A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments

Beyond the Gut: The intratumoral microbiome's influence on tumorigenesis and treatment response

The intratumoral microbiome (TM) refers to the microorganisms in the tumor tissues, including bacteria, fungi, viruses, and so on, and is distinct from the gut microbiome and circulating microbiota. TM is strongly associated with tumorigenesis, progression, metastasis, and response to therapy. This paper highlights the current status of TM. Tract sources, adjacent normal tissue, circulatory system, and concomitant tumor co-metastasis are the main origin of TM. The advanced techniques in TM analysis are comprehensively summarized. Besides, TM is involved in tumor progression through several mechanisms, including DNA damage, activation of oncogenic signaling pathways (phosphoinositide 3-kinase [PI3K], signal transducer and activator of transcription [STAT], WNT/β-catenin, and extracellular regulated protein kinases [ERK]), influence of cytokines and induce inflammatory responses, and interaction with the tumor microenvironment (anti-tumor immunity, pro-tumor immunity, and microbial-derived metabolites). Moreover, promising directions of TM in tumor therapy include immunotherapy, chemotherapy, radiotherapy, the application of probiotics/prebiotics/synbiotics, fecal microbiome transplantation, engineered microbiota, phage therapy, and oncolytic virus therapy. The inherent challenges of clinical application are also summarized. This review provides a comprehensive landscape for analyzing TM, especially the TM-related mechanisms and TM-based treatment in cancer.

Environmental microbial diversity and water pollution characteristics resulted from 150 km coastline in Quanzhou Bay offshore area

As a typical transitional area between the land and sea, the offshore area is subjected to the triple synergistic pressure from the ocean, land, and atmosphere at the same time, and has obvious characteristics such as complex and diverse chemical, physical, and biological processes, coupled and changeable environmental factors, and sensitive and fragile ecological environment. With the deepening of the urbanization process, the offshore area has gradually become the final receptions of pollutants produced by industry, agriculture, and service industries, and plays a key role in the global environmental geochemical cycle of pollutants. In this study, the Quanzhou Bay offshore area was selected as the research object. Sediment and water samples were collected from 8 sampling points within about 150 km of coastline in the Quanzhou Bay offshore area. 16s rDNA high-throughput sequencing method was used to investigate the variation rule of microbial diversity in the offshore area, and multi-parameter water quality analysis was carried out at the same time. The results showed that the distribution characteristics of microbial communities and water quality in the Quanzhou Bay offshore area showed significant differences in different latitudes and longitudes. This difference is closely related to the complexity of offshore area. This study can provide scientific support for protecting and improving the ecological environment of offshore areas.

Characterization of Silver Carbonate Nanoparticles Biosynthesized Using Marine Actinobacteria and Exploring of Their Antimicrobial and Antibiofilm Activity

Bacterial resistance to different antimicrobial agents is growing with alarming speed, especially when bacterial cells are living in biofilm. Hybrid nanoparticles, synthesized through the green method, hold promise as a potential solution to this challenge. In this study, 66 actinomycete strains were isolated from three distinct marine sources: marine sediment, the algae Codium bursa, and the marine sponge Chondrosia reniformis. From the entirety of the isolated strains, one strain, S26, identified as Saccharopolyspora erythrea, was selected based on its taxonomic position and significant antimicrobial activity. Using the biomass of the selected marine Actinobacteria, the green synthesis of eco-friendly silver carbonate nanoparticles (BioAg2CO3NPs) is reported for the first time in this pioneering study. The BioAg2CO3NPs were characterized using different spectroscopic and microscopic analyses; the synthesized BioAg2CO3NPs primarily exhibit a triangular shape, with an approximate size of 100 nm. Biological activity evaluation indicated that the BioAg2CO3NPs exhibited good antimicrobial activity against all tested microorganisms and were able to remove 58% of the biofilm formed by the Klebsiella pneumoniae kp6 strain.

Paracrocinitomix mangrovi gen. nov., sp. nov., isolated from a mangrove sediment: proposal of two new families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov., and emended description of the family Schleiferiaceae

A Gram-stain-negative and short rod-shaped bacterial strain designated GM2-3-6-6^T was obtained from a mangrove sediment. Cells were light yellow-pigmented, catalase-positive and oxidase-positive. Carotenoid pigment was produced. Phylogeny of the 16S rRNA gene showed that strain GM2-3-6-6^T was affiliated to the family Crocinitomicaceae, sharing maximum sequence similarities with Crocinitomix algicola 0182^T, C. catalasitica IFO 15977^T, and Putridiphycobacter roseus SM1701^T of 93.8%, 93.6%, and 92.5%, respectively. The average nucleotide identity values, digital DNA-DNA hybridization estimates and average amino acid identity values between strain GM2-3-6-6^T and the three close relatives were 68.6-68.8%, 18.5-19.2%, and 59.0-62.3%, respectively. The complete circular genome of strain GM2-3-6-6^T was 4,365,762 bp in length with a DNA G + C content of 35.0%. The respiratory quinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, two unidentified phospholipids, one unidentified aminoglycolipid, one unidentified aminolipid and four other unidentified lipids. The major fatty acids were iso-C_15:0, iso-C_15:1 G, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), and iso-C_17:0 3-OH. Based on genomic, phenotypic, and chemotaxonomic characterizations, strain GM2-3-6-6^T represents a novel species of a novel genus, for which the name Paracrocinitomix mangrovi gen. nov., sp. nov. is proposed. The type strain is GM2-3-6-6^T (= MCCC 1K04831^T = KCTC 82931^T). Additionally, phylogenomic analysis of the type strains of the family Schleiferiaceae and family Cryomorphaceae related members including uncultivated bacteria, was performed using the Genome Taxonomic Database toolkit (GTDB-Tk). Based on 16S rRNA gene phylogeny and genomic features, two novel families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov. are proposed. An emended description of the family Schleiferiaceae is also proposed.

iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments

Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an "one strain many compounds" approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products.

Horizontal Transfer of Virulence Factors by Pathogenic Enterobacteria to Marine Saprotrophic Bacteria during Co-Cultivation in Biofilm

Environmental problems associated with marine pollution and climate warming create favorable conditions for the penetration and survival of pathogenic bacteria in marine ecosystems. These microorganisms have interspecific competitive interactions with marine bacteria. Co-culture, as an important research strategy that mimics the natural environment of bacteria, can activate silent genes or clusters through interspecies interactions. The authors used modern biotechnology of co-cultivation to dynamically study intercellular interactions between different taxa of bacteria—pathogenic enterobacteria Yersinia pseudotuberculosis and Listeria monocytogenes and saprotrophic marine bacteria Bacillus sp. and Pseudomonas japonica isolated in summer from the coastal waters of the recreational areas of the Sea of Japan. The results of the experiments showed that during the formation of polycultural biofilms, horizontal transfer of genes encoding some pathogenicity factors from Y. pseudotuberculosis and L. monocytogenes to marine saprotrophic bacteria with different secretion systems is possible. It was previously thought that this was largely prevented by the type VI secretion system (T6SS) found in marine saprotrophic bacteria. The authors showed for the first time the ability of marine bacteria Bacillus sp. and P. japonica to biofilm formation with pathogenic enterobacteria Y. pseudotuberculosis and L. monocytogenes, saprophytic bacteria with type III secretion system (T3SS). For the first time, a marine saprotrophic strain of Bacillus sp. Revealed manifestations of hyaluronidase, proteolytic and hemolytic activity after cultivation in a polycultural biofilm with listeria. Saprotrophic marine bacteria that have acquired virulence factors from pathogenic enterobacteria, including antibiotic resistance genes, could potentially play a role in altering the biological properties of other members of the marine microbial community. In addition, given the possible interdomain nature of intercellular gene translocation, acquired virulence factors can be transferred to marine unicellular and multicellular eukaryotes. The results obtained contribute to the paradigm of the epidemiological significance and potential danger of anthropogenic pollution of marine ecosystems, which creates serious problems for public health and the development of marine culture as an important area of economic activity in coastal regions.

Hanstruepera crassostreae He et al. 2018 is a later heterotypic synonym of Pseudobizionia ponticola Park et al. 2018 and transfer of Pseudobizionia ponticola to the genus Hanstruepera as Hanstruepera ponticola comb. nov

The 16S rRNA gene sequences of Pseudobizionia ponticola MM-14^T and Hanstruepera crassostreae L53^T shared 100 % sequence similarity. This study aimed to clarify the taxonomic position of the two species. Whole-genome comparisons showed that P. ponticola MM-14^T and H. crassostreae L53^T shared average nucleotide identity of 97.52 %, digital DNA-DNA hybridization of 75.30 % and average amino acid identity of 96.98 %. These values exceeded the threshold of bacterial species delineation. Furthermore, average amino acid identities of P. ponticola MM-14^T and H. crassostreae L53^T in comparison with Hanstruepera neustonica CC-PY-50^T were 82.04 and 82.11 %, respectively. Phylogenetic analysis based on 16S rRNA gene and 120 bacterial conserved single-copy genes also supported that P. ponticola MM-14^T and H. crassostreae L53^T belonged to the genus Hanstruepera. Phenotypic and chemical taxonomic properties compared between P. ponticola MM-14^T and H. crassostreae L53^T were nearly identical. Colonies of the two species on marine agar plates were orange-pigmented, circular and smooth. Flexirubin-type pigments were present in both H. crassostreae L53^T and P. ponticola MM-14^T. The major fatty acids composition of the two species consisted of iso-C_15 : 1 G, iso-C_15 : 0, and iso-C_17 : 0 3-OH, similar to H. neustonica CC-PY-50^T. Based on priority, H. crassostreae He et al. 2018 is a later heterotypic synonym of P. ponticola Park et al. 2018, and P. ponticola should be transferred to the genus Hanstruepera as Hanstruepera ponticola comb. nov.

Oceanobacter mangrovi Sp. Nov., a Novel Poly-β-hydroxybutyrate Accumulating Bacterium Isolated from Mangrove Sediment

A Gram-stain-negative, rod-shaped, motile, mesophilic, and aerobic bacterial strain, designated SM2-42 ^T was isolated from a mangrove sediment. Catalase activity and oxidase activity were positive. Growth was observed at 20 °C-40 °C, pH 6.0-8.0, and in the presence of 0.5-5.0% NaCl. Cells of strain SM2-42 ^T contained poly-β-hydroxybutyrate granules. The 16S rRNA gene of strain SM2-42 ^T had maximum sequence similarity with Oceanobacter kriegii 197 ^T of 97.1%. Phylogenetic analysis based on 16S rRNA gene sequence and 120 conserved concatenated proteins indicated that strain SM2-42 ^T was affiliated to the genus Oceanobacter and formed a monophyletic branch with O. kriegii 197 ^T. The average nucleotide identity and digital DNA-DNA hybridization values between strain SM2-42 ^T and O. kriegii 197 ^T were 76.43% and 21.60%, respectively. The major isoprenoid quinone was Q-8. The major fatty acids (> 10%) comprised C_16:0, summed feature 8 (C_18:1ω7c and C_18:1 ω6c), C_18:0, and summed feature 3 (C_16:1ω7c and/or C_16:1 ω6c). The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The draft genome size was 5,115,008 bp with DNA G + C content of 54.3%. Based on phylogenetic analyses and whole genomic comparisons, strain SM2-42 ^T represented a novel species, for which the name Oceanobacter mangrovi sp. nov. was proposed. The type strain was SM2-42 ^T (= MCCC 1K06300^T = KCTC 82938 ^T).