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PloS One 2020Vermicompost application has been shown to promote plant growth, alter the rhizosphere microbiome, and suppress plant pathogens. These beneficial properties are often...
Vermicompost application has been shown to promote plant growth, alter the rhizosphere microbiome, and suppress plant pathogens. These beneficial properties are often attributed to the activity of vermicompost-associated microorganisms. However, little is known about the microbial shifts that occur in the rhizosphere after vermicompost application. To better understand the impact of vermicompost treatments on the assembly of rhizosphere bacterial communities, 16S rDNA communities of vermicompost and rhizospheres of each peat- and soil-grown tomatoes were profiled after conventional fertigation, irrigation without additional nutrients, and addition of three different vermicompost-extracts. The full dataset consisted of 412 identified genera, of which 317 remained following stringent quality filtration. Tomato rhizosphere microbiome responses to treatments were complex and unique between peat and soil growth substrates. Direct colonization of vermicompost-origin taxa into rhizospheres was limited, with genera Photobacterium and Luteimonas colonizing peat rhizospheres, genera Truepera, Phenylobacterium, and Lysinibacillus colonizing soil rhizospheres, and genus Pelagibius appearing in both soil and peat rhizospheres. Further patterns of differential abundance and presence/absence between treatments highlight vermicompost-mediated effects on rhizosphere microbiome assembly as an interplay of rhizosphere medium, direct colonization of vermicompost-origin taxa and vermicompost-induced shifts in the rhizosphere microbial community. This exploratory analysis is intended to provide an initial look at 16S community composition of vermicompost and the effects of vermicompost treatment on the rhizosphere microbiome assembly to highlight interactions of potential merit for subsequent investigations.
Topics: Bacteria; Composting; Solanum lycopersicum; Rhizosphere
PubMed: 32251438
DOI: 10.1371/journal.pone.0230577 -
Scientific Reports May 2017Mitochondria-targeted antioxidants are known to alleviate mitochondrial oxidative damage that is associated with a variety of diseases. Here, we showed that SkQ1, a...
Mitochondria-targeted antioxidants are known to alleviate mitochondrial oxidative damage that is associated with a variety of diseases. Here, we showed that SkQ1, a decyltriphenyl phosphonium cation conjugated to a quinone moiety, exhibited strong antibacterial activity towards Gram-positive Bacillus subtilis, Mycobacterium sp. and Staphylococcus aureus and Gram-negative Photobacterium phosphoreum and Rhodobacter sphaeroides in submicromolar and micromolar concentrations. SkQ1 exhibited less antibiotic activity towards Escherichia coli due to the presence of the highly effective multidrug resistance pump AcrAB-TolC. E. coli mutants lacking AcrAB-TolC showed similar SkQ1 sensitivity, as B. subtilis. Lowering of the bacterial membrane potential by SkQ1 might be involved in the mechanism of its bactericidal action. No significant cytotoxic effect on mammalian cells was observed at bacteriotoxic concentrations of SkQ1. Therefore, SkQ1 may be effective in protection of the infected mammals by killing invading bacteria.
Topics: Anti-Bacterial Agents; Antioxidants; Bacillus subtilis; Escherichia coli; HeLa Cells; Humans; Mitochondria; Mycobacterium; Photobacterium; Plastoquinone; Rhodobacter sphaeroides; Staphylococcus aureus
PubMed: 28469140
DOI: 10.1038/s41598-017-00802-8 -
Microbiology Spectrum Jan 2018Major concerns surround the use of antimicrobial agents in farm-raised fish, including the potential impacts these uses may have on the development of...
Major concerns surround the use of antimicrobial agents in farm-raised fish, including the potential impacts these uses may have on the development of antimicrobial-resistant pathogens in fish and the aquatic environment. Currently, some antimicrobial agents commonly used in aquaculture are only partially effective against select fish pathogens due to the emergence of resistant bacteria. Although reports of ineffectiveness in aquaculture due to resistant pathogens are scarce in the literature, some have reported mass mortalities in larvae caused by resistant to trimethoprim-sulfamethoxazole, chloramphenicol, erythromycin, and streptomycin. Genetic determinants of antimicrobial resistance have been described in aquaculture environments and are commonly found on mobile genetic elements which are recognized as the primary source of antimicrobial resistance for important fish pathogens. Indeed, resistance genes have been found on transferable plasmids and integrons in pathogenic bacterial species in the genera , , , , and . Class 1 integrons and IncA/C plasmids have been widely identified in important fish pathogens ( spp., spp., spp., spp., and spp.) and are thought to play a major role in the transmission of antimicrobial resistance determinants in the aquatic environment. The identification of plasmids in terrestrial pathogens ( serotypes, , and others) which have considerable homology to plasmid backbone DNA from aquatic pathogens suggests that the plasmid profiles of fish pathogens are extremely plastic and mobile and constitute a considerable reservoir for antimicrobial resistance genes for pathogens in diverse environments.
Topics: Animals; Anti-Bacterial Agents; Aquaculture; Bacteria; Drug Resistance, Multiple, Bacterial; Fish Diseases; Fisheries; Fishes; Interspersed Repetitive Sequences; Microbial Sensitivity Tests
PubMed: 29372680
DOI: 10.1128/microbiolspec.ARBA-0017-2017 -
Scientific Reports Mar 2024It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume....
It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray-Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray-Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.
Topics: Animals; Phylogeny; Microbiota; Gastrointestinal Microbiome; Salmon; Tuna; Seafood; Photobacterium; Pseudomonas
PubMed: 38443405
DOI: 10.1038/s41598-024-55938-1 -
Environmental Microbiome Oct 2023Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic...
BACKGROUND
Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, viruses and eukaryotic microbes, are referred to coral holobionts. Among them, coral diseases, mainly caused by Vibrio spp., have significantly contributed to the loss of coral cover and diversity. Habitat filtering across the globe has led to a variety structure of marine bacterial communities. Coral species, quantity and characteristics are significant differences between the Xisha Islands and Daya Bay (Guangdong Province). Thus, the Vibrio communities may be distinct between coral rich and poor areas.
RESULTS
Through comparison of Vibrio dynamics between coral-rich (Xisha Islands) and coral-poor (Daya Bay) locations, we uncovered differences in Vibrio abundance, diversity, community composition and assembly mechanisms associated with corals. The higher abundance of Vibrio in coral rich areas may indicate a strong interaction between vibrios and corals. V. campbellii, Paraphotobacterium marinum and V. caribbeanicus were widely distributed in both coral rich and poor areas, likely indicating weak species specificity in the coral-stimulated growth of Vibrio. Random-forest prediction revealed Vibrio species and Photobacterium species as potential microbial indicators in the coral rich and coral poor areas, respectively. Ecological drift rather than selection governed the Vibrio community assembly in the Xisha Islands. Comparatively, homogenizing selection was more important for the Daya Bay community, which may reflect a role of habitat filtration.
CONCLUSION
This study revealed the different distribution pattern and assembly mechanism of Vibrio spp. between coral rich and poor areas, providing the background data for the research of Vibrio community in coral reef areas and may help the protection of coral reef at the biological level. The main reasons for the difference were different number and species of corals, environmental (e.g., temperature) and spatial factors. It reflected the strong interaction between Vibrio and corals, and provided a new perspective for the investigation of Vibrio in coral reef ecosystem.
PubMed: 37872593
DOI: 10.1186/s40793-023-00532-7 -
Frontiers in Microbiology 2023Recirculating aquaculture systems (RAS) pose unique challenges in microbial community management since they rely on a stable community with key target groups, both in...
Recirculating aquaculture systems (RAS) pose unique challenges in microbial community management since they rely on a stable community with key target groups, both in the RAS environment and in the host (in this case, ). Our goal was to determine how much of the sole microbiome is inherited from the egg stage, and how much is acquired during the remainder of the sole life cycle in an aquaculture production batch, especially regarding potentially probiotic and pathogenic groups. Our work comprises sole tissue samples from 2 days before hatching and up to 146 days after hatching (-2 to 146 DAH), encompassing the egg, larval, weaning, and pre-ongrowing stages. Total DNA was isolated from the different sole tissues, as well as from live feed introduced in the first stages, and 16S rRNA gene was sequenced (V6-V8 region) using the Illumina MiSeq platform. The output was analysed with the DADA2 pipeline, and taxonomic attribution with SILVAngs version 138.1. Using the Bray-Curtis dissimilarity index, both age and life cycle stage appeared to be drivers of bacterial community dissimilarity. To try to distinguish the inherited (present since the egg stage) from the acquired community (detected at later stages), different tissues were analysed at 49, 119 and 146 DAH (gill, intestine, fin and mucus). Only a few genera were inherited, but those that were inherited accompany the sole microbiome throughout the life cycle. Two genera of potentially probiotic bacteria ( and ) were already present in the eggs, while others were acquired later, in particularly, forty days after live feed was introduced. The potentially pathogenic genera and were inherited from the eggs, while and seemed to be acquired at 49 and 119 DAH, respectively. Significant co-occurrence was found between and both and . On the other hand, significantly negative correlations were detected between and , , and . Our work reinforces the importance of life cycle studies, which can contribute to improve production husbandry strategies. However, we still need more information on this topic as repetition of patterns in different settings is essential to confirm our findings.
PubMed: 37434707
DOI: 10.3389/fmicb.2023.1188876 -
Nature Communications Apr 2019Chemoenzymatic modification of cell-surface glycan structures has emerged as a complementary approach to metabolic oligosaccharide engineering. Here, we identify...
Chemoenzymatic modification of cell-surface glycan structures has emerged as a complementary approach to metabolic oligosaccharide engineering. Here, we identify Pasteurella multocida α2-3-sialyltransferase M144D mutant, Photobacterium damsela α2-6-sialyltransferase, and Helicobacter mustelae α1-2-fucosyltransferase, as efficient tools for live-cell glycan modification. Combining these enzymes with Helicobacter pylori α1-3-fucosyltransferase, we develop a host-cell-based assay to probe glycan-mediated influenza A virus (IAV) infection including wild-type and mutant strains of H1N1 and H3N2 subtypes. At high NeuAcα2-6-Gal levels, the IAV-induced host-cell death is positively correlated with haemagglutinin (HA) binding affinity to NeuAcα2-6-Gal. Remarkably, an increment of host-cell-surface sialyl Lewis X (sLe) exacerbates the killing by several wild-type IAV strains and a previously engineered mutant HK68-MTA. Structural alignment of HAs from HK68 and HK68-MTA suggests formation of a putative hydrogen bond between Trp222 of HA-HK68-MTA and the C-4 hydroxyl group of the α1-3-linked fucose of sLe, which may account for the enhanced host cell killing of that mutant.
Topics: Animals; Bacterial Proteins; Biological Assay; CHO Cells; Cricetulus; Dogs; Glycosyltransferases; Healthy Volunteers; Helicobacter mustelae; Hemagglutinins; Host-Pathogen Interactions; Humans; Influenza A Virus, H1N1 Subtype; Influenza A Virus, H3N2 Subtype; Influenza, Human; Intravital Microscopy; Luciferases, Bacterial; Lung; Madin Darby Canine Kidney Cells; Metabolic Engineering; Microscopy, Fluorescence; Molecular Imaging; Oligosaccharides; Pasteurella multocida; Recombinant Proteins; Sialyl Lewis X Antigen; Staining and Labeling
PubMed: 30996301
DOI: 10.1038/s41467-019-09608-w -
Animal Microbiome May 2022Invertebrates are a very attractive subject for studying host-microbe interactions because of their simple gut microbial community and host diversity. Studying the...
BACKGROUND
Invertebrates are a very attractive subject for studying host-microbe interactions because of their simple gut microbial community and host diversity. Studying the composition of invertebrate gut microbiota and the determining factors is essential for understanding their symbiotic mechanism. Cephalopods are invertebrates that have similar biological properties to vertebrates such as closed circulation system, an advanced nervous system, and a well-differentiated digestive system. However, it is not currently known whether their microbiomes have more in common with vertebrates or invertebrates. This study reports on the microbial composition of six cephalopod species and compares them with other mollusk and marine fish microbiomes to investigate the factors that shape the gut microbiota.
RESULTS
Each cephalopod gut consisted of a distinct consortium of microbes, with Photobacterium and Mycoplasma identified as core taxa. The gut microbial composition of cephalopod reflected their host phylogeny, the importance of which was supported by a detailed oligotype-level analysis of operational taxonomic units assigned to Photobacterium and Mycoplasma. Photobacterium typically inhabited multiple hosts, whereas Mycoplasma tended to show host-specific colonization. Furthermore, we showed that class Cephalopoda has a distinct gut microbial community from those of other mollusk groups or marine fish. We also showed that the gut microbiota of phylum Mollusca was determined by host phylogeny, habitat, and diet.
CONCLUSION
We have provided the first comparative analysis of cephalopod and mollusk gut microbial communities. The gut microbial community of cephalopods is composed of distinctive microbes and is strongly associated with their phylogeny. The Photobacterium and Mycoplasma genera are core taxa within the cephalopod gut microbiota. Collectively, our findings provide evidence that cephalopod and mollusk gut microbiomes reflect host phylogeny, habitat, and diet. It is hoped that these data can contribute to future studies on invertebrate-microbe interactions.
PubMed: 35527289
DOI: 10.1186/s42523-022-00184-x -
Applied and Environmental Microbiology May 2019spp. are ubiquitous marine bacteria with high metabolism flexibility and genome plasticity. Previous studies have revealed the dynamics of planktonic vibrios in...
spp. are ubiquitous marine bacteria with high metabolism flexibility and genome plasticity. Previous studies have revealed the dynamics of planktonic vibrios in relation to environmental forces, such as temperature and salinity. However, little is known about ecology in benthic environments. Here, we elucidate the abundance, diversity, and spatial distribution of spp. in sediments of the Chinese marginal seas, with a wide spatial range from north to south covering the Yellow Sea (YS), East China Sea (ECS), and South China Sea (SCS). Quantitative analysis showed that spp. were most abundant in the SCS (∼9.04 × 10 copies/g) compared to the YS (∼1.00 × 10 copies/g) and ECS (∼8.86 × 10 copies/g). community compositions derived from Illumina sequencing of -specific 16S rRNA genes varied significantly between sampling areas, which was reflected by a strong distance-decay pattern. The spatial distribution of was governed by a joint effect of spatial and environmental factors (especially temperature, salinity, and SiO), and their respective pure effects explained only a small fraction of the community variation. Moreover, we identified the most prominent operational taxonomic units (OTUs) that were partitioned in these sea areas. Whereas OTU20 and were prevalent in the YS, and , and , , and were prevalent in the ECS and SCS, respectively. Our study demonstrated clear spatial heterogeneity of spp. in sediments of the Chinese marginal seas, laying a foundation for fully understanding the marine ecology and the ecological roles of the species. is an important component of natural marine microbial populations in terms of pathogenicity and roles in carbon cycling. Compared to the marine pelagic environment, our knowledge of the diversity and distribution pattern of spp. in sediment is limited. Here, we show higher abundance in Chinese marginal seas than in other studied sediments. There was a clear spatial differentiation of abundance and community composition in different sea areas. The benthic community displayed a strong distance-decay pattern across a wide spatial range, which was formed under the combined effects of spatial and environmental factors. These results provide deep insights into the ecological dynamics of and its environmental controls, facilitating a more comprehensive understanding of the marine ecology.
Topics: Biodiversity; China; Geologic Sediments; Oceans and Seas; Vibrio
PubMed: 30877118
DOI: 10.1128/AEM.03064-18 -
Journal of Clinical Microbiology Feb 2023Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness... (Review)
Review
Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum ) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the , , and genera. Valid and effectively published novel members of the Streptococcus, , and genera are additionally described from disease pathogenesis perspectives.
Topics: Humans; Planctomycetes; Bacteria; Gram-Negative Bacteria; Phylogeny
PubMed: 36719221
DOI: 10.1128/jcm.01426-22