changes linked with the advancement of cervical cancer. It also scrutinizes the databases from past studies on the microbiota during healthy and cancerous stages, drawing connections between prior findings concerning the role of the microbiota in the progression of cervical cancer. Preliminary findings identify spp., spp., spp., and spp., as potential biomarkers for cervical cancer progression. spp., spp., and spp. were identified as potential biomarkers for HPVs (+), while spp. may be indicative of HPV (-). However, the study's limitations, including potential biases and methodological constraints, underscore the need for further research to validate these findings and delve deeper into the microbiota's role in HPV development. Despite these limitations, the review provides valuable insights into microbiota trends during cervical cancer progression, offering direction for future research. The review summarizes key findings from previous studies on microbiota during healthy and cancerous stages, as well as other conditions such as CIN, SIL, HPV (+), and HPV (-), indicating a promising area for further investigation. The consistent presence of HPV across all reported cervical abnormalities, along with the identification of distinct bacterial genera between cancerous and control samples, suggests a potential link that merits further exploration. In conclusion, a more profound understanding of the microbial landscape could elucidate the pathogenesis of cervical diseases and inform future strategies for diagnosis, prevention, and treatment.
PubMed: 38389527
DOI: 10.3389/fmicb.2024.1352778 -
Synthetic and Systems Biotechnology Sep 2023Methanol has recently gained significant attention as a potential carbon substrate for the production of fuels and chemicals, owing to its high degree of reduction,...
Methanol has recently gained significant attention as a potential carbon substrate for the production of fuels and chemicals, owing to its high degree of reduction, abundance, and low price. Native methylotrophic yeasts and bacteria have been investigated for the production of fuels and chemicals. Alternatively, synthetic methylotrophic strains are also being developed by reconstructing methanol utilization pathways in model microorganisms, such as Owing to the complex metabolic pathways, limited availability of genetic tools, and methanol/formaldehyde toxicity, the high-level production of target products for industrial applications are still under development to satisfy commercial feasibility. This article reviews the production of biofuels and chemicals by native and synthetic methylotrophic microorganisms. It also highlights the advantages and limitations of both types of methylotrophs and provides an overview of ways to improve their efficiency for the production of fuels and chemicals from methanol.
PubMed: 37384124
DOI: 10.1016/j.synbio.2023.06.001 -
Ecology and Evolution Dec 2021The obligate mutualistic basidiomycete fungus, , mediates nutrition of leaf-cutting ants with carbons from vegetal matter. In addition, diazotrophic Enterobacteriales in...
The obligate mutualistic basidiomycete fungus, , mediates nutrition of leaf-cutting ants with carbons from vegetal matter. In addition, diazotrophic Enterobacteriales in the fungus garden and intestinal Rhizobiales supposedly mediate assimilation of atmospheric nitrogen, and Entomoplasmatales in the genus , as well as other yet unidentified strains, supposedly mediate ant assimilation of other compounds from vegetal matter, such as citrate, fructose, and amino acids. Together, these nutritional partners would support the production of high yields of leafcutter biomass. In the present investigation, we propose that three phylogenetically distinct and culturable diazotrophs in the genera , and integrate this symbiotic nutrition network, facilitating ant nutrition on nitrogen. Strains in these genera were often isolated and directly sequenced in 16S rRNA libraries from the ant abdomen, together with the nondiazotrophs and . These five isolates were underrepresented in libraries, suggesting that none of them is dominant . Libraries have been dominated by four uncultured Rhizobiales strains in the genera , and and, only in ants, by the Entomoplasmatales in the genus . also presented small amounts of two other uncultured Entomoplasmatales strains, and . The absence of Entomoplasmatales in workers implicates that the association with these bacteria is not mandatory for ant biomass production. Most of the strains that we detected in South American ants were genetically similar with strains previously described in association with leafcutters from Central and North America, indicating wide geographic dispersion, and suggesting fixed ecological services.
PubMed: 35003632
DOI: 10.1002/ece3.8213