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Haloalkane dehalogenase, LinB, is a member of the α/ß hydrolase family of enzymes. It has a wide range of halogenated substrates, but, has been mostly studied in context of degradation of hexachlorocyclohexane (HCH) isomers, especially ß-HCH (5-12% of total HCH isomers), which is the most recalcitrant and persistent among all the HCH isomers. LinB was identified to directly act on ß-HCH in a one or two step transformation which decreases its toxicity manifold. Thereafter, many studies focused on LinB including its structure determination using X-ray crystallographic studies, structure comparison with other haloalkane dehalogenases, substrate specificity and kinetic studies, protein engineering and site-directed mutagenesis studies in search of better catalytic activity of the enzyme. LinB was mainly identified and characterized in bacteria belonging to sphingomonads. Detailed sequence comparison of LinB from different sphingomonads further revealed the residues critical for its activity and ability to catalyze either one or two step transformation of ß-HCH. Association of LinB with IS6100 elements is also being discussed in detail in sphingomonads. In this review, we summarized vigorous efforts done by different research groups on LinB for developing better bioremediation strategies against HCH contamination. Also, kinetic studies, protein engineering and site directed mutagenesis studies discussed here forms the basis of further exploration of LinB's role as an efficient enzyme in bioremediation projects.
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Hexaclorocicloexano , Hidrolases , Hidrolases/metabolismo , Hidrolases/genética , Hidrolases/química , Hexaclorocicloexano/metabolismo , Especificidade por Substrato , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/química , Cinética , Biodegradação Ambiental , Cristalografia por Raios X , Mutagênese Sítio-Dirigida , Sphingomonas/enzimologia , Sphingomonas/genética , Sphingomonas/metabolismoRESUMO
The present study used whole-genome data to clarify the taxonomic assignment of two closely related Williamsia species. Genomic information for 10 type strains was available at the time of conducting this analysis. One group of type strains was found to be conspecific, namely Williamsia muralis Kämpfer et al. 1999 and Williamsia marianensis Pathom-aree et al. 2006. The 16S rRNA gene sequences showed 99â% similarity between these type strains. Whole-genome-based comparisons showed that Williamsia muralis DSM 44343T and Williamsia marianensis DSM 44944T shared 98.07â% average nucleotide identity, 98.29â% average amino acid identity and 84.80â% digital DNA-DNA hybridization values. These values exceeded the threshold values for bacterial species delineation. Further, phylogenomic analysis based on the core genomes of the strains under study confirmed that Williamsia muralis DSM 44343T and Williamsia marianensis DSM 44944T formed a monophyletic clade. Based on this evidence, we propose the reclassification of Williamsia marianensis Pathom-aree et al. 2006 as a later heterotypic synonym of Williamsia muralis Kämpfer et al. 1999.
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DNA Bacteriano , Genoma Bacteriano , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , RNA Ribossômico 16S/genética , DNA Bacteriano/genética , Técnicas de Tipagem BacterianaRESUMO
Ever since the isolation of Amycolatopsis mediterranei in 1957, this strain has been the focus of research worldwide. In the last 60 years or more, our understanding of the taxonomy, development of cloning vectors and conjugation system, physiology, genetics, genomics, and biosynthetic pathway of rifamycin B production in A. mediterranei has substantially increased. In particular, the development of cloning vectors, transformation system, characterization of the rifamycin biosynthetic gene cluster, and the regulation of rifamycin B production by the pioneering work of Heinz Floss have made the rifamycin polyketide biosynthetic gene cluster (PKS) an attractive target for extensive genetic manipulations to produce rifamycin B analogues which could be effective against multi-drug-resistant tuberculosis. Additionally, a better understanding of the regulation of rifamycin B production and the application of newer genomics tools, including CRISPR-assisted genome editing systems, might prove useful to overcome the limitations associated with low production of rifamycin analogues.
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Actinomycetales , Rifamicinas , Amycolatopsis , Vias Biossintéticas/genética , Rifamicinas/metabolismoRESUMO
The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, ß-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.
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Biodegradação Ambiental , Simulação por Computador , Genoma Bacteriano , Hexaclorocicloexano , Filogenia , Sphingomonadaceae , Sphingomonadaceae/genética , Sphingomonadaceae/metabolismo , Sphingomonadaceae/classificação , Hexaclorocicloexano/metabolismo , Ilhas Genômicas , Transferência Genética HorizontalRESUMO
Endosymbiotic relationships between ciliates and others are critical for their ecological roles, physiological adaptations, and evolutionary implications. These can be obligate and facultative. Symbionts often provide essential nutrients, contribute to the ciliate's metabolism, aid in digestion, and offer protection against predators or environmental stressors. In turn, ciliates provide a protected environment and resources for their symbionts, facilitating their survival and proliferation. Ultrastructural and full-cycle rRNA approaches are utilized to identify these endosymbionts. Fluorescence in situ hybridization using "species- and group-specific probes" which are complementary to the genetic material (DNA or RNA) of a particular species or group of interest represent convenient tools for their detection directly in the environment. A systematic survey of these endosymbionts has been conducted using both traditional and metagenomic approaches. Ciliophora and other protists have a wide range of prokaryotic symbionts, which may contain potentially pathogenic bacteria. Ciliates can establish symbiotic relationships with a variety of hosts also, ranging from protists to metazoans. Understanding ciliate symbiosis can provide useful insights into the complex relationships that drive microbial communities and ecosystems in general.
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DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.
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Código de Barras de DNA Taxonômico , DNA , Código de Barras de DNA Taxonômico/métodos , RNA Ribossômico 16S/genética , Plantas/genética , Archaea/genéticaRESUMO
The taxonomic status of 43 Psychrobacter species was examined based upon the genome sequences of their type strains. Three groups of type strains were found to be conspecific, Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) and Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) and Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835); and Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006), Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956). For all three groups, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values are > 97.69% and > 80.2%, respectively. This conclusion is supported by similarities in morphology, growth properties, and fatty acid compositions. Based on this evidence, we propose the reclassification of Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as a later heterotypic synonym of Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) as a later heterotypic synonym of Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835), and Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as later heterotypic synonyms of Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006).
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Psychrobacter , Psychrobacter/genética , Filogenia , DNA Bacteriano/genéticaRESUMO
Strains P8930T and 478 were isolated from Antarctic glaciers located on James Ross Island and King George Island, respectively. They comprised Gram-stain-negative short rod-shaped cells forming pink pigmented colonies and exhibited identical 16S rRNA gene sequences and highly similar MALDI TOF mass spectra, and hence were assigned as representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences assigned both isolates to the genus Pedobacter and showed Pedobacter frigidisoli and Pedobacter terrae to be their closest phylogenetic neighbours, with 97.4 and 97.2â% 16S rRNA gene sequence similarities, respectively. These low similarity values were below the threshold similarity value of 98.7%, confirming the delineation of a new bacterial species. Further genomic characterization included whole-genome sequencing accompanied by average nucleotide identity (ANI) and digital DNA-DNA hybridization calculations, and characterization of the genome features. The ANI values between P8930T and P. frigidisoli RP-3-11T and P. terrae DSM 17933T were 79.7 and 77.6â%, respectively, and the value between P. frigidisoli RP-3-11T and P. terrae DSM 17933T was 77.7â%, clearly demonstrating the phylogenetic distance and the novelty of strain P8930T. Further characterization included analysis of cellular fatty acids, quinones and polar lipids, and comprehensive biotyping. All the obtained results proved the separation of strains P8930T and 478 from the other validly named Pedobacter species, and confirmed that they represent a new species for which the name Pedobacter fastidiosus sp. nov. is proposed. The type strain is P8930T (=CCM 8938T=LMG 32098T).
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Pedobacter , Regiões Antárticas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ecossistema , Ácidos Graxos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
The genus Paracoccus represents a taxonomically diverse group comprising more than 80 novel species isolated from various pristine and polluted environments. The species are characterized as coccoid-shaped Gram-negative bacteria with versatile metabolic attributes and classified as autotrophs, heterotrophs and/or methylotrophs. The present study highlights the up-to-date global taxonomic diversity and critically discusses the significance of genome analysis for identifying the genomic determinants related to functional attributes mainly bioplastic synthesis and biodegradation potential that makes these isolates commercially viable. The analysis accentuates polyphasic and genomic attributes of Paracoccus spp. which could be harnessed for commercial applications and emphasizes the need of integrating genome-based computational analysis for evolutionary species and functional diversification. The work reflects on the underexplored genetic potential for bioplastic synthesis which can be harnessed using advanced genomic methods. It also underlines the degradation potential and possible use of naturally-occurring pollutant-degrading Paracoccus isolates for the development of a biodegradation system and efficient removal of contaminants. The work contemplates plausible use of such potent isolates to establish the plant-microbe interaction, contributing toward contaminated land reclamation. Overall, the work signifies the need and application of genome analysis to identify and explore the prospective potential of Paracoccus spp. for environmental application toward achieving sustainability.
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Paracoccus , Xenobióticos , Técnicas de Tipagem Bacteriana , Biodegradação Ambiental , DNA Bacteriano/genética , Ácidos Graxos/análise , Genômica , Paracoccus/genética , Paracoccus/metabolismo , Filogenia , Estudos Prospectivos , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Xenobióticos/metabolismoRESUMO
Antibiotic resistance is one of the major growing concerns for public health. Conventional antibiotics act on a few predefined targets and, with time, several bacteria have developed resistance against a large number of antibiotics. The WHO has suggested that antibiotic resistance is at a crisis stage and identification of new antibiotics and targets could be the only approach to bridge the gap. Filamentous Temperature Sensitive-Mutant Z (Fts-Z) is one of the promising and less explored antibiotic targets. It is a highly conserved protein and plays a key role in bacterial cell division by introducing a cytokinetic Z-ring formation. In the present article, the potential of over 165 cyanobacterial compounds with reported antibiotic activity against the catalytic core domain in the Fts-Z protein of the Bacillus subtilis was studied. The identified cyanobacterial compounds were screened using the GLIDE module of Maestro v-2019-2 followed by 100-ns molecular dynamics (MD) simulation. Ranking of the potential compound was performed using dock score and MMGBSA based free energy. The study reported that the docking score of aphanorphine (-6.010 Kcalmol-1) and alpha-dimorphecolic acid (ADMA) (-6.574 Kcalmol-1) showed significant role with respect to the reported potential inhibitor PC190723 (-4.135 Kcalmol-1). A 100 ns MD simulation infers that Fts-Z ADMA complex has a stable conformation throughout the progress of the simulation. Both the compounds, i.e., ADMA and Aphanorphine, were further considered for In-vitro validation by performing anti-bacterial studies against B. subtilis by agar well diffusion method. The results obtained through In-vitro studies confirm that ADMA, a small molecule of cyanobacterial origin, is a potential compound with an antibacterial activity that may act by inhibiting the novel target Fts-Z and could be a great drug candidate for antibiotic development.
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Bacillus subtilis , Cianobactérias , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Proteínas de Bactérias/metabolismo , Cianobactérias/metabolismo , Proteínas do Citoesqueleto/metabolismo , Proteínas Mutantes/metabolismoRESUMO
Hydrolytic dehalogenases form an important class of dehalogenases that include haloacid dehalogenase, haloalkane dehalogenase, haloacetate dehalogenase, and atrazine chlorohydrolase. These enzymes are involved in biodegradation of various environmental pollutants and therefore it is important to understand their phylogeny. In the present study, it was found that the enzymes haloalkane and haloacetate dehalogenases share a common ancestry with enzymes such as carboxyesterase, epoxide hydrolase, and lipases, which can be traced to ancestral α/ß hydrolase fold enzyme. Haloacid dehalogenases and atrazine chlorohydrolases have probabaly evolved from ancestral enzymes with phosphatase and deaminases activity, respectively. These findings were supported by the similarities in the secondary structure, key catalytic motifs and placement of catalytic residues. The phylogeny of haloalkane dehalogenases and haloacid dehalogenases differs from 16S rRNA gene phylogeny, suggesting spread through horizontal gene transfer. Hydrolytic dehalogenases are polyphyletic and do not share a common evolutionay history, the functional similarities are due to convergent evolution. The present study also identifies key functional residues, mutating which, can help in generating better enzymes for clean up of the persistent environmental pollutants using enzymatic bioremediation. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-022-01043-8.
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Titanium dioxide nanoparticles (TiO2NPs) usage is increasing in everyday consumer products, hence, assessing their toxic impacts on living organisms and environment is essential. Various studies have revealed the significant role of TiO2NPs physicochemical properties on their toxicity. However, TiO2NPs are still poorly characterized with respect to their physicochemical properties, and environmental factors influencing their toxicity are either ignored or are too complex to be assessed under laboratory conditions. The outcomes of these studies are diverse and inconsistent due to lack of standard protocols. TiO2NPs toxicity also differs for in vivo and in vitro systems, which must also be considered during standardization of protocols to maintain uniformity and reproducibility of results. This review critically evaluates impact of different physicochemical parameters of TiO2NPs and other experimental conditions, employed in different laboratories in determining their toxicity towards bacteria. These important observations may be helpful in evaluation of environmental risks posed by these nanoparticles and this can further assist regulatory bodies in policymaking.
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A rigorous exploration of microbial diversity has revealed its presence on Earth, deep oceans, and vast space. The presence of microbial life in diverse environmental conditions, ranging from moderate to extreme temperature, pH, salinity, oxygen, radiations, and altitudes, has provided the necessary impetus to search for them by extending the limits of their habitats. Microbiology started as a distinct science in the mid-nineteenth century and has provided inputs for the betterment of mankind during the last 150 years. As beneficial microbes are assets and pathogens are detrimental, studying both have its own merits. Scientists are nowadays working on illustrating the microbial dynamics in Earth's subsurface, deep sea, and polar regions. In addition to studying the role of microbes in the environment, the microbe-host interactions in humans, animals and plants are also unearthing newer insights that can help us to improve the health of the host by modulating the microbiota. Microbes have the potential to remediate persistent organic pollutants. Antimicrobial resistance which is a serious concern can also be tackled only after monitoring the spread of resistant microbes using disciplines of genomics and metagenomics The cognizance of microbiology has reached the top of the world. Space Missions are now looking for signs of life on the planets (specifically Mars), the Moon and beyond them. Among the most potent pieces of evidence to support the existence of life is to look for microbial, plant, and animal fossils. There is also an urgent need to deliberate and communicate these findings to layman and policymakers that would help them to take an adequate decision for better health and the environment around us. Here, we present a glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity.
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The present study was carried out to clarify the taxonomic assignment of two closely related Amycolatopsis species. Genomic information for 48 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Amycolatopsis eurytherma Kim et al. 2002 and Amycolatopsis thermoflava Chun et al. 1999, are conspecific. The 16S rRNA gene sequences of the two species possess 98.85â% sequence similarity. Further, whole-genome comparisons showed that A. eurytherma DSM 44348T and A. thermoflava N1165T shared 98.75â% average nucleotide identity, 98.63â% average amino acid identity and 87.8â% digital DNA-DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. eurytherma DSM 44348T and A. thermoflava N1165T formed a monophyletic clade. Based on this evidence we propose the reclassification of Amycolatopsis eurytherma Kim et al. 2002 as a later heterotypic synonym of Amycolatopsis thermoflava Chun et al. 1999.
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Genoma Bacteriano , Filogenia , Amycolatopsis/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Genômica , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensis DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA-DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans.
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Deinococcus/classificação , Filogenia , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Genômica , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
ß-Hexachlorocyclohexane (ß-HCH) is a remnant from former HCH pesticide production. Its removal from the environment gained attention in the last few years since it is the most stable HCH isomer. However, knowledge about the transformation of ß-HCH in soil-plant systems is still limited. Therefore, experiments with a contaminated field soil were conducted to investigate the transformation of ß-HCH in soil-plant systems by compound specific isotope analysis (CSIA). The results showed that the δ13C and δ37Cl values of ß-HCH in the soil of the planted control remained stable, revealing no transformation due to a low bioavailability. Remarkably, an increase of the δ13C and δ37Cl values in soil and plant tissues of the spiked treatments were observed, indicating the transformation of ß-HCH in both the soil and the plant. This was surprising as previously it was shown that wheat is unable to transform ß-HCH when growing in hydroponic culture or garden soil. Thus, results of this work indicate for the first time that a microbial community of the soil inoculated the wheat and then facilitated the transformation of ß-HCH in the wheat, which may have implications for the development of phytoremediation concepts. A high abundance of HCH degraders belonging to Sphingomonas sp., Mycobacterium sp., and others was detected in the ß-HCH-treated bulk and rhizosphere soil, potentially supporting the biotransformation.
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Hexaclorocicloexano , Poluentes do Solo , Biodegradação Ambiental , Hexaclorocicloexano/análise , Isótopos , Solo , Poluentes do Solo/análise , TriticumRESUMO
The present study reports the functional annotation of complete genome of methylotrophic bacterium Paracoccus sp. strain AK26. The 3.6 Mb genome with average GC content of 65.7% was distributed across five replicons; including chromosome (2.7 Mb) and four extrachromosomal replicons pAK1 (471Kb), pAK2 (189Kb), pAK3 (129Kb) and pAK4 (84 Kb). Interestingly, nearly 23% of the Cluster of Orthologous Group (COG) of proteins were annotated on extrachromosomal replicons and 185Kb genome content was attributed to segregated 19 genomic island regions. Among the four replicons, pAK4 was identified as essential and integral part of the genome, as supported by codon usage, GC content (66%) and synteny analysis. Comparative genome analysis for methylotrophy showed mechanistic variations in oxidation and assimilation of C1 compounds among closely related Paracoccus spp. Collectively, present study reports the functional characterization and genomic architecture of strain AK26 and provides genetic basis for quinone and isoprenoid based secondary metabolites synthesis using strain AK26.
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Genoma Bacteriano , Paracoccus/genética , Proteínas de Bactérias/genética , Carbono/metabolismo , Cromossomos Bacterianos , Regulação Bacteriana da Expressão Gênica , Redes Reguladoras de Genes , Paracoccus/metabolismo , Plasmídeos/genética , Replicon , Estresse Fisiológico/genéticaRESUMO
Members of genus Sphingopyxis are known to thrive in diverse environments. Genomes of 21 Sphingopyxis strains were selected. Phylogenetic analysis was performed using GGDC, AAI and core-SNP showed agreement at sub-species level. Based on our results, we propose that both S. baekryungensis DSM16222 and Sphingopyxis sp. LPB0140 strains should not be included under genus Sphingopyxis. Core-analysis revealed, 1422 genes were shared which included essential pathways and genes for conferring adaptation against stress environment. Polyhydroxybutyrate degradation, anaerobic respiration, type IV secretion were notable abundant pathways and exopolysaccharide, hyaluronic acid production and toxin-antitoxin system were differentially present families. Interestingly, genome of S. witflariensis DSM14551, Sphingopyxis sp. MG and Sphingopyxis sp. FD7 provided a hint of probable pathogenic abilities. Protein-Protein Interactome depicted that membrane proteins and stress response has close integration with core-proteins while aromatic compounds degradation and virulence ability formed a separate network. Thus, these should be considered as strain specific attributes.
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Genoma Bacteriano , Sphingomonadaceae/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Filogenia , Mapas de Interação de Proteínas , Sphingomonadaceae/classificação , Sphingomonadaceae/metabolismo , Estresse Fisiológico , Sistemas Toxina-AntitoxinaRESUMO
The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.
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Bacillus/genética , Genoma Bacteriano , Animais , Bacillus/classificação , Bacillus/isolamento & purificação , Bacillus/metabolismo , Bovinos , Genômica , Filogenia , Metabolismo Secundário/genéticaRESUMO
The taxonomic classification of metabolically versatile Paracoccus spp. has been so far performed using polyphasic approach. The topology of single gene phylogenies, however, has highlighted ambiguous species assignments. In the present study, genome based multi-gene phylogenies and overall genome related index were used for species threshold assessment. Comprehensive phylogenomic analysis of Paracoccus genomes (n = 103) showed concordant clustering of strains across multi-gene marker set phylogenies (nMC = 0.08-0.14); as compared to 16S rDNA phylogeny (nMC = 0.37-0.42) suggesting robustness of multi gene phylogenies in drawing phylogenetic inferences. Functional gene content distribution across the genus showed that only 1.7% gene content constitutes the core genome highlighting the significance of extensive genomic variability in the evolution of Paracoccus spp. Further, genome metrics were used to validate characterized strains, identifying classification anomalies (n = 13), and based on this, genome derived taxonomic amendments were notified in present study. Conclusively, validated metric tools can be employed on whole genome sequences, including draft assemblies, for the assessment and assignment of uncharacterized strains and species level ascription of newly isolated Paracoccus strains in future.