scholarly journals Insights into the cultured bacterial fraction of corals

2020 ◽  
Author(s):  
Michael Sweet ◽  
Helena Villela ◽  
Tina Keller-Costa ◽  
Rodrigo Costa ◽  
Stefano Romano ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Comprehensive Overview ◽  
Associated Bacteria ◽  
Reef Restoration ◽  
Coral Holobiont ◽  
Metabolic Interactions ◽  
And Function

Abstract Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite the putative importance of bacteria, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable, coral-associated bacteria. A total of 3055 isolates from 52 studies were considered by our meta-survey. Of these, 1045 had full length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterial-coral symbioses among them. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features - not previously described for coral-bacterial symbioses - involved in host colonization and host-symbiont recognition, antiviral defence mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning, and guide the selection of probiotic candidates to promote coral resilience and improve reef restoration efforts.

scholarly journals Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1421
Author(s):  
Yuqiang Zhao ◽  
Yanxin Wang ◽  
Chengyao Xia ◽  
Xu Li ◽  
Xianfeng Ye ◽  
...  
Keyword(s):  
Extracellular Enzymes ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Predatory Behavior ◽  
Phytopathogenic Fungi ◽  
Plant Diseases ◽  
Comparative Genomic ◽  
Comprehensive Overview ◽  
Circular Chromosome ◽  
Pan Genome

Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced, annotated, and compared with 10 other Corallococcus species. The strain EGB genome was assembled as a single circular chromosome of 9.4 Mb with 7916 coding genes. Phylogenomics analysis showed that strain EGB was most closely related to Corallococcus interemptor AB047A, and it was inferred to be a novel species within the Corallococcus genus. Comparative genomic analysis revealed that the pan-genome of Corallococcus genus was large and open. Only a small proportion of genes were specific to strain EGB, and most of them were annotated as hypothetical proteins. Subsequent analyses showed that strain EGB produced abundant extracellular enzymes such as chitinases and β-(1,3)-glucanases, and proteases to degrade the cell-wall components of phytopathogenic fungi. In addition, 35 biosynthetic gene clusters potentially coding for antimicrobial compounds were identified in the strain EGB, and the majority of them were present in the dispensable pan-genome with unexplored metabolites. Other genes related to secretion and regulation were also explored for strain EGB. This study opens new perspectives in the greater understanding of the predatory behavior of strain EGB, and facilitates a potential application in the biocontrol of fungal plant diseases in the future.

scholarly journals Oxygenation properties of hemoglobin and the evolutionary origins of isoform multiplicity in an amphibious air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris)

2019 ◽  
Author(s):  
Jay F. Storz ◽  
Chandrasekhar Natarajan ◽  
Magnus K. Grouleff ◽  
Michael Vandewege ◽  
Federico G. Hoffmann ◽  
...  
Keyword(s):  
Globin Gene ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Air Breathing ◽  
Aerial Respiration ◽  
Evolutionary Origins ◽  
Amino Acid Divergence ◽  
Boleophthalmus Pectinirostris ◽  
And Function

ABSTRACTAmong the numerous lineages of teleost fish that have independently transitioned from obligate water-breathing to facultative air-breathing, evolved properties of hemoglobin (Hb)-O2 transport may have been shaped by the prevalence and severity of aquatic hypoxia (which influences the extent to which fish are compelled to switch to aerial respiration) as well as the anatomical design of air-breathing structures and the cardiovascular system. Here we examine the structure and function of Hbs in an amphibious, facultative air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris). We also characterized the genomic organization of the globin gene clusters of the species and we integrated phylogenetic and comparative genomic analyses to unravel the duplicative history of the genes that encode the subunits of structurally distinct mudskipper Hb isoforms (isoHbs). The B. pectinirostris isoHbs exhibit high intrinsic O2-affinities, similar to those of hypoxia-tolerant, water-breathing teleosts, and remarkably large Bohr effects. Genomic analysis of conserved synteny revealed that the genes that encode the α-type subunits of the two main adult isoHbs are members of paralogous gene clusters that represent products of the teleost-specific whole-genome duplication. Experiments revealed no appreciable difference in the oxygenation properties of co-expressed isoHbs in spite of extensive amino acid divergence between the alternative α-chain subunit isoforms. It therefore appears that the ability to switch between aquatic and aerial respiration does not necessarily require a division of labor between functionally distinct isoHbs with specialized oxygenation properties.Summary statementThe blue-spotted mudskipper routinely switches between aquatic and aerial respiration. This respiratory versatility is associated with properties of hemoglobin-oxygen transport that are similar to those found in hypoxia-adapted water-breathing fishes.

scholarly journals Taxogenomic and Comparative Genomic Analysis of the Genus Saccharomonospora Focused on the Identification of Biosynthetic Clusters PKS and NRPS

2021 ◽  
Vol 12 ◽  
Author(s):  
Ninfa Ramírez-Durán ◽  
Rafael R. de la Haba ◽  
Blanca Vera-Gargallo ◽  
Cristina Sánchez-Porro ◽  
Scarlett Alonso-Carmona ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Marine Habitats ◽  
Speciation Event ◽  
Halophilic Actinobacteria

Actinobacteria are prokaryotes with a large biotechnological interest due to their ability to produce secondary metabolites, produced by two main biosynthetic gene clusters (BGCs): polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS). Most studies on bioactive products have been carried out on actinobacteria isolated from soil, freshwater or marine habitats, while very few have been focused on halophilic actinobacteria isolated from extreme environments. In this study we have carried out a comparative genomic analysis of the actinobacterial genus Saccharomonospora, which includes species isolated from soils, lake sediments, marine or hypersaline habitats. A total of 19 genome sequences of members of Saccharomonospora were retrieved and analyzed. We compared the 16S rRNA gene-based phylogeny of this genus with evolutionary relationships inferred using a phylogenomic approach obtaining almost identical topologies between both strategies. This method allowed us to unequivocally assign strains into species and to identify some taxonomic relationships that need to be revised. Our study supports a recent speciation event occurring between Saccharomonospora halophila and Saccharomonospora iraqiensis. Concerning the identification of BGCs, a total of 18 different types of BGCs were detected in the analyzed genomes of Saccharomonospora, including PKS, NRPS and hybrid clusters which might be able to synthetize 40 different putative products. In comparison to other genera of the Actinobacteria, members of the genus Saccharomonospora showed a high degree of novelty and diversity of BGCs.

scholarly journals Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 298
Author(s):  
Despoina Konstantinou ◽  
Rafael V. Popin ◽  
David P. Fewer ◽  
Kaarina Sivonen ◽  
Spyros Gkelis
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Genome Reduction ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Symbiotic Relationships ◽  
Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

scholarly journals Pseudonocardia abyssalis sp. nov. and Pseudonocardia oceani sp. nov., two novel actinomycetes isolated from the deep Southern Ocean

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Jonathan Parra ◽  
Sylvia Soldatou ◽  
Liam M. Rooney ◽  
Katherine R. Duncan
Keyword(s):  
Fatty Acid ◽  
Southern Ocean ◽  
Type Strain ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Distinct Species ◽  
Diaminopimelic Acid ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Content Type

The actinomycetes strains KRD168T and KRD185T were isolated from sediments collected from the deep Southern Ocean and, in this work, they are described as representing two novel species of the genus Pseudonocardia through a polyphasic approach. Despite sharing >99 % 16S rRNA gene sequence similarity with other members of the genus, comparative genomic analysis allowed species delimitation based on average nucleotide identity and digital DNA–DNA hybridization. The KRD168T genome is characterized by a size of 6.31 Mbp and a G+C content of 73.44 mol%, while the KRD185T genome has a size of 6.82 Mbp and a G+C content of 73.98 mol%. Both strains contain meso-diaminopimelic acid as the diagnostic diamino acid, glucose as the major whole-cell sugar, MK-8(H4) as a major menaquinone and iso-branched hexadecanoic acid as a major fatty acid. Biochemical and fatty acid analyses also revealed differences between these strains and their phylogenetic neighbours, supporting their status as distinct species. The names Pseudonocardia abyssalis sp. nov. (type strain KRD168T=DSM 111918T=NCIMB 15270T) and Pseudonocardia oceani (type strain KRD185T=DSM 111919T=NCIMB 15269T) are proposed.

scholarly journals Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

2020 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Bora Lim ◽  
Si Hong Park ◽  
Bryna Rackerby ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Analysis ◽  
23S Rrna ◽  
Lactobacillus Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
23S Rrna Gene ◽  
Species Specific

Abstract Background Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus , and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

scholarly journals Neonatal Salivary Analysis Reveals Global Developmental Gene Expression Changes in the Premature Infant

2010 ◽  
Vol 56 (3) ◽  
pp. 409-416 ◽  
Author(s):  
Jill L Maron ◽  
Kirby L Johnson ◽  
David M Rocke ◽  
Michael G Cohen ◽  
Albert J Liley ◽  
...  
Keyword(s):  
Gene Expression ◽  
System Development ◽  
Newborn Care ◽  
Genomic Analysis ◽  
Nervous System Development ◽  
Comparative Genomic ◽  
Tissue Development ◽  
Bioinformatics Analyses ◽  
Noninvasive Technique ◽  
And Function

Abstract Background: There is an important need to develop noninvasive biomarkers to detect disease in premature neonates. Our objective was to determine if salivary genomic analysis provides novel information about neonatal expression of developmental genes. Methods: Saliva (50–200 μL) was prospectively collected from 5 premature infants at 5 time points: before, starting, and advancing enteral nutrition; at the introduction of oral feeds; and at advanced oral feeds. Salivary RNA was extracted, amplified, and hybridized onto whole-genomic microarrays. Results: Bioinformatics analyses identified 9286 gene transcripts with statistically significant gene expression changes across individuals over time. Of these genes, 3522 (37.9%) were downregulated, and 5764 (62.1%) were upregulated. Gene expression changes were highly associated with developmental pathways. Significantly downregulated expression was seen in embryonic development, connective tissue development and function, hematologic system development and function, and survival of the organism (10−14 < P < 10−3). Conversely, genes associated with behavior, nervous system development, tissue development, organ development, and digestive system development were significantly upregulated (10−11 < P < 10−2). Conclusions: Comparative genomic salivary analyses provide robust, comprehensive, real-time information regarding nearly all organs and tissues in the developing preterm infant. This innovative and noninvasive technique represents a new approach for monitoring health, disease, and development in this vulnerable patient population. By comparing these data in healthy infants with data from infants who develop medical complications, we expect to identify new biomarkers that will ultimately improve newborn care.

scholarly journals Comparative Genomic Analysis of Phylogenetically Closely Related Hydrogenobaculum sp. Isolates from Yellowstone National Park

2013 ◽  
Vol 79 (9) ◽  
pp. 2932-2943 ◽  
Author(s):  
Christine Romano ◽  
Seth D'Imperio ◽  
Tanja Woyke ◽  
Konstantinos Mavromatis ◽  
Roger Lasken ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Marker Gene ◽  
Genomic Analysis ◽  
Mercury Resistance ◽  
Nitrate Respiration ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Content Type ◽  
Outflow Channel

ABSTRACTWe describe the complete genome sequences of four closely relatedHydrogenobaculumsp. isolates (≥99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different fromHydrogenobaculumsp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite [As(III)] oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRISPR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum ofHydrogenobaculumgenotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.

scholarly journals Simultaneous detection of 37 Lactobacillus species using a real-time PCR assay based on whole-genome sequence analysis

2020 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Bora Lim ◽  
Si Hong Park ◽  
Bryna Rackerby ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Real Time ◽  
Real Time Pcr ◽  
Genomic Analysis ◽  
23S Rrna ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Species Specific

Abstract BackgroundLactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. ResultsTo select species-specific sequences or genes, a total of 143 Lactobacillus complete genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the real-time polymerase chain reaction (PCR) with the standard curve were confirmed. The real-time PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This Real-time PCR method was designed to detect 37 Lactobacillus species in a single reaction. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. ConclusionsThe method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus, and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

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