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International Journal of Environmental... Mar 2022Lake Vostok is the deepest lake of Antarctica but has poor accessibility for study due to a thick glacial cover, however, water samples of this lake have become...
Lake Vostok is the deepest lake of Antarctica but has poor accessibility for study due to a thick glacial cover, however, water samples of this lake have become available for study just recently. Previously, only the microbiome of the ice cover samples was characterized. Here we report results of bacteriological seeding with subsequent identification of the heterotrophic microorganisms (bacteria and micellar fungi) present by 16S rDNA sequencing as well as results of a direct molecular study of the water microbiome. Surprisingly, the data obtained gave evidence of a predominant occurrence of common chemoorganotrophs that were rather psychrotolerant than psychrophilic. We isolated and described strains belonging to eight heterotrophic microbial species able to grow in a rich medium: six bacterial strains belonging to the species and , , , sp. and ; and two fungal strains belonging to sp. and . Direct study of 16S rDNA purified water samples confirmed the predominance of the , , and () .
Topics: Antarctic Regions; DNA, Ribosomal; Lakes; Microbiota; Sphingomonadaceae; Water; Water Microbiology
PubMed: 35409708
DOI: 10.3390/ijerph19074025 -
PloS One 2020The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to...
The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.
Topics: Actinobacteria; Bacteriophages; Base Composition; DNA, Viral; Genes, Viral; Genetic Variation; Genome, Viral; Genomics; Phylogeny; Viral Fusion Proteins
PubMed: 32555720
DOI: 10.1371/journal.pone.0234636 -
Foods (Basel, Switzerland) Nov 2023The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages...
The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages on the composition and function of donkey milk microbiota. The milk samples were collected at 1, 30, 60, 90, 120, 150, and 180 days post-delivery. The result showed that the microbial composition and functions in donkey milk were significantly affected by different lactation stages. The dominant bacterial phyla in donkey milk are (60%) and (22%). (39%), (4%), and (2%) were the predominant bacterial genera detected in all milk samples. In the mature milk, the abundance of lactic acid bacteria (7%) was higher. (5%) and (3%) were more plentiful in milk samples from middle and later lactation stages (90-180 d). Furthermore, the pathogens and and thermoduric bacteria , , and were also detected. Donkey milk is rich in beneficial bacteria and also poses a potential health risk. The above findings have improved our understanding of the composition and function changes of donkey milk microbiota, which is beneficial for the rational utilization of donkey milk.
PubMed: 38231735
DOI: 10.3390/foods12234272 -
Frontiers in Microbiology 2020The microbiota that spoil long-life micro-filtered milk generally includes species of the genus . The metabolic properties of this of microorganisms that could...
Phenotypic and Genotypic Investigation of Two Representative Strains of Microbacterium Species Isolated From Micro-Filtered Milk: Growth Capacity and Spoilage-Potential Assessment.
The microbiota that spoil long-life micro-filtered milk generally includes species of the genus . The metabolic properties of this of microorganisms that could potentially modify the quality of micro-filtered milk are still unexplored when compared to better-known microorganisms, such as the spore-forming and spp., and Gram-negative contaminants, such as species of the genera and . In this preliminary study, two strains of ( 18H and sp. 2C) isolated from micro-filtered milk were characterized in depth, both phenotypically and genotypically, to better understand their role in long-term milk spoilage. The study highlights the ability of these strains to produce high cell numbers and low acidification in micro-filtered milk under storage and shelf-life conditions. Phenotypic analyses of the two sp. isolates revealed that both strains have low proteolytic and lipolytic activity. In addition, they have the ability to form biofilms. This study aims to be a preliminary investigation of milk-adapted strains of the genus, which are able to grow to high cellular levels and perform slight but not negligible acidification that could pose a potential risk to the final quality of micro-filtered milk. Furthermore, 18H and sp. 2C were genotypically characterized in relation to the characteristics of interest in the milk environment. Some protein-encoding genes involved in lactose metabolism were found in the genomes, such as β-galactosidase, lactose permease, and L-lactate dehydrogenase. The phenotypically verified proteolytic ability was supported in the genomes by several genes that encode for proteases, peptidases, and peptide transferases.
PubMed: 33193134
DOI: 10.3389/fmicb.2020.554178 -
International Journal of Environmental... Sep 2022Due to the ecotoxicity of 17β-estradiol (E2), residual E2 in the environment poses potential risks to human and animal health and ecosystems. Biodegradation is...
Due to the ecotoxicity of 17β-estradiol (E2), residual E2 in the environment poses potential risks to human and animal health and ecosystems. Biodegradation is considered one of the most effective strategies to remove E2 from the environment. Here, a novel, efficient E2-degrading bacterial strain MZT7 was isolated from activated sludge and characterized. The genome of strain MZT7 contained 4,011,347 bp nucleotides with 71.26% G + C content and 3785 coding genes. There was 86.7% transformation efficiency of 10 mg/L E2 by strain MZT7 after incubation for 5 d at optimal temperature (30 °C) and pH (7.0). This strain was highly tolerant to ranges in pH (5.0-11.0), temperature (20-40 °C), and salinity (2-8%). Adding sources of carbon (glucose, maltose, sucrose, or lactose) or nitrogen sources (urea, peptone, or beef extract) promoted the degradation of E2 by strain MZT7. However, when yeast extract was added as a nitrogen source, the degradation efficiency of E2 was inhibited. Metabolites were analyzed by LC-MS and three metabolic pathways of E2 degradation were proposed. Further, the intermediates dehydroepiandrosterone and androsta-1,4-diene-3,17-dione were detected, as well as identification of and genes by KEGG, confirming one E2 degradation pathway. This study provided some insights into E2 biodegradation.
Topics: Animals; Bacteria; Biodegradation, Environmental; Cattle; Ecosystem; Estradiol; Humans; Microbacterium; Nitrogen
PubMed: 36078812
DOI: 10.3390/ijerph191711097 -
Microbiology Resource Announcements Nov 2023We purified two novel bacteriophages from soil collected in Sioux County, Iowa: BAjuniper and Tedro. These bacteriophages were isolated from the host, . BAjuniper was...
We purified two novel bacteriophages from soil collected in Sioux County, Iowa: BAjuniper and Tedro. These bacteriophages were isolated from the host, . BAjuniper was assigned to cluster EB, and Tedro was assigned to cluster EF. Both phages display genomes typical of other phages in their clusters.
PubMed: 37905824
DOI: 10.1128/MRA.00793-23 -
Frontiers in Microbiology 2023The deep-sea covers over 70% of the Earth's surface and harbors predominantly uncharacterized bacterial communities. Actinobacteria are the major prokaryotic source of...
The deep-sea covers over 70% of the Earth's surface and harbors predominantly uncharacterized bacterial communities. Actinobacteria are the major prokaryotic source of bioactive natural products that find their way into drug discovery programs, and the deep-sea is a promising source of biotechnologically relevant actinobacteria. Previous studies on actinobacteria in deep-sea sediments were either regionally restricted or did not combine a community characterization with the analysis of their bioactive potential. Here we characterized the actinobacterial communities of upper layers of deep-sea sediments from the Arctic and the Atlantic (Azores and Madeira) ocean basins, employing 16S rRNA metabarcoding, and studied the biosynthetic potential of cultivable actinobacteria retrieved from those samples. Metabarcoding analysis showed that the actinobacterial composition varied between the sampled regions, with higher abundance in the Arctic samples but higher diversity in the Atlantic ones. Twenty actinobacterial genera were detected using metabarcoding, as a culture-independent method, while culture-dependent methods only allowed the identification of nine genera. Isolation of actinobacteria resulted on the retrieval of 44 isolates, mainly associated with , , and genera. Some of these isolates were only identified on a specific sampled region. Chemical extracts of the actinobacterial isolates were subsequently screened for their antimicrobial, anticancer and anti-inflammatory activities. Extracts from two strains demonstrated activity against . Additionally, eight extracts (obtained from , , , , and isolates) showed significant activity against at least one of the tested cancer cell lines (HepG2 and T-47D). Furthermore, 15 actinobacterial extracts showed anti-inflammatory potential in the RAW 264.4 cell model assay, with no concomitant cytotoxic response. Dereplication and molecular networking analysis of the bioactive actinobacterial extracts showed the presence of some metabolites associated with known natural products, but one of the analyzed clusters did not show any match with the natural products described as responsible for these bioactivities. Overall, we were able to recover taxonomically diverse actinobacteria with different bioactivities from the studied deep-sea samples. The conjugation of culture-dependent and -independent methods allows a better understanding of the actinobacterial diversity of deep-sea environments, which is important for the optimization of approaches to obtain novel chemically-rich isolates.
PubMed: 37065153
DOI: 10.3389/fmicb.2023.1158441 -
Biology Nov 2023Two novel strains of sp. and sp. were identified from the intestine of olive flounder () and characterized in vitro as potential probiotics. Feeds without probiotic...
Two novel strains of sp. and sp. were identified from the intestine of olive flounder () and characterized in vitro as potential probiotics. Feeds without probiotic and with a 50:50 mixture of these two strains (1 × 10 CFU/g feed) were denoted as the control and Pro diets, respectively. Three randomly selected tanks (20 flounders/tank, ~11.4 g each) were used for each diet replication. After 8 weeks of feeding, the growth and feed utilization of the flounder in the Pro group improved ( < 0.05) compared to the control. Among four immune parameters, only myeloperoxidase activity was elevated in the Pro group. Serum biochemistry, intestinal microbial richness (Chao1), and diversity (Shannon index) remained unchanged ( ≥ 0.05), but phylogenetic diversity was enriched in the Pro fish intestine. Significantly lower Firmicutes and higher Proteobacteria were found in the Pro diet; the genus abundance in the control and Pro was as follows: > > and > > , respectively. Microbial linear discriminant scores and a cladogram analysis showed significant modulation. Therefore, the combination of two host-associated probiotics improved the growth and intestinal microbial population of flounder and could be supplemented in the Korean flounder industry.
PubMed: 37998042
DOI: 10.3390/biology12111443 -
Microbiology Resource Announcements Nov 2022Phages Cassita and Fransoyer were isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The genomes of Cassita and Fransoyer are...
Phages Cassita and Fransoyer were isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The genomes of Cassita and Fransoyer are 61,868 bp and 62,277 bp, respectively, with direct terminal repeats. Both phages exhibit siphoviral morphology and are predicted to have lytic life cycles.
PubMed: 36287072
DOI: 10.1128/mra.00885-22 -
Microbiology Resource Announcements Nov 2022Anseraureola, Pondwater, and Yasuo are bacteriophages with siphovirus morphology that infect Microbacterium foliorum NRRL B-24224. They were isolated from soil collected...
Anseraureola, Pondwater, and Yasuo are bacteriophages with siphovirus morphology that infect Microbacterium foliorum NRRL B-24224. They were isolated from soil collected in Amherst, Massachusetts, and have genome lengths between 17,362 bp and 17,453 bp. These phages each contain 25 predicted protein-coding genes and are assigned to phage cluster EE.
PubMed: 36227095
DOI: 10.1128/mra.00849-22