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

Análise em larga escala da expressão diferencial de Corynebacterium pseudotuberculosis em resposta a estresses abióticos

Exportado OPUSMade available in DSpace on 2019-08-14T20:21:06Z (GMT). No. of bitstreams: 1 tese_completa_2011.pdf: 5508692 bytes, checksum: 05a09899a66ecb14396adaeda2e067ee (MD5) Previous issue date: 31Uma nova tecnologia de sequenciamento de cDNA tem permitido uma análise detalhada e aprofundada dos transcritos em procariotos. Corynebacterium pseudotuberculosis, uma bactéria causadora de doenças, como a linfadenite caseosa, que trazem grandes prejuízos econômicos para o agronegócio mundial, foi o alvo de nossos estudos. Neste contexto, caracterizamos o perfil transcricional diferencial deste microrganismo em algumas condições que simulam o ambiente encontrado pela bactéria no hospedeiro no processo de infecção como, estresse osmótico (2M), térmico (50°C) e acidez (pH=5). No presente estudo escolhemos a plataforma SOLiDTM para tentar compreender o desenvolvimento da doença e a modulação da resposta a partir dos genes envolvidos no processo da infecção. Conseguimos detectar todas as regiões transcricionalmente ativas preditas no genoma (2057 genes), sendo que na condição controle (condição fisiológica normal), foi possível observar que 97,58% dos genes são transcritos, apresentando 2,42% de região não transcrita com valor de RPKM (Reads Per Kilobase of coding sequence per Million mapped) igual a zero. Nas condições de estresse osmótico, estresse térmico e acidez, 98,05%, 97,34%, 97,81% dos genes são transcritos, respectivamente. Dos 2064 transcritos do estresse osmótico, 48,01% foram considerados diferencialmente expressos em relação ao controle, 45,68% genes considerados diferencialmente expressos no térmico e no estresse ácido, 48,08%. Grande parte dos genes em todas as condições, induzidos ou reprimidos foi composta por proteínas de funções desconhecidas (hipotéticas) confirmando quão pouco este microrganismo é caracterizado. As análises revelaram uma forte correlação entre resposta ao estresse ácido e expressão de genes relacionados à virulência. O processo de regulação da transcrição e adesão celular estão entre os principais resultados do Blast2GO. No estresse osmótico processo de reparo e transporte transmembrana foram destaques, além do processo de adesão. No estresse térmico, menor número de genes diferencialmente expressos fizeram parte da análise e entre os principais processos estão o de oxidoredução e catabólico de ATP, gerando energia para célula sobreviver no ambiente hostil. Dentro do core estimulon (genes compartilhados entre os estresses), genes de virulência se destacaram, demonstrando que já no inicio da fase exponencial a bactéria regula a transcrição para uma resposta específica e adaptativa. Entre os reprimidos, os genes envolvidos no processo metabólico e biossintéticos foram os mais representados, demonstrando redução no crescimento, que é uma importante estratégia de ajuste da fisiologia celular para uma nova condição. O presente estudo permitiu criar um catálogo gênico que é utilizado como recurso para sobrevivência dentro de ambientes prejudiciais e conseguir escapar da resposta imune do hospedeiro. Estes resultados nos permitem sugerir possíveis candidatos à obtenção de vacinas eficientes com potencial redução das perdas no agronegócio, em estudos futuros.A new cDNA sequencing technology has allowed deep analysis of prokaryotic transcripts. Corynebacterium pseudotuberculosis, our study target, is a bacterium responsible for several diseases, such as caseous lymphadenitis that causes important economic losses in global agrobusinesses. In this context, we characterized its differential transcriptional profile in some conditions that mimic the environment found during an infectious process, namely osmotic (2M), termic (50°C) and acid (pH=5) stresses. For this work, SOLiDTM platform was chosen to try to understand the development of the disease and modulation of the response from the genes involved in the infectious process. All transcriptionally active regions that were predicted in the genome (2057 genes) were detected, observing 97,58% of transcript genes under the control condition, and 2,42% of non-transcribed regions with a RPKM value (Reads Per Kilobase of coding sequence per Million mapped) equal to zero. During conditions of osmotic, termic and acid stresses, 98,05%, 97,34% and 97,81% of genes, respectively, were found to be transcribed. During osmotic stress, 48,01% of the transcripts were considered differentially expressed with relation to the control, whereas during termic and acid stress, 45,68% and 48,08% respectively were found. It was observed that most genes for all stresses were formed by proteins of unknown function (hypothetical), highlighting the need for more information about this microorganism. Our analysis revealed a strong relationship between acid stress response and gene expression of genes previously associated to virulence. The process of transcription regulation and cell adhesion are among the main results of Blast2GO. During osmotic stress, repair process and transmembrane transport, as well as adhesion process, were highlighted. During heat shock, fewer differentially expressed genes were part of the analysis and oxidoreduction processes and ATP catabolic process were among the main energy generators for cell survival in the hostile environment. Within the core estimulon (genes shared between the stresses), virulence genes stood out, demonstrating that already at the beginning of the exponential phase the bacteria regulates the transcription for a specific and adaptive response. Among the repressed genes, those involved in metabolic and biosynthesis were the most represented, demonstrating reduced growth, an important strategy for adjusting cell physiology to a new condition. The present study allowed the creation of a gene catalog that can be used as a resource for survival in adverse environments and escape of the host immune response. These results allow us to suggest, in future studies, possible candidates for efficient vaccines regarding potential loss reduction in agribusinesses

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

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

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

Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina

In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis PAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium