scholarly journals Phenogenomic characterization of a newly domesticated and novel species from the genus Verrucosispora

2021 ◽  
Author(s):  
Sarah J. Kennedy ◽  
Celine Grace F. Atkinson ◽  
Brooke R. Tomlinson ◽  
Lauren Hammond ◽  
Prahathees Eswara ◽  
...  
Keyword(s):  
Dark Matter ◽  
Novel Species ◽  
Gene Clusters ◽  
Genetic Redundancy ◽  
Rich Media ◽  
Genotypic Analysis ◽  
Initial Recovery ◽  
Gene Status ◽  
Mixed Approach ◽  
Static Conditions

The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental gap in our knowledge of microbial diversity. Herein we present the domestication of such an organism: a previously uncultured, novel species from the rare-Actinomycetes genus Verrucosispora . Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media, but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic atrophy through a mixed approach of pseudogenization and reversion of pseudogenization of amino acid metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread SNP, indel and pseudogene-impactful mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability. Importance The majority of environmental bacteria cannot be cultured within the laboratory. Understanding why only certain environmental isolates can be recovered is key to unlocking the abundant microbial dark matter that is widespread on our planet. In this study we present not only the culturing but domestication of just such an organism. Although initial recovery took >4 months, we were able to isolate distinct, sub-passaged offspring from the originating colony within mere weeks. A phenotypic and genotypic analysis of our generational strains revealed that adaptation to life in the lab occurred as a result of wholesale mutational changes. These permitted an enhanced ability for growth in nutrient rich media, but came at the expense of reduced genomic flexibility. We suggest that without dynamic natural environmental stressors our domesticated strains effectively underwent genomic atrophy as they adapted to static conditions experienced in the laboratory.

scholarly journals Phenogenomic characterization of a newly domesticated and novel species from the genus Verrucosispora

2021 ◽  
Author(s):  
Sarah Kennedy ◽  
Celine Atkinson ◽  
Brooke Tomlinson ◽  
Lauren Hammond ◽  
Prahathees J. Eswara ◽  
...  
Keyword(s):  
Amino Acids ◽  
Novel Species ◽  
Gene Clusters ◽  
Genetic Redundancy ◽  
Biosynthetic Gene Clusters ◽  
Rare Actinomycetes ◽  
Rich Media ◽  
Initial Recovery ◽  
Gene Status

The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental hole in our knowledge of microbial diversity. Herein we present the domestication of such an organism: a previously uncultured, novel species from the rare-Actinomycetes genus Verrucosispora. Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media, but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic decay through the pseudogenization of amino acids metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread SNP, indel and pseudogene mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability.

scholarly journals Ex Vivo Culture Models of Hidradenitis Suppurativa for defining molecular pathogenesis and treatment efficacy of novel drugs

2021 ◽  
Author(s):  
Kayla Goliwas ◽  
Mahendra P Kashyap ◽  
Jasim Khan ◽  
Rajesh Sinha ◽  
Zhiping Weng ◽  
...  
Keyword(s):  
Hidradenitis Suppurativa ◽  
Ex Vivo ◽  
Drug Efficacy ◽  
Culture Method ◽  
Gene Clusters ◽  
Dynamic Expression ◽  
Novel Drugs ◽  
Culture Models ◽  
Ex Vivo Culture ◽  
Gene Status

Hidradenitis suppurativa (HS) is a complex inflammatory and debilitating skin disease for which no effective treatment is available. This is partly because of the unavailability of suitable human or animal models with which exact pathobiology of the disease can be defined. Here, we describe the development of air-liquid (A-L) interface, liquid-liquid/liquid-submersion (L-S) and bioreactor (Bio) ex vivo skin culture models. All three ex vivo platforms were effective for culturing skin samples up to day-14, with the tissue architecture and integrity remaining intact for at least 3 days for healthy skin while for 14 days for HS skin. Up to day-3, no significant differences were observed in % early apoptotic cells among all three platforms. However, an increase was observed in late apoptotic/necrotic cells in HS skin at day-3 in A-L and Bio culture of HS skin. These cultures efficiently support the growth of various cells populations, including keratinocytes and immune cells. Profiling of the inflammatory genes using HS skin from these ex vivo cultures showed dynamic expression changes at day-3 and day-14. All of these cultures are necessary to represent the inflammatory gene status of HS skin at day-0 suggesting that not all gene clusters are identically altered in each culture method. Similarly, cytokine/chemokine profiling of the supernatant from vehicle- and drug-treated ex vivo HS cultures again showed better prediction of drug efficacy against HS. Overall, development of these three systems collectively provide a powerful tool to uncover the pathobiology of HS progression and screen various drugs against HS.

scholarly journals Predatory Organisms with Untapped Biosynthetic Potential: Descriptions of Novel Corallococcus Species C. aberystwythensis sp. nov., C. carmarthensis sp. nov., C. exercitus sp. nov., C. interemptor sp. nov., C. llansteffanensis sp. nov., C. praedator sp. nov., C. sicarius sp. nov., and C. terminator sp. nov.

2019 ◽  
Vol 86 (2) ◽  
Author(s):  
Paul G. Livingstone ◽  
Oliver Ingleby ◽  
Susan Girdwood ◽  
Alan R. Cookson ◽  
Russell M. Morphew ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Novel Species ◽  
Methyl Esters ◽  
Gene Clusters ◽  
Distinct Species ◽  
Antimicrobial Activities ◽  
Biologically Active ◽  
Active Metabolites ◽  
Taxonomic Assignment ◽  
Content Type

ABSTRACT Corallococcus spp. are common soil-dwelling organisms which kill and consume prey microbes through the secretion of antimicrobial substances. Two species of Corallococcus have been described previously (Corallococcus coralloides and Corallococcus exiguus). A polyphasic approach, including biochemical analysis of fatty acid methyl esters, substrate utilization, and sugar assimilation assays, was taken to characterize eight Corallococcus species strains and the two type strains. The genomes of all strains, including that of C. exiguus DSM 14696T (newly reported here), shared an average nucleotide identity below 95% and digital DNA-DNA hybridization scores of less than 70%, indicating that they belong to distinct species. In addition, we characterized the prey range and antibiotic resistance profile of each strain, illustrating the diversity of antimicrobial activity and, thus, the potential for drug discovery within the Corallococcus genus. Each strain gave a distinct profile of properties, which together with their genomic differences supports the proposal of the eight candidate strains as novel species. The eight candidates are as follows: Corallococcus exercitus sp. nov. (AB043AT = DSM 108849T = NBRC 113887T), Corallococcus interemptor sp. nov. (AB047AT = DSM 108843T = NBRC 113888T), Corallococcus aberystwythensis sp. nov. (AB050AT = DSM 108846T = NBRC 114019T), Corallococcus praedator sp. nov. (CA031BT = DSM 108841T = NBRC 113889T), Corallococcus sicarius sp. nov. (CA040BT = DSM 108850T = NBRC 113890T), Corallococcus carmarthensis sp. nov. (CA043DT = DSM 108842T = NBRC 113891T), Corallococcus llansteffanensis sp. nov. (CA051BT = DSM 108844T = NBRC 114100T), and Corallococcus terminator sp. nov. (CA054AT = DSM 108848T = NBRC 113892T). IMPORTANCE Corallococcus is a genus of predators with broad prey ranges, whose genomes contain large numbers of gene clusters for secondary metabolite biosynthesis. The physiology and evolutionary heritage of eight Corallococcus species strains were characterized using a range of analyses and assays. Multiple metrics confirmed that each strain belonged to a novel species within the Corallococcus genus. The strains exhibited distinct patterns of drug resistance and predatory activity, which mirrored their possession of diverse sets of biosynthetic genes. The breadth of antimicrobial activities observed within the Corallococcus genus highlights their potential for drug discovery and suggests a previous underestimation of both their taxonomic diversity and biotechnological potential. Taxonomic assignment of environmental isolates to novel species allows us to begin to characterize the diversity and evolution of members of this bacterial genus with potential biotechnological importance, guiding future bioprospecting efforts for novel biologically active metabolites and antimicrobials.

scholarly journals Knoellia locipacati sp. nov., from soil of the Demilitarized Zone in South Korea

2012 ◽  
Vol 62 (2) ◽  
pp. 342-346 ◽  
Author(s):  
Na-Ri Shin ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Mi-Ja Jung ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
South Korea ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Mycolic Acids ◽  
Demilitarized Zone ◽  
Genotypic Analysis

A Gram-positive, aerobic, rod- or coccus-shaped, non-motile bacterium, designated DMZ1T, was isolated from soil of the Demilitarized Zone, South Korea. Strain DMZ1T grew optimally at 30 °C, at pH 7–8 and with 1 % (w/v) NaCl. The isolate showed high 16S rRNA gene sequence similarity with Knoellia aerolata 5317S-21T (98.2 %). The cell-wall sugars were glucose and ribose. The peptidoglycan amino acids were meso-diaminopimelic acid, glutamic acid and glycine. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The polar lipids were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and five unknown phospholipids. The isolate did not contain mycolic acids. The DNA G+C content was 72.6 mol%. The isolate showed <28 % DNA–DNA relatedness with members of the genus Knoellia. Phylogenetic, phenotypic and genotypic analysis indicated that strain DMZ1T represents a novel species of the genus Knoellia, for which the name Knoellia locipacati sp. nov. is proposed. The type strain is DMZ1T ( = KACC 15114T  = JCM 17313T).

scholarly journals Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134

Microbiology ◽  
2009 ◽  
Vol 155 (11) ◽  
pp. 3641-3651 ◽  
Author(s):  
Danilo Pérez-Pantoja ◽  
Raúl A. Donoso ◽  
Miguel A. Sánchez ◽  
Bernardo González
Keyword(s):  
Aromatic Compounds ◽  
Gene Clusters ◽  
Cupriavidus Necator ◽  
Gene Products ◽  
Genetic Redundancy ◽  
Rt Pcr ◽  
Cell Extracts ◽  
Maleylacetate Reductase ◽  
Encoding Genes

Maleylacetate reductases (MAR) are required for biodegradation of several substituted aromatic compounds. To date, the functionality of two MAR-encoding genes (tfdF I and tfdF II) has been reported in Cupriavidus necator JMP134(pJP4), a known degrader of aromatic compounds. These two genes are located in tfd gene clusters involved in the turnover of 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3-CB). The C. necator JMP134 genome comprises at least three other genes that putatively encode MAR (tcpD, hqoD and hxqD), but confirmation of their functionality and their role in the catabolism of haloaromatic compounds has not been assessed. RT-PCR expression analyses of C. necator JMP134 cells exposed to 2,4-D, 3-CB, 2,4,6-trichlorophenol (2,4,6-TCP) or 4-fluorobenzoate (4-FB) showed that tfdF I and tfdF II are induced by haloaromatics channelled to halocatechols as intermediates. In contrast, 2,4,6-TCP only induces tcpD, and any haloaromatic compounds tested did not induce hxqD and hqoD. However, the tcpD, hxqD and hqoD gene products showed MAR activity in cell extracts and provided the MAR function for 2,4-D catabolism when heterologously expressed in MAR-lacking strains. Growth tests for mutants of the five MAR-encoding genes in strain JMP134 showed that none of these genes is essential for degradation of the tested compounds. However, the role of tfdF I/tfdF II and tcpD genes in the expression of MAR activity during catabolism of 2,4-D and 2,4,6-TCP, respectively, was confirmed by enzyme activity tests in mutants. These results reveal a striking example of genetic redundancy in the degradation of aromatic compounds.

scholarly journals Dark matter effect attributed to the inherent structure of cosmic space

2019 ◽  
Vol 28 (06) ◽  
pp. 1950082 ◽  
Author(s):  
T. G. Tenev ◽  
M. F. Horstemeyer
Keyword(s):  
Dark Matter ◽  
Spherically Symmetric ◽  
Gravitational Effects ◽  
Ordinary Matter ◽  
Symmetric Configuration ◽  
Inherent Structure ◽  
Cosmic Space ◽  
Matter Effect ◽  
Static Conditions ◽  
Weak Gravity

We propose that anomalous gravitational effects currently attributed to dark matter can alternatively be explained as a manifestation of the inherent structure of space at galactic length scales. Specifically, we show that the inherent curvature of space amplifies the gravity of ordinary matter such that the effect resembles the presence of the hypothetical hidden mass. Our study is conducted in the context of weak gravity, nearly static conditions, and spherically symmetric configuration, and leverages the Cosmic Fabric model of space developed by Tenev and Horstemeyer [T. G. Tenev and M. F. Horstemeyer, Int. J. Mod. Phys. D 27 (2018) 1850083; T. G. Tenev and M. F. Horstemeyer, Rep. Adv. Phys. Sci. 2 (2018) 1850011, arXiv:1808.08804].

scholarly journals Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications

2021 ◽  
Vol 2 ◽  
Author(s):  
Tomás A. Rush ◽  
Him K. Shrestha ◽  
Muralikrishnan Gopalakrishnan Meena ◽  
Margaret K. Spangler ◽  
J. Christopher Ellis ◽  
...  
Keyword(s):  
Natural Products ◽  
Applied Research ◽  
Novel Species ◽  
Gene Clusters ◽  
Initial Step ◽  
Biosynthetic Gene Clusters ◽  
Research Fields ◽  
Fungal Organisms ◽  
Development Goals ◽  
Potential Impact

Natural products derived from microbes are crucial innovations that would help in reaching sustainability development goals worldwide while achieving bioeconomic growth. Trichoderma species are well-studied model fungal organisms used for their biocontrol properties with great potential to alleviate the use of agrochemicals in agriculture. However, identifying and characterizing effective natural products in novel species or strains as biological control products remains a meticulous process with many known challenges to be navigated. Integration of recent advancements in various “omics” technologies, next generation biodesign, machine learning, and artificial intelligence approaches could greatly advance bioprospecting goals. Herein, we propose a roadmap for assessing the potential impact of already known or newly discovered Trichoderma species for biocontrol applications. By screening publicly available Trichoderma genome sequences, we first highlight the prevalence of putative biosynthetic gene clusters and antimicrobial peptides among genomes as an initial step toward predicting which organisms could increase the diversity of natural products. Next, we discuss high-throughput methods for screening organisms to discover and characterize natural products and how these findings impact both fundamental and applied research fields.

scholarly journals The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Gordon Webster ◽  
Alex J. Mullins ◽  
Aimee S. Bettridge ◽  
Cerith Jones ◽  
Edward Cunningham-Oakes ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Novel Species ◽  
Wood Decay ◽  
Gene Clusters ◽  
Antagonistic Activity ◽  
Biosynthetic Gene Clusters ◽  
Decay Fungi ◽  
Content Type ◽  
Wood Decay Fungi ◽  
Novel Taxa

Three strains of fungus-associated Burkholderiales bacteria with antagonistic activity against Gram-negative plant pathogens were genome sequenced to investigate their taxonomic placement and potential for antimicrobial specialized metabolite production. The selected strains were identified as novel taxa belonging to the genus Paraburkholderia and carry multiple biosynthetic gene clusters.

scholarly journals Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov.

2020 ◽  
Vol 12 (12) ◽  
pp. 2289-2302 ◽  
Author(s):  
James Chambers ◽  
Natalie Sparks ◽  
Natashia Sydney ◽  
Paul G Livingstone ◽  
Alan R Cookson ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Draft Genome ◽  
Gene Clusters ◽  
Single Species ◽  
Genomic Variation ◽  
Biosynthetic Gene Clusters ◽  
Multicellular Development ◽  
Pan Genome ◽  
Novel Drug

Abstract Members of the predatory Myxococcales (myxobacteria) possess large genomes, undergo multicellular development, and produce diverse secondary metabolites, which are being actively prospected for novel drug discovery. To direct such efforts, it is important to understand the relationships between myxobacterial ecology, evolution, taxonomy, and genomic variation. This study investigated the genomes and pan-genomes of organisms within the Myxococcaceae, including the genera Myxococcus and Corallococcus, the most abundant myxobacteria isolated from soils. Previously, ten species of Corallococcus were known, whereas six species of Myxococcus phylogenetically surrounded a third genus (Pyxidicoccus) composed of a single species. Here, we describe draft genome sequences of five novel species within the Myxococcaceae (Myxococcus eversor, Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis, Myxococcus vastator, Pyxidicoccus caerfyrddinensis, and Pyxidicoccus trucidator) and for the Pyxidicoccus type species strain, Pyxidicoccus fallax DSM 14698T. Genomic and physiological comparisons demonstrated clear differences between the five novel species and every other Myxococcus or Pyxidicoccus spp. type strain. Subsequent analyses of type strain genomes showed that both the Corallococcus pan-genome and the combined Myxococcus and Pyxidicoccus (Myxococcus/Pyxidicoccus) pan-genome are large and open, but with clear differences. Genomes of Corallococcus spp. are generally smaller than those of Myxococcus/Pyxidicoccus spp. but have core genomes three times larger. Myxococcus/Pyxidicoccus spp. genomes are more variable in size, with larger and more unique sets of accessory genes than those of Corallococcus species. In both genera, biosynthetic gene clusters are relatively enriched in the shell pan-genomes, implying they grant a greater evolutionary benefit than other shell genes, presumably by conferring selective advantages during predation.

scholarly journals A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
David Wylensek ◽  
Thomas C. A. Hitch ◽  
Thomas Riedel ◽  
Afrizal Afrizal ◽  
Neeraj Kumar ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bile Acids ◽  
Sequence Data ◽  
Novel Species ◽  
Meta Analysis ◽  
Gene Clusters ◽  
In Vitro Assays ◽  
The Novel ◽  
Strain Collection

AbstractOur knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.

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