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Microbiological Research Mar 2020Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge...
Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15.
Topics: Aquatic Organisms; Base Composition; DNA, Bacterial; Genome, Bacterial; Genomics; Malaysia; Phenomics; Photobacterium; Phylogeny; Seawater; Sequence Analysis, DNA
PubMed: 31945517
DOI: 10.1016/j.micres.2020.126410 -
Frontiers in Oncology 2022Commensal microbiota have been proven to colonize the mammary gland, but whether their composition is altered in patients with breast cancer (BC) remains elusive. This...
BACKGROUND
Commensal microbiota have been proven to colonize the mammary gland, but whether their composition is altered in patients with breast cancer (BC) remains elusive. This study intends to explore the breast microbiome differences between benign and malignant diseases and to investigate the impact of neoadjuvant chemotherapy (NAC) on the breast microbiota in patients with BC.
METHODS
Breast normal adipose tissues (NATs) were collected from 79 patients with BC and 15 controls between July 2019 and November 2021. The BC group consisted of 29 patients who had received NAC and 50 who were non-NAC patients. Participants diagnosed with benign breast disease were recruited as controls. 16S rRNA gene sequencing was used to analyze the bacterial diversity of NATs.
RESULTS
The community structure of the NAT microbiome was significantly different between the BC and control groups. decreased (47.40% versus 39.74%), whereas increased (15.71% versus 25.33%) in patients with BC when compared with that in control tissues. Nine genera were enriched in BC NATs, and four genera levels increased in the control group. The associations between differential bacterial genera and breast tumor grade were calculated by Spearman's correlation. The results showed that tumor grade was positively associated with the relative abundance of and negatively related to , , , and . Moreover, menopause was associated with the microbiota composition change of non-NAC BC patients and related to the significant reduction in the abundance level of , , and . In addition, NAC was related to the beta diversity of patients with BC and associated with the decrease of and in postmenopausal patients. Of note, Tax4Fun functional prediction analysis revealed that the metabolic state was more exuberant in the BC group with upregulating of multiple metabolism-related pathways.
CONCLUSION
Our results offer new insight into the relationship between NAC and breast microbiota and help to better characterize the breast microbial dysbiosis that occurs in patients with BC. Further epidemiological studies with larger sample size and well-designed animal experiments are required to elucidate the role of breast microbiota in the therapeutic outcome of BC.
PubMed: 36172155
DOI: 10.3389/fonc.2022.926920 -
Molecules (Basel, Switzerland) Jul 2022This study aimed to evaluate the antibacterial activity in vitro of and extracts against potentially pathogenic bacteria for Pacific white shrimp. Furthermore, the...
This study aimed to evaluate the antibacterial activity in vitro of and extracts against potentially pathogenic bacteria for Pacific white shrimp. Furthermore, the extracts with higher inhibitory activity were analyzed to identify compounds responsible for bacterial inhibition and evaluate their effect on motility and biofilm formation. and extracts were prepared using methanol, acetone, and hexane by ultrasound. The minimum inhibitory concentration (MIC) of the extracts was determined against and . The polyphenol profile of those extracts showing the highest bacterial inhibition were determined. Besides, the bacterial swimming and swarming motility and biofilm formation were determined. The highest inhibitory activity against the four pathogens was found with the acetonic extract of leaf (MIC of 50 mg/mL for spp. and 25 mg/mL for spp.) and the methanol extract of flower (MIC of 50 mg/mL for all pathogens tested). Both extracts affected the swarming and swimming motility and the biofilm formation of the tested bacteria. The main phenolic compounds related to bacteria inhibition were naringin, vanillic acid, and rosmarinic acid, whilst hesperidin, kaempferol pentosyl-rutinoside, and rhamnetin were related to bacteria inhibition.
Topics: Animals; Anti-Bacterial Agents; Methanol; Microbial Sensitivity Tests; Penaeidae; Plant Extracts; Vibrio parahaemolyticus
PubMed: 35889267
DOI: 10.3390/molecules27144397 -
Microbial Genomics Dec 2022The Pacific oyster (PO), , is an important commercial marine species but periodically experiences large stock losses due to disease events known as summer mortality....
The Pacific oyster (PO), , is an important commercial marine species but periodically experiences large stock losses due to disease events known as summer mortality. Summer mortality has been linked to environmental perturbations and numerous viral and bacterial agents, indicating this disease is multifactorial in nature. In 2013 and 2014, several summer mortality events occurred within the Port Stephens estuary (NSW, Australia). Extensive culture and molecular-based investigations were undertaken and several potentially pathogenic species were identified. To improve species identification and genomically characterise isolates obtained from this outbreak, whole-genome sequencing (WGS) and subsequent genomic analyses were performed on 48 bacterial isolates, as well as a further nine isolates from other summer mortality studies using the same batch of juveniles. Average nucleotide identity (ANI) identified most isolates to the species level and included members of the , , and genera, with species making up more than two-thirds of all species identified. Construction of a phylogenomic tree, ANI analysis, and pan-genome analysis of the 57 isolates represents the most comprehensive culture-based phylogenomic survey of during a PO summer mortality event in Australian waters and revealed large genomic diversity in many of the identified species. Our analysis revealed limited and inconsistent associations between isolate species and their geographical origins, or host health status. Together with ANI and pan-genome results, these inconsistencies suggest that to determine the role that microbes may have in Pacific oyster summer mortality events, isolate identification must be at the taxonomic level of strain. Our WGS data (specifically, the accessory genomes) differentiated bacterial strains, and coupled with associated metadata, highlight the possibility of predicting a strain's environmental niche and level of pathogenicity.
Topics: Animals; Crassostrea; Phylogeny; Gammaproteobacteria; Australia; Vibrio; Disease Outbreaks
PubMed: 36748707
DOI: 10.1099/mgen.0.000883 -
Frontiers in Immunology 2021Cobia () is a marine fish of high economic value that grows at a fast rate. However, intensive fish farming has led to disease outbreaks in cobia cultures, which is...
Cobia () is a marine fish of high economic value that grows at a fast rate. However, intensive fish farming has led to disease outbreaks in cobia cultures, which is highly costly to the industry. The impact of infectious diseases on cobia production has led to the inappropriate and increased use of chemicals and antibiotics, which negatively affects the environment and human health and promotes the spread of drug-resistant pathogens. Hence, prophylactic measurements, such as the use of immunomodulators, are required to improve the health of cultured animals against pathogens. In this study, we examined the effects of water extract (SSWE) in cobia and . We found that treatment with SSWE could significantly increase the expression of cytokines (e.g., , , , , and ) and chemokines (e.g., ) in primary cultured head kidney leukocytes. Intraperitoneal injection of SSWE (20 μg/g body weight) promoted higher expression of , , , , chemokines (e.g., ), and antibodies (e.g., ) in head kidney and spleen tissues of the fish compared with other dose levels. Additionally, we describe for the second time (only after India) of the isolation of subsp. () from a deadly epizootic in cage-farmed cobia. An intraperitoneal inoculation of SSWE before challenge showed that SSWE treatment could delay the onset of mortality of cobia. Finally, fish that received SSWE intraperitoneally before infection with exhibited elevated expression of Th1-type cytokines, namely, , , , and . At the same time, the expression of Th2-related factors (such as in the head kidney, and and in the spleen) were lower for the fish that received SSWE instead of PBS before the challenge. The results indicate that SSWE treatment facilitates the induction of Th1-type cytokines in cobia to fight against infection and has the potential to be used as an immunostimulant and vaccine adjuvant for fish.
Topics: Animals; Biological Products; Cytokines; Fish Diseases; Host-Pathogen Interactions; Immunity, Innate; Inflammation Mediators; Mortality; Photobacterium; Rhodophyta; Th1 Cells; Transcriptome
PubMed: 35140710
DOI: 10.3389/fimmu.2021.801501 -
Applied and Environmental Microbiology Jul 2023Coral reefs are among the most biodiverse ecosystems, providing habitats for various organisms. Studies on coral bleaching have been increasing recently, but little is...
Coral reefs are among the most biodiverse ecosystems, providing habitats for various organisms. Studies on coral bleaching have been increasing recently, but little is known about the distribution and community assembly of coral pathogenic bacteria (e.g., several species). We elucidated the distribution pattern and interaction relationships of total bacteria and spp. in sediments from the Xisha Islands, which are characterized by their high coverage and diversity of coral resources. spp. showed significantly higher relative abundance values in the Xisha Islands (1.00 × 10 copies/g) than in other areas (approximately 1 × 10 to 9.04 × 10 copies/g), indicating that the coral bleaching event of 2020 may have promoted the bloom of vibrios. A spatial shift in community composition was observed between the northern (Photobacterium rosenbergii and Vibrio ponticus) and southern (Vibrio ishigakensis and Vibrio natriegens) sites, accompanied by a clear distance-decay pattern. The spatial distance and coral species (e.g., and ) had much greater correlations with the community than did environmental factors. However, complex mechanisms may exist in the community assembly of spp. due to the large proportion of unexplained variation. Stochastic processes may play an important role, as shown by the neutral model. Vibrio harveyi had the highest relative abundance (77.56%) and niche breadth, compared to other species, and it was negatively correlated with Acroporidae, likely reflecting its strong competitive ability and adverse effects on specific corals. Our study provides insights into the bloom and underlying assembly mechanisms of sedimentary vibrios in the Xisha Islands, thereby contributing to identify the potential indicator of coral bleaching and provide inspiration for the environmental management of coral reef areas. Coral reefs exert important roles in maintaining the sustainability of marine ecosystems but decline worldwide due to various drivers, especially pathogenic microorganisms. Here, we investigated the distribution pattern and interactions of total bacteria and spp. in the sediments from Xisha Islands during the coral bleaching event of 2020. Our results showed that the abundances of (1.00 × 10 copies/g) were high across the whole sites, indicating the bloom of sedimentary spp. Coral pathogenic species were abundant in the sediments, likely reflecting adverse effects on several kinds of corals. The compositions of the spp. were separated by geographical location, which was mainly attributable to the spatial distance and coral species. Overall, this work contributes by providing evidence for the outbreak of coral pathogenic vibrios. The pathogenic mechanism of the dominant species (especially V. harveyi) should be comprehensively considered by laboratory infection experiments in the future.
Topics: Animals; Ecosystem; Coral Bleaching; Islands; Coral Reefs; Anthozoa; Vibrio
PubMed: 37314342
DOI: 10.1128/aem.00543-23 -
International Journal of Molecular... Aug 2022The genus is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. sp. CCB-ST2H9 was isolated from estuarine...
The genus is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with , forming a distinct clade with , , and . The core genome of was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA-DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against spp. Intriguingly, clustering based on BGCs profiles grouped , , , , and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genomics; Multigene Family; Photobacterium; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 36077108
DOI: 10.3390/ijms23179712 -
Microbial Genomics Apr 2021Despite the recent advances in sequencing technologies, the complete assembly of multi-chromosome genomes of the , often containing several plasmids, remains...
Despite the recent advances in sequencing technologies, the complete assembly of multi-chromosome genomes of the , often containing several plasmids, remains challenging. Using a combination of Oxford Nanopore MinION long reads and short Illumina reads, we fully sequenced, closed and curated the genomes of two strains of a primary aquatic pathogen subsp. isolated in Australia. These are also the first genome sequences of subsp. isolated in Oceania and, to our knowledge, in the Southern hemisphere. We also investigated the phylogenetic relationships between Australian and overseas isolates, revealing that Australian subsp. are more closely related to the Asian and American strains rather than to the European ones. We investigated the mobilome and present new evidence showing that a host specialization process and progressive adaptive evolution to fish are ongoing in subsp. , and are largely mediated by transposable elements, predominantly in chromosome 2, and by plasmids. Finally, we identified two novel potential virulence determinants in subsp. - a chorismate mutase gene, which is ubiquitously retained and co-localized with the AIP56 apoptogenic toxin-encoding gene on the pPHDP10 plasmid, and transfer-messenger RNA gene located on the main chromosome, homologous to a critical-to-virulence determinant in . Our study describes, to our knowledge, the only fully closed and manually curated genomes of subsp. available to date, offering new insights into this important fish pathogen and its evolution.
Topics: Bacterial Proteins; Chromosome Mapping; DNA Transposable Elements; Evolution, Molecular; Genome, Bacterial; Photobacterium; Phylogeny; Virulence Factors
PubMed: 33885359
DOI: 10.1099/mgen.0.000562 -
International Journal of Environmental... Mar 2019The single toxicity (IC) of zinc (Zn) and 11 nitro-substituted benzenes to were determined, respectively. On basis of single toxicity, the joint toxicity of binary...
The single toxicity (IC) of zinc (Zn) and 11 nitro-substituted benzenes to were determined, respectively. On basis of single toxicity, the joint toxicity of binary mixtures of Zn and 11 nitro-substituted benzenes at different Zn concentrations of 0.2 IC, 0.5 IC, and 0.8 IC were measured. The joint toxicity was evaluated by toxic unit (TU) and additive index (AI) methods. The results indicated that the joint toxicity was not only depending on the Zn concentrations but also on the substituted groups of nitro-substituted benzenes. The quantitative structure-activity relation (QSAR) equations were developed and the results showed that the toxicity of nitro-substituted benzenes has different joint effect at the different Zn concentrations. At the Zn concentration of 0.2 IC, the binary joint effects were mainly antagonism and the joint toxicity was negatively related to descriptors called VE2_B(p) and TIC3. At the Zn concentration of 0.5 IC and 0.8 IC, the binary joint effects were mainly antagonism and simple addition, and the joint toxicity was related to the same descriptor Eig06_ AEA(dm). It indicated that the joint toxic actions were similar when combined at the medium and high concentrations of Zn.
Topics: Benzene; Photobacterium; Quantitative Structure-Activity Relationship; Zinc
PubMed: 30909451
DOI: 10.3390/ijerph16061041 -
Antioxidants (Basel, Switzerland) Jun 2022Phospholipids have an important antioxidant effect on animals. The effects of different dietary phospholipid sources on the growth, antioxidant activity, immunity, and...
Phospholipids have an important antioxidant effect on animals. The effects of different dietary phospholipid sources on the growth, antioxidant activity, immunity, and gut microbiota of female broodstock of Pacific white shrimp were investigated. Four isoproteic and isolipid semi-purified diets containing 4% soybean lecithin (SL), egg yolk lecithin (EL), or krill oil (KO) and a control diet without phospholipid supplementation were fed to female broodstock of (34.7 ± 4.2 g) for 28 days. The growth performance, antioxidative capacity, and innate immunity of the female broodstock fed phospholipid supplemented diets were improved regardless of sources compared with the control shrimp. The effects on growth and antioxidant capacity in female shrimp fed the KO diet were highest. The innate immunity of female shrimp fed the EL and KO diets were significantly higher than shrimp fed the SL diet. Dietary phospholipid supplementation increased gut microbiota diversity and richness, and the Chao1 and ACE values in the KO group were significantly higher than in the control group. The richness of Proteobacteria, , and decreased, whereas the richness of Firmicutes and Bacteroidetes increased in the shrimp fed the KO diet compared with the shrimp fed the SL and EL diets. The interactions of gut microbiota in shrimp fed the KO diet were the most complex, and the positive interaction was the largest among all the treatments. The functional genes of gut microbiota in shrimp fed the KO diet were significantly enriched in lipid metabolism and terpenoid/polyketide metabolism pathways. Spearman correlation analysis showed that had significantly positive correlations with antioxidant activity (total antioxidant capacity, superoxide dismutase, glutathione peroxidase), immune enzyme activity (phenoloxidase and lysozyme), and immune gene expression (C-type lectin 3, Caspase-1). All findings suggest that dietary phospholipids supplementation can improve the growth and health status of female broodstock. Krill oil is more beneficial in improving the antioxidant capacity and innate immunity than other dietary phospholipid sources. Furthermore, krill oil can help establish the intestinal immune barrier by increasing the richness of and promote the growth of female shrimp. may be involved in iron metabolism to improve the antioxidant capacity of female shrimp.
PubMed: 35740040
DOI: 10.3390/antiox11061143