Comparative Genomic Analysis of Members of the GeneraMethanosphaeraandMethanobrevibacterReveals Distinct Clades with Specific Potential Metabolic Functions

MethanobrevibacterandMethanosphaeraspecies represent some of the most prevalent methanogenic archaea in the gastrointestinal tract of animals and humans and play an important role in this environment. The aim of this study was to identify genomic features that are shared or specific for members of each genus with a special emphasis of the analysis on the assimilation of nitrogen and acetate and the utilization of methanol and ethanol for methanogenesis. Here, draft genome sequences ofMethanobrevibacter thaueristrain DSM 11995T,Methanobrevibacter woeseistrain DSM 11979T, andMethanosphaera cuniculistrain 4103Tare reported and compared to those of 16 otherMethanobrevibacterandMethanosphaeragenomes, including genomes of the 13 currently available types of strains of the two genera. The comparative genome analyses indicate that among other genes, the absence of molybdopterin cofactor biosynthesis is conserved inMethanosphaeraspecies but reveals also that the three species share a core set of more than 300 genes that distinguishes the genusMethanosphaerafrom the genusMethanobrevibacter. Multilocus sequence analysis shows that the genusMethanobrevibactercan be subdivided into clades, potentially new genera, which may display characteristic specific metabolic features. These features include not only the potential ability of nitrogen fixation and acetate assimilation in a clade comprised ofMethanobrevibacterspecies from the termite gut andMethanobrevibacter arboriphilusstrains but also the potential capability to utilize ethanol and methanol in a clade comprisingMethanobrevibacter woliniistrain DSM 11976T,Mbb.sp. AbM4, andMbb. boviskoreanistrain DSM 25824T.

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Comparative Genomic Analysis of the Biotechnological Potential of the Novel Species Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T

Diversity ◽

10.3390/d11110204 ◽

2019 ◽

Vol 11 (11) ◽

pp. 204

Author(s):

Dominik Rutz ◽

David Frasson ◽

Martin Sievers ◽

Jochen Blom ◽

Fabio Rezzonico ◽

...

Keyword(s):

New Species ◽

Plant Pathogens ◽

Draft Genome ◽

Genomic Analysis ◽

Yield Potential ◽

Comparative Genomic ◽

Genomic Features ◽

Two New Species ◽

Genes Encoding ◽

Potential Applications

In recent years, the use of whole-cell biocatalysts and biocatalytic enzymes in biotechnological applications originating from the genus Pseudomonas has greatly increased. In 2014, two new species within the Pseudomonas putida group were isolated from Swiss forest soil. In this study, the high quality draft genome sequences of Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T were used in a comparative genomics approach to identify genomic features that either differed between these two new species or to selected members of the P. putida group. The genomes of P. wadenswilerensis CCOS 864T and P. reidholzensis CCOS 865T were found to share genomic features for the degradation of aromatic compounds or the synthesis of secondary metabolites. In particular, genes encoding for biocatalytic relevant enzymes belonging to the class of oxidoreductases, proteases and isomerases were found, that could yield potential applications in biotechnology. Ecologically relevant features revealed that both species are probably playing an important role in the degradation of soil organic material, the accumulation of phosphate and biocontrol against plant pathogens.

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Draft Genome Sequences for Seven Streptococcus parauberis Isolates from Wild Fish in the Chesapeake Bay: TABLE 1

Genome Announcements ◽

10.1128/genomea.00741-16 ◽

2016 ◽

Vol 4 (4) ◽

Cited By ~ 1

Author(s):

Ashley Haines ◽

Emily Nebergall ◽

Elvira Besong ◽

Kimaya Council ◽

Onaysha Lambert ◽

...

Keyword(s):

Chesapeake Bay ◽

Draft Genome ◽

Morone Saxatilis ◽

Genomic Analysis ◽

Comparative Genomic ◽

Streptococcus Iniae ◽

Genome Sequences ◽

Streptococcus Uberis ◽

Animal Hosts ◽

Streptococcus Parauberis

Streptococcus parauberis is a pathogen of cattle and fish, closely related Streptococcus uberis and Streptococcus iniae . We report the genomes of seven S. parauberis strains recovered from striped bass ( Morone saxatilis ) in the Chesapeake Bay. The availability of these genomes will allow comparative genomic analysis of Chesapeake Bay S. parauberis strains versus S. parauberis cultured from other animal hosts and geographic regions.

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Comparative genomics of two Shewanella xiamenensis strains isolated from a pilgrim before and during travels to the Hajj

Gut Pathogens ◽

10.1186/s13099-021-00404-w ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Thongpan Leangapichart ◽

Linda Hadjadj ◽

Philippe Gautret ◽

Jean-Marc Rolain

Keyword(s):

Genome Size ◽

Pathogenic Bacteria ◽

Capsular Polysaccharide ◽

Draft Genome ◽

Water Environment ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Comparative Genomic ◽

Whole Genome ◽

Genome Sequences

Abstract Background Shewanella xiamenensis has been reported in water environment and in patients and can act as the originator of oxacillinase in gram-negative bacteria. In order to assess genome plasticity and its functional properties related diarrhea symptoms in pilgrim, comparisons of draft genome sequences of the two isolates were conducted with other closely related genomes. Results We isolated S. xiamenensis 111B and 111D strains from a pilgrim before travels to the Hajj and during travels with diarrhea symptom, respectively. Whole-genome sequencing showed that draft genome size of 111B strain was 5,008,191 bp, containing 49 kb of a putative plasmid. The genome size of 111D was 4,964,295 bp containing 225 kb of a putative plasmid that shared the backbone sequences with the hospital wastewater strain T17. Comparatively, two Hajj strains are identical at 97.3% identity and 98.7% coverage. They are closely related to river water strain, AS58 by SNPs analysis. Notably, a novel blaOXA-48 allele blaOXA-547 was identified in 111D, sharing 99.5% identity with blaOXA-546 and blaOXA-894. Multiple copies of virulence specific genes, such as capsular polysaccharide biosynthesis, O-antigen and lasB (vibriolysin related gene) have been identified specifically in 111D, but absent in 111B strain. Conclusions The whole genome sequences of S. xiamenensis strain 111B and 111D, including comparative genomic analysis, highlight here the potential for virulence factors that might be related to the cause of diarrhea in humans and also indicate the possible acquisition of pathogenic bacteria, including antibiotic resistance genes or plasmids during the Hajj.

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Genomic Features and Comparative Genomic Analysis of novel Bacillus glycinifermentans strain JRCGR-1

10.21203/rs.3.rs-902697/v1 ◽

2021 ◽

Author(s):

Asad Karim ◽

poirot olivier ◽

Ambrina Khatoon ◽

Matthieu Legendre

Keyword(s):

Core Genome ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Public Database ◽

Genome Sequences ◽

Genomic Features ◽

The Public ◽

Comparative Genomics Analysis ◽

High Level

Abstract To the best of our knowledge, only six B. glycinifermentans sp. genome sequences are available in the public database. Here, we performed genome sequencing and comparative genomics analysis of B. glycinifermentans strain JRCGR-1. Cluster analysis of strain JRCGR-1 genes showed that 92.6% of genes were present in the orthogroups and 7.4% genes were not assigned to any group. The pangenome size was calculated at 8329 genes and presented an open genome characteristic. Phylogeny based on the pan and core genome demonstrated that all the B. glycinifermentans strains belong to the same clade. The strain JRCGR-1, ANI, TETRA and DDH values were in the range of 96.1-99.04%, 0.996-997, 73.5–84.7%, respectively. The strain JRCGR genome exhibits a high level of synteny with multiple locations in B. sonorensis sp. and B. licheniformis sp. The finding of the current study provides knowledge that facilitates a better understanding of this at the genomic level.

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Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

Tropical Animal Health and Production ◽

10.1007/s11250-021-02877-y ◽

2021 ◽

Vol 53 (4) ◽

Author(s):

Jean N. Hakizimana ◽

Jean B. Ntirandekura ◽

Clara Yona ◽

Lionel Nyabongo ◽

Gladson Kamwendo ◽

...

Keyword(s):

Complete Genome ◽

African Swine Fever Virus ◽

Gc Content ◽

Genomic Analysis ◽

African Swine Fever ◽

Eastern Africa ◽

Nucleotide Identity ◽

Comparative Genomic ◽

Genome Sequences ◽

Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

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Draft Genome Sequences of Three Bacterial Isolates from Cultures of the Marine Diatom Thalassiosira rotula

Genome Announcements ◽

10.1128/genomea.00316-17 ◽

2017 ◽

Vol 5 (18) ◽

Cited By ~ 3

Author(s):

Nathan S. Garcia ◽

Cheuk-Man Yung ◽

Katherine M. Davis ◽

Tatiana Rynearson ◽

Dana E. Hunt

Keyword(s):

Heterotrophic Bacteria ◽

Draft Genome ◽

Marine Diatom ◽

Bacterial Isolates ◽

Genome Sequences ◽

Metabolic Functions

ABSTRACT Phytoplankton often both provision and depend on heterotrophic bacteria. In order to investigate these relationships further, we sequenced draft genomes of three bacterial isolates from cultures of the marine diatom Thalassiosira rotula to identify metabolic functions that may support interactions with T. rotula.

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Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production

FEMS Yeast Research ◽

10.1093/femsyr/foz034 ◽

2019 ◽

Vol 19 (4) ◽

Cited By ~ 3

Author(s):

Débora Trichez ◽

Andrei S Steindorff ◽

Carlos E V F Soares ◽

Eduardo F Formighieri ◽

João R M Almeida

Keyword(s):

Renewable Resources ◽

Xylose Reductase ◽

Genomic Analysis ◽

Product Yield ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Brazilian Cerrado ◽

Genome Sequences ◽

Yeast Strains ◽

Spathaspora Passalidarum

ABSTRACT Xylitol is a five-carbon polyol of economic interest that can be produced by microbial xylose reduction from renewable resources. The current study sought to investigate the potential of two yeast strains, isolated from Brazilian Cerrado biome, in the production of xylitol as well as the genomic characteristics that may impact this process. Xylose conversion capacity by the new isolates Spathaspora sp. JA1 and Meyerozyma caribbica JA9 was evaluated and compared with control strains on xylose and sugarcane biomass hydrolysate. Among the evaluated strains, Spathaspora sp. JA1 was the strongest xylitol producer, reaching product yield and productivity as high as 0.74 g/g and 0.20 g/(L.h) on xylose, and 0.58 g/g and 0.44 g/(L.h) on non-detoxified hydrolysate. Genome sequences of Spathaspora sp. JA1 and M. caribbica JA9 were obtained and annotated. Comparative genomic analysis revealed that the predicted xylose metabolic pathway is conserved among the xylitol-producing yeasts Spathaspora sp. JA1, M. caribbica JA9 and Meyerozyma guilliermondii, but not in Spathaspora passalidarum, an efficient ethanol-producing yeast. Xylitol-producing yeasts showed strictly NADPH-dependent xylose reductase and NAD+-dependent xylitol-dehydrogenase activities. This imbalance of cofactors favors the high xylitol yield shown by Spathaspora sp. JA1, which is similar to the most efficient xylitol producers described so far.

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Whole-Genome Sequences and Classification of Streptococcus agalactiae Strains Isolated from Laboratory-Reared Long-Evans Rats (Rattus norvegicus)

Genome Announcements ◽

10.1128/genomea.01435-16 ◽

2017 ◽

Vol 5 (1) ◽

Cited By ~ 4

Author(s):

C. Bodi Winn ◽

J. Dzink-Fox ◽

Y. Feng ◽

Z. Shen ◽

V. Bakthavatchalu ◽

...

Keyword(s):

Streptococcus Agalactiae ◽

Genomic Analysis ◽

Opportunistic Pathogen ◽

Comparative Genomic ◽

Whole Genome ◽

Genome Sequences ◽

Content Type ◽

Long Evans ◽

Fatal Septicemia

ABSTRACT In collaboration with the CDC’s Streptococcus Laboratory, we report here the whole-genome sequences of seven Streptococcus agalactiae bacteria isolated from laboratory-reared Long-Evans rats. Four of the S. agalactiae isolates were associated with morbidity accompanied by endocarditis, metritis, and fatal septicemia, providing an opportunity for comparative genomic analysis of this opportunistic pathogen.

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Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000226 ◽

2015 ◽

Vol 65 (Pt_7) ◽

pp. 2104-2109 ◽

Cited By ~ 48

Author(s):

Christopher A. Dunlap ◽

Soo-Jin Kim ◽

Soon-Wo Kwon ◽

Alejandro P. Rooney

Keyword(s):

Bacillus Amyloliquefaciens ◽

Type Strain ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Genomic Analysis ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Growth Promoters ◽

Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

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Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations

PeerJ ◽

10.7717/peerj.3266 ◽

2017 ◽

Vol 5 ◽

pp. e3266 ◽

Cited By ~ 10

Author(s):

Emma C. Wallace ◽

Lina M. Quesada-Ocampo

Keyword(s):

Downy Mildew ◽

Draft Genome ◽

Model Organism ◽

Genomic Analysis ◽

Population Level ◽

Comparative Genomic ◽

Pathogen Population ◽

Pseudoperonospora Humuli ◽

Hyaloperonospora Arabidopsidis

Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P. cubensis predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire of P. cubensis to that of the model organism Hyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from P. cubensis transcripts differed significantly from H. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product in P. cubensis isolates, and 83 microsatellites demonstrated transferability to P. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified in P. cubensis isolates. Analysis of Pseudoperonospora isolates from diverse hosts and locations revealed higher diversity in P. cubensis compared to P. humuli isolates. These microsatellites will be useful in efforts to better understand relationships within Pseudoperonospora species and P. cubensis on a population level.

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