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MSystems Apr 2021Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the...
Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum , family , the genus includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and 's evolutionary history, we performed tandem genomic analyses with phenotyping of 85 accessions. Phylogenomic analysis of the family reveals that basal members of the clade are spp., a group of often-pathogenic organisms. exhibited two broad growth patterns in our phenotypic screen: one group that we called the "flexible ecotype" (FE) had the ability to grow between 4 and 37°C, and the other, which we called the "restricted ecotype" (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in colonizations of gnotobiotic mice, only FE strains persist. Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for , which likely evolved from a pathobiont. Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus , particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.
PubMed: 33850039
DOI: 10.1128/mSystems.00258-21 -
Microorganisms Aug 2020Surfactants, both synthetic and natural, are used in a wide range of industrial applications, including the degradation of petroleum hydrocarbons. Organisms from extreme...
Surfactants, both synthetic and natural, are used in a wide range of industrial applications, including the degradation of petroleum hydrocarbons. Organisms from extreme environments are well-adapted to the harsh conditions and represent an exciting avenue of discovery of naturally occurring biosurfactants, yet microorganisms from cold environments have been largely overlooked for their biotechnological potential as biosurfactant producers. In this study, four cold-adapted bacterial isolates from Antarctica are investigated for their ability to produce biosurfactants. Here we report on the physical properties and chemical structure of biosurfactants from the genera , , and . These organisms were able to grow on diesel, motor oil, and crude oil at 4 °C. Putative identification showed the presence of sophorolipids and rhamnolipids. Emulsion index test () activity ranged from 36.4-66.7%. Oil displacement tests were comparable to 0.1-1.0% sodium dodecyl sulfate (SDS) solutions. Data presented herein are the first report of organisms of the genus to produce biosurfactants and their metabolic capabilities to degrade diverse petroleum hydrocarbons. The organisms' ability to produce biosurfactants and grow on different hydrocarbons as their sole carbon and energy source at low temperatures (4 °C) makes them suitable candidates for the exploration of hydrocarbon bioremediation in low-temperature environments.
PubMed: 32756528
DOI: 10.3390/microorganisms8081183 -
Applied and Environmental Microbiology Jan 2022Dimethylsulfoniopropionate (DMSP) is one of the most abundant organic sulfur compounds in the oceans, which is mainly degraded by bacteria through two pathways, a...
Dimethylsulfoniopropionate (DMSP) is one of the most abundant organic sulfur compounds in the oceans, which is mainly degraded by bacteria through two pathways, a cleavage pathway and a demethylation pathway. Its volatile catabolites dimethyl sulfide (DMS) and methanethiol (MT) in these pathways play important roles in the global sulfur cycle and have potential influences on the global climate. Intense DMS/DMSP cycling occurs in the Arctic. However, little is known about the diversity of cultivable DMSP-catabolizing bacteria in the Arctic and how they catabolize DMSP. Here, we screened DMSP-catabolizing bacteria from Arctic samples and found that bacteria of four genera (, , and ) could grow with DMSP as the sole carbon source, among which and are predominant. Four representative strains ( sp. K31L, sp. K222D, sp. K632G, and sp. G41H) from different genera were selected to probe their DMSP catabolic pathways. All these strains produce DMS and MT simultaneously during their growth on DMSP, indicating that all strains likely possess the two DMSP catabolic pathways. On the basis of genomic and biochemical analyses, the DMSP catabolic pathways in these strains were proposed. Bioinformatic analysis indicated that most and bacteria have the potential to catabolize DMSP via the demethylation pathway and that only a small portion of strains may catabolize DMSP via the cleavage pathway. This study provides novel insights into DMSP catabolism in marine bacteria. Dimethylsulfoniopropionate (DMSP) is abundant in the oceans. The catabolism of DMSP is an important step of the global sulfur cycle. Although are widespread in the oceans, the contribution of in global DMSP catabolism is not fully understood. Here, we found that bacteria of four genera belonging to (, , and ), which were isolated from Arctic samples, were able to grow on DMSP. The DMSP catabolic pathways of representative strains were proposed. Bioinformatic analysis indicates that most and bacteria have the potential to catabolize DMSP via the demethylation pathway and that only a small portion of strains may catabolize DMSP via the cleavage pathway. Our results suggest that novel DMSP dethiomethylases/demethylases may exist in , and and that may be important participants in the marine environment, especially in polar DMSP cycling.
Topics: Bacteria; Carbon-Sulfur Lyases; Humans; Sulfides; Sulfonium Compounds; Sulfur
PubMed: 34788071
DOI: 10.1128/AEM.01806-21 -
BMC Veterinary Research Jan 2023An important food-producing sector in Egypt is aquaculture and fisheries; however, several pathogenic microorganisms lead to high mortalities and significant economic...
An important food-producing sector in Egypt is aquaculture and fisheries; however, several pathogenic microorganisms lead to high mortalities and significant economic losses. The occurrence of Psychrobacter glacincola infection among 180 wild marine fishes collected from the Red sea at Hurghada, Egypt were investigated in the present study. The disease prevalence rate was 6.7%. The recovered isolates were subjected to biochemical and molecular identification. The study also investigated pathogenicity and the antibiogram profile of the recovered isolates. The clinical examination of the infected fish revealed various signs that included lethargy and sluggish movement, hemorrhages and ulcers on the body and the operculum, scale loss, and fin congestion and rot, especially at the tail fin. Furthermore, during postmortem examination, congestion of the liver, spleen, and kidney was observed. Interestingly, 12 isolates were recovered and were homogenous bacteriologically and biochemically. The phylogenetic analysis based on 16S rRNA gene confirmed that MRB62 identified strain was closely related the genus Psychrobacter and identified as P. glacincola and was pathogenic to Rhabdosargus haffara fish, causing 23.3% mortality combined with reporting a series of clinical signs similar to that found in naturally infected fishes. The present study also showed that P. glacincola isolates were sensitive to all antibiotics used for sensitivity testing. Our findings add to the body of knowledge regarding the occurrence of pathogenic P. glacincola infection in Egyptian marine fishes and its potential effects on fish. Future large-scale surveys exploring this bacterium among other freshwater and marine fishes in Egypt would be helpful for the implementation of effective strategies for the prevention and control of this infection are warranted.
Topics: Animals; Psychrobacter; Egypt; RNA, Ribosomal, 16S; Phylogeny; Indian Ocean; Fishes
PubMed: 36717850
DOI: 10.1186/s12917-022-03542-8 -
Data in Brief Apr 2022Bacteria of the genus are known for their psychrophilic characteristics, being extremophilic organisms capable of surviving and reproducing in hostile environments of...
Bacteria of the genus are known for their psychrophilic characteristics, being extremophilic organisms capable of surviving and reproducing in hostile environments of low temperature and high pressure. Among many of the genus characteristics, there is the ability to produce enzymes and molecules of industrial biotechnology importance, such as pigments and proteins related to heavy metal bioremediation. The bacterium strain LAMA 639 was isolated from sediments from the Walvis Ridge ocean crest at a depth of 4.400 m (33.40 S 2.35 E). It is a nonmotile, halotolerant, cream-colored gram-negative aerobic bacterium. Its cultivation was performed in marine agar plates and inoculated into test tubes with NaCl at an optimal temperature of 30 °C and with shaking at 100 rpm. Genome extraction was performed with the DNeasy Blood & Tissue Kit (QIAGEN®). Sequencing was performed by Macrogen using the NovaSeq® 6000 platform (Illumina) applying the whole genome shotgun (WGS) method. Thereafter, 14.712.526 reads of 151 bp were generated, totaling 2.2 G bp with a GC content of 42.9%. Assembly and mapping were performed with a CLC Genomics Workbench. The best assembly considered was the one with the lowest number of contigs and the highest base length pair. The assemblies were evaluated using QUAST, and the best resulting variant was selected for annotation. Genome annotation was performed with RAST and PATRIC; the antiSMASH tool was used for secondary metabolites; NaPDoS was used for domains; and three-dimensional structural prediction of relevant proteins was performed using Phyre2. Annotation with ClassicRAST generated 2,891 coding sequences (CDSs) distributed in 402 subsystems. Annotation with PATRIC generated 2,896 coding sequences, among them 776 hypothetical proteins. The antiSMASH tool visualized a beta-lactone cluster in contig 06. In the search for natural products with NaPDoS, two ketosynthase domains were identified. The search for relevant proteins was performed using the AMFEP list as a criterion. From these data, 34 possible enzymes with biotechnological potential were found. Finally, the organism is presented as a new reference regarding the potential of deep-sea marine bacteria, demonstrating that, from the annotated and cured genome, it is possible to find in its genetic repertory products of interest for biotechnological applications.
PubMed: 35242911
DOI: 10.1016/j.dib.2022.107927 -
Microorganisms Jun 2022The gut microbiome is a unique marker for cetaceans' health status, and the microbiome composition of their skin wounds can indicate a potential infection from their...
The gut microbiome is a unique marker for cetaceans' health status, and the microbiome composition of their skin wounds can indicate a potential infection from their habitat. Our study provides the first comparative analysis of the microbial communities from gut regions and skin wounds of an individual Indo-Pacific finless porpoise (). Microbial richness increased from the foregut to the hindgut with variation in the composition of microbes. (67.51% ± 5.10%), (22.00% ± 2.60%), and (10.47% ± 5.49%) were the dominant phyla in the gastrointestinal tract, while Proteobacteria (76.11% ± 0.54%), (22.00% ± 2.60%), and (10.13% ± 0.49%) were the dominant phyla in the skin wounds. The genera , , , , , and , considered potential pathogens for mammals, were identified in the gut and skin wounds of the stranded Indo-Pacific finless porpoise. A comparison of the gut microbiome in the Indo-Pacific finless porpoise and other cetaceans revealed a possible species-specific gut microbiome in the Indo-Pacific finless porpoise. There was a significant difference between the skin wound microbiomes in terrestrial and marine mammals, probably due to habitat-specific differences. Our results show potential species specificity in the microbiome structure and a potential threat posed by environmental pathogens to cetaceans.
PubMed: 35889014
DOI: 10.3390/microorganisms10071295 -
IScience Oct 2023Alcohol-related liver disease (ALD) is one of the leading causes of liver-related death worldwide. However, roles of oral microbiota in regulating the progression of ALD...
Alcohol-related liver disease (ALD) is one of the leading causes of liver-related death worldwide. However, roles of oral microbiota in regulating the progression of ALD remain unknown. Here, we fed mice with control or ethanol diet to establish chronic-plus-binge ALD model. 16S ribosomal DNA sequencing was performed on oral and cecum samples. We demonstrated that alcohol drinking influenced bacterial richness, microbial structure, and composition in oral samples of ethanol-fed mice compared with control mice. Alcohol consumption also remodeled relationships among oral microbes and altered functions of oral microbiota. Furthermore, oral microbiota, such as , , , and were closely associated with ALD parameters. Finally, we observed , , and possibly translocated along with oral-gut axis and positively correlated with the severity of ALD. Altogether, alcohol consumption reprogramed composition and functions of oral microbiota to promote ALD progression, suggesting that oral microbes might become a new target for ALD therapy.
PubMed: 37810215
DOI: 10.1016/j.isci.2023.107977 -
Nature Feb 2024To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In...
To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.
Topics: Bacterial Proteins; Peptide Elongation Factor Tu; Protein Biosynthesis; Ribosomal Proteins; Ribosomes; Psychrobacter; Cryoelectron Microscopy; Cold-Shock Response; Peptide Termination Factors
PubMed: 38355796
DOI: 10.1038/s41586-024-07041-8 -
International Journal of Food Science 2021Yellow cured codfish has a typical yellow colour, distinctive taste, and low salt content due to its special curing process of the raw salted codfish involving several...
Yellow cured codfish has a typical yellow colour, distinctive taste, and low salt content due to its special curing process of the raw salted codfish involving several soaks in water of the raw salted codfish, alternated with drying steps. The purpose of this study was to assess the main functional groups of bacteria involved in this process and relate them with physicochemical properties of the product. A total of 28 codfish from Iceland were supplied by two local companies. Seven stages of the curing process were analyzed. From each of these seven stages, four fish samples were collected to carry out the microbial and physicochemical analyses (moisture, salt content, pH, total volatile basic nitrogen (TVB-N), and trimethylamine nitrogen (TMA-N)). Bacteria counts were performed using the MPN method and adequate culture media for aerobic, proteolytic, sulphite-reducing, biogenic amine, and trimethylamine-producing and ammonifying bacteria. Strains isolated from the highest dilutions with microbial growth were used to characterize the predominant bacteria. The results showed that total aerobic counts increased from 3.9 log MPN/g in raw salted codfish to 5.9 log MPN/g in the final. Proteolytic, ammonifying, and trimethylamine bacteria producers also increased to 8, 7.5, and 6.5 log MPN/g, respectively. The salt content decreases (from 17% until 8%) and moisture increases (53% until 67%) during the salted-raw-codfish soaking, favoring sulphite-reducing and biogenic amine-producing species, confirming that desalting enhances potential spoilers. The subsequent drying step benefits proteolytic, ammonifying, and trimethylamine-producing bacteria, with a corresponding non-protein-nitrogen content (TVB-N and TMA-N) increase. The dominant bacteria during yellow curing belong to the genera , , , and with a clear positive correlation between the content of and and TVB-N and TMA-N concentration. spp. are the dominant bacteria in the steps where the product has a higher salt concentration; thus, it could be particularly useful as an indicator to control the industrially yellow curing process and could have an important role in the development of the final characteristics of this product.
PubMed: 34778447
DOI: 10.1155/2021/6072731 -
Frontiers in Microbiology 2020Autoimmune diseases are increasingly linked to aberrant gut microbiome and relevant metabolites. However, the association between vitiligo and the gut microbiome remains...
Autoimmune diseases are increasingly linked to aberrant gut microbiome and relevant metabolites. However, the association between vitiligo and the gut microbiome remains to be elucidated. Thus, we conducted a case-control study through 16S rRNA sequencing and serum untargeted-metabolomic profiling based on 30 vitiligo patients and 30 matched healthy controls. In vitiligo patients, the microbial composition was distinct from that of healthy controls according to the analysis on α- and β-diversity ( < 0.05), with a characteristic decreased ratio. Meanwhile, the levels of 23 serum metabolites (including taurochenodeoxycholate and L-NG-monomethyl-arginine) in the vitiligo patients were different from those in the healthy individuals and showed significant correlations with some microbial markers. We found that , , and were correlated significantly with disease duration and serum IL-1β level in vitiligo patients. And was identified as the most predictive features for vitiligo by machine learning analysis ("importance" = 0.0236). Finally, combining multi-omics data and joint prediction models with accuracies up to 0.929 were established with dominant contribution of and . Our findings replenished the previously unknown relationship between gut dysbiosis and vitiligo circulating metabolome and enrolled the gut-skin axis into the understanding of vitiligo pathogenesis.
PubMed: 33381090
DOI: 10.3389/fmicb.2020.592248