The Space-Exposed Kombucha Microbial Community Member Komagataeibacter oboediens Showed Only Minor Changes in Its Genome After Reactivation on Earth

Komagataeibacter is the dominant taxon and cellulose-producing bacteria in the Kombucha Microbial Community (KMC). This is the first study to isolate the K. oboediens genome from a reactivated space-exposed KMC sample and comprehensively characterize it. The space-exposed genome was compared with the Earth-based reference genome to understand the genome stability of K. oboediens under extraterrestrial conditions during a long time. Our results suggest that the genomes of K. oboediens IMBG180 (ground sample) and K. oboediens IMBG185 (spaceexposed) are remarkably similar in topology, genomic islands, transposases, prion-like proteins, and number of plasmids and CRISPR-Cas cassettes. Nonetheless, there was a difference in the length of plasmids and the location of cas genes. A small difference was observed in the number of protein coding genes. Despite these differences, they do not affect any genetic metabolic profile of the cellulose synthesis, nitrogen-fixation, hopanoid lipids biosynthesis, and stress-related pathways. Minor changes are only observed in central carbohydrate and energy metabolism pathways gene numbers or sequence completeness. Altogether, these findings suggest that K. oboediens maintains its genome stability and functionality in KMC exposed to the space environment most probably due to the protective role of the KMC biofilm. Furthermore, due to its unaffected metabolic pathways, this bacterial species may also retain some promising potential for space applications

The Transcriptional Regulatory Network of Corynebacterium pseudotuberculosis

Parise D, Dornelles Parise MT, Pinto Gomide AC, et al. The Transcriptional Regulatory Network of Corynebacterium pseudotuberculosis. Microorganisms. 2021;9(2): 415.Corynebacterium pseudotuberculosis is a Gram-positive, facultative intracellular, pathogenic bacterium that infects several different hosts, yielding serious economic losses in livestock farming. It causes several diseases including oedematous skin disease (OSD) in buffaloes, ulcerative lymphangitis (UL) in horses, and caseous lymphadenitis (CLA) in sheep, goats and humans. Despite its economic and medical-veterinary importance, our understanding concerning this organism's transcriptional regulatory mechanisms is still limited. Here, we review the state of the art knowledge on transcriptional regulatory mechanisms of this pathogenic species, covering regulatory interactions mediated by two-component systems, transcription factors and sigma factors. Key transcriptional regulatory players involved in virulence and pathogenicity of C. pseudotuberculosis, such as the PhoPR system and DtxR, are in the focus of this review, as these regulators are promising targets for future vaccine design and drug development. We conclude that more experimental studies are needed to further understand the regulatory repertoire of this important zoonotic pathogen, and that regulators are promising targets for future vaccine design and drug development

Glutamicibacter creatinolyticus strain LGCM 259 infection in a horse: first genetic characterization

Abstract Glutamicibacter creatinolyticus (formerly Arthrobacter creatinolyticus) belonged to the family Microccaceae. It plays a significant role in many ecosystems: soil, water, air, cheese, plant, and it was associated to urinary tract infections and bacteremia in humans [1]. Recently, G. creatinolyticus LGCM 259 (LGCM-259) was isolated from diffuse subcutaneous nodules adherent to muscular tissues from a mare in Italy. Objectives Since the identification is only possible using 16S rRNA and MALDI- TOF sequence analyses11, this study was carried out to: -characterize LGCM-259 with a complete DNA sequence and annotation; -identify genes encoding virulence factors. Materials and methods By comparative analyses among four isolated species of different habitats, available in the NCBI database, chromosomal sequencing using Hiseq technology (Illumina, USA) was conducted. The genome of LGCM-259 was automatically annotated using PROKKA. A phylogenomic tree and the presence of virulence genes were generated by Phylogenomic Tree Tool in Pathosystems Resource Integration Center (version-3.5.17), and BLASTp against the Virulence Factor Database (VFDB), respectively. Results LGCM-259 strain was sequenced and assembled in a circular chromosome, which exhibits a length of 3.3 Mb, with a G+C content of 66.4%, and a total of 2882 CDSs, 4 clusters of rRNAS (5S, 16S, and 23S), and 61 tRNA genes, respectively. The locus tag LGCM259_1698, LGCM259_0905 and LGCM259_1698 may be involved in multiple drug resistance to Rifampin, Elfamycin, and Fluoroquinolone (rpoB, tufA, tufB). The genome also displayed copper tolerance genes (copZ, csoR_1, cutC, aniA, pcoC), resistance to heavy metals such as arsenic, cobalt-zinc-cadmium (cobT, cobS, cadA), and chrome composts which are serious environmental contaminants. Conclusion The LGCM 259 strain’s genome was first characterize and its chromosome sequence has been deposited in the NCBI database under accession number CP034412. It affects animals and carries important bacterial virulence factors that are essential in cell viability and pathogenicity

Glutamicibacter creatinolyticus strain LGCM 259 infection in a horse: first genetic characterization

Abstract Glutamicibacter creatinolyticus (formerly Arthrobacter creatinolyticus) belonged to the family Microccaceae. It plays a significant role in many ecosystems: soil, water, air, cheese, plant, and it was associated to urinary tract infections and bacteremia in humans [1]. Recently, G. creatinolyticus LGCM 259 (LGCM-259) was isolated from diffuse subcutaneous nodules adherent to muscular tissues from a mare in Italy. Objectives Since the identification is only possible using 16S rRNA and MALDI- TOF sequence analyses11, this study was carried out to: -characterize LGCM-259 with a complete DNA sequence and annotation; -identify genes encoding virulence factors. Materials and methods By comparative analyses among four isolated species of different habitats, available in the NCBI database, chromosomal sequencing using Hiseq technology (Illumina, USA) was conducted. The genome of LGCM-259 was automatically annotated using PROKKA. A phylogenomic tree and the presence of virulence genes were generated by Phylogenomic Tree Tool in Pathosystems Resource Integration Center (version-3.5.17), and BLASTp against the Virulence Factor Database (VFDB), respectively. Results LGCM-259 strain was sequenced and assembled in a circular chromosome, which exhibits a length of 3.3 Mb, with a G+C content of 66.4%, and a total of 2882 CDSs, 4 clusters of rRNAS (5S, 16S, and 23S), and 61 tRNA genes, respectively. The locus tag LGCM259_1698, LGCM259_0905 and LGCM259_1698 may be involved in multiple drug resistance to Rifampin, Elfamycin, and Fluoroquinolone (rpoB, tufA, tufB). The genome also displayed copper tolerance genes (copZ, csoR_1, cutC, aniA, pcoC), resistance to heavy metals such as arsenic, cobalt-zinc-cadmium (cobT, cobS, cadA), and chrome composts which are serious environmental contaminants. Conclusion The LGCM 259 strain’s genome was first characterize and its chromosome sequence has been deposited in the NCBI database under accession number CP034412. It affects animals and carries important bacterial virulence factors that are essential in cell viability and pathogenicity

Complete genome analysis of Glutamicibacter creatinolyticus from mare abscess and comparative genomics provide insight of diversity and adaptation for Glutamicibacter

Bacteria of the genusGlutamicibacterare considered ubiquitous because they can be found in soil, water and air. They have already been isolated from different habitats, including different types of soil, clinical samples, cheese and plants. Glutamicibacter creatinolyticus is a Gram-positive bacterium important to various biotechnological processes, however, as a pathogen it is associated to urinary tract infections and bacteremia. Recently,Glutamicibacter creatinolyticusLGCM 259 was isolated from a mare, which displayed several diffuse subcutaneous nodules with heavy vascularization. In this study, sequencing, genomic analysis ofG. creatinolyticusLGCM 259 and comparative analyseswere performedamong 4representatives of different members of genusfromdifferent habitats, available in the NCBI database. The LGCM 259 strain's genome carries important factors of bacterial virulence that are essential in cell viability, virulence, and pathogenicity. Genomic islands were predicted for 4 members of genusGlutamicibacter,showing ahigh number of GEIs,which may reflect a high interspecific diversity and a possible adaptive mechanism responsible for the survival of each species in its specific niche. Furthermore,G. creatinolyticusLGCM 259 sharessyntenicregions, albeit with a considerable loss of genes, in relation to the other species. In addition,G. creatinolyticusLGCM 259 presentsresistancegenes to 6 differentclasses ofantibiotics and heavy metals, such as: copper, arsenic, chromium and cobalt-zinc-cadmium.Comparative genomicsanalysescouldcontribute to the identification of mobile genetic elements particular to the speciesG. creatinolyticuscompared to other members of genus. The presence of specific regions inG. creatinolyticuscould be indicative of their rolesin host adaptation, virulence, and the characterization ofastrain that affects animals

Comparative Genomics and In Silico Evaluation of Genes Related to the Probiotic Potential of Bifidobacterium breve 1101A

Bifidobacterium breve is among the first microorganisms colonizing the intestinal tract in humans and is a predominant species in the gut microbiota of newborns and children. This bacterium is widely used in the probiotic industry due to its capacity to improve host health. The search for new targets with probiotic properties is an increasing trend with the help of next-generation sequencing as they facilitate the characterization of the bacterial features. B. breve 1101A was isolated from the faeces of healthy children in Brazil and therefore could play a protective role in the gut. To investigate the beneficial properties of this strain, the present study performed a comprehensive characterization of the genetic features involved in the bacterium resistance and adaptation to gastrointestinal conditions, production of nutrients, and immunomodulatory compounds. Furthermore, this study carried out the prediction of genomic elements (plasmids, prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes) to evaluate the safety of B. breve 1101A. A comparative genomics approach using 45 B. breve complete genomes based on pangenome and phylogenomic analysis was also performed to identify specific genes in B. breve 1101A. The prediction of genetic elements, possibly safety-related, did not detect plasmids, but only one incomplete prophage, two non-functional CRISPR systems, and seven genomic islands. Additionally, three antibiotic resistance genes were identified: ileS (resistance to mupirocin), rpoB, and erm(X). In the comparative genomic analysis, the pangenome was revealed to be open, and B. breve 1101A presented 63 unique genes associated with several processes, such as transmembrane transport, membrane components, DNA processes, and carbohydrate metabolism. In conclusion, B. breve 1101A is potentially safe and well-adapted for intestinal disorder therapeutics, although the role of its unique genetic repertoire needs further investigation

Transcriptome analysis of Corynebacterium pseudotuberculosis biovar Equi in two conditions of the environmental stress

Corynebacterium pseudotuberculosis has been widely studied in an effort to understand its biological evolution. Transcriptomics has revealed possible candidates for virulence and pathogenicity factors of strain 1002 (biovar Ovis). Because C. pseudotuberculosis is classified into two biovars, Ovis and Equi, it was interesting to assess the transcriptional profile of biovar Equi strain 258, the causative agent of ulcerative lymphangitis. The genome of this strain was re-sequenced; the reassembly was completed using optical mapping technology, and the sequence was subsequently re-annotated. Two growth conditions that occur during the host infection process were simulated for the transcriptome: the osmotic and acid medium. Genes that may be associated with the microorganism's resilience under unfavorable conditions were identified through RNAseq, including genes present in pathogenicity islands. The RT-qPCR was performed to confirm the results in biological triplicate for each condition for some genes. The results extend our knowledge of the factors associated with the spread and persistence of C. pseudotuberculosis during the infection process and suggest possible avenues for studies related to the development of vaccines, diagnosis, and therapies that might help minimize damage to agribusinesses.Fil: Gomide, Anne Cybelle Pinto. Universidade Federal de Minas Gerais; BrasilFil: Ibraim, Izabela Coimbra. Universidade Federal de Minas Gerais; BrasilFil: Alves, Jorianne T. C.. Universidade Federal do Pará; BrasilFil: de Sá, Pablo Gomes. Federal Rural University Of Amazonia; BrasilFil: de Oliveira Silva, Yuri Rafael. Universidade Federal do Pará; BrasilFil: Santana, Mariana Passos. Universidade Federal de Minas Gerais; BrasilFil: Marques Da Silva, Wanderson. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Folador, Edson Luiz. Universidade Federal Da Paraiba; BrasilFil: Mariano, Diego C. B.. Universidade Federal de Minas Gerais; BrasilFil: de Paula Castro, Thiago Luiz. Universidade Federal da Bahia; BrasilFil: Barbosa, Silvanira. Universidade Federal do Pará; BrasilFil: Dorella, Fernanda Alves. Universidade Federal de Minas Gerais; BrasilFil: Carvalho, Alex F.. Universidade Federal de Minas Gerais; BrasilFil: Pereira, Felipe L.. Universidade Federal de Minas Gerais; BrasilFil: Leal, Carlos A. G.. Universidade Federal de Minas Gerais; BrasilFil: Figueiredo, Henrique C. P.. Universidade Federal de Minas Gerais; BrasilFil: Azevedo, Vasco. Universidade Federal de Minas Gerais; BrasilFil: Silva, Artur. Universidade Federal do Pará; BrasilFil: Folador, Adriana Ribeiro Carneiro. Universidade Federal do Pará; Brasi

Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation

Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia. © 2022 Institut Pasteu

The space-exposed Kombucha microbial community member Komagataeibacter oboediens showed only minor changes in its genome after reactivation on earth

Komagataeibacter is the dominant taxon and cellulose-producing bacteria in the Kombucha Microbial Community (KMC). This is the first study to isolate the K. oboediens genome from a reactivated space-exposed KMC sample and comprehensively characterize it. The space-exposed genome was compared with the Earth-based reference genome to understand the genome stability of K. oboediens under extraterrestrial conditions during a long time. Our results suggest that the genomes of K. oboediens IMBG180 (ground sample) and K. oboediens IMBG185 (spaceexposed) are remarkably similar in topology, genomic islands, transposases, prion-like proteins, and number of plasmids and CRISPR-Cas cassettes. Nonetheless, there was a difference in the length of plasmids and the location of cas genes. A small difference was observed in the number of protein coding genes. Despite these differences, they do not affect any genetic metabolic profile of the cellulose synthesis, nitrogen-fixation, hopanoid lipids biosynthesis, and stress-related pathways. Minor changes are only observed in central carbohydrate and energy metabolism pathways gene numbers or sequence completeness. Altogether, these findings suggest that K. oboediens maintains its genome stability and functionality in KMC exposed to the space environment most probably due to the protective role of the KMC biofilm. Furthermore, due to its unaffected metabolic pathways, this bacterial species may also retain some promising potential for space applications.The National Academy of Sciences of Ukraine, Scientific productivity scholarships were supported by the CNPq (Brazil) and a CAPES/PrInt (Brazil) grant.https://www.frontiersin.org/journals/microbiologydm2022BiochemistryGeneticsMicrobiology and Plant Patholog