Genomic analysis of Helicobacter himalayensis sp. nov. isolated from Marmota himalayana

Abstract Background: Helicobacter himalayensis was isolated from Marmota himalayana in the Qinghai-Tibet Plateau, China, and is a new non-H. pylori species, with unclear taxonomy, phylogeny, and pathogenicity. Results: A comparative genomic analysis was performed between the H. himalayensis type strain 80(YS1)T and other the genomes of Helicobacter species present in the National Center for Biotechnology Information (NCBI) database to explore the molecular evolution and potential pathogenicity of H. himalayensis. H. himalayensis 80(YS1)T formed a clade with H. cinaedi and H. hepaticus that was phylogenetically distant from H. pylori. The H. himalayensis genome showed extensive collinearity with H. hepaticus and H. cinaedi. However, it also revealed a low degree of genome collinearity with H. pylori. The genome of 80(YS1)T comprised 1,829,936 bp, with a 39.89% GC content, a predicted genomic island, and 1,769 genes. Comparatively, H. himalayensis has more genes for functions in “cell wall/membrane/envelope biogenesis” and “coenzyme transport and metabolism” sub-branches than the other compared helicobacters, and its genome contained 42 virulence factors genes, including that encoding cytolethal distending toxin (CDT). Conclusions: We characterized the H. himalayensis 80(YS1)T genome, its phylogenetic position, and its potential pathogenicity. However, further understanding of the pathogenesis of this potentially pathogenic bacterium is required, which might help to manage H. himalayensis-induced diseases.

Download Full-text

Genomic analysis of Helicobacter himalayensis sp. nov. isolated from Marmota himalayana

10.21203/rs.3.rs-55448/v2 ◽

2020 ◽

Author(s):

Shouhui Hu ◽

Lina Niu ◽

Lei Wu ◽

Xiaoxue Zhu ◽

Yu Cai ◽

...

Keyword(s):

Gc Content ◽

Genomic Analysis ◽

Tibet Plateau ◽

Phylogenetic Position ◽

Comparative Genomic ◽

Low Degree ◽

Membrane Envelope ◽

H Pylori ◽

Potential Pathogenicity ◽

Qinghai Tibet Plateau

Abstract Background: Helicobacter himalayensis was isolated from Marmota himalayana in the Qinghai-Tibet Plateau, China, and is a new non-H. pylori species, with unclear taxonomy, phylogeny, and pathogenicity.Results: A comparative genomic analysis was performed between the H. himalayensis type strain 80(YS1) and other the genomes of Helicobacter species present in the National Center for Biotechnology Information (NCBI) database to explore the molecular evolution and potential pathogenicity of H. himalayensis. H. himalayensis 80(YS1)T formed a clade with H. cinaedi and H. hepaticus that was phylogenetically distant from H. pylori. The H. himalayensis genome showed extensive collinearity with H. hepaticus and H. cinaedi. However, it also revealed a low degree of genome collinearity with H. pylori. The genome of 80(YS1)T comprised 1,829,936 bp, with a 39.89% GC content, a predicted genomic island, and 1,769 genes. Comparatively, H. himalayensis has more genes for functions in “cell wall/membrane/envelope biogenesis” and “coenzyme transport and metabolism” sub-branches than the other compared helicobacters, and its genome contained 42 virulence factors genes, including that encoding cytolethal distending toxin (CDT).Conclusions: We characterized the H. himalayensis 80(YS1)T genome, its phylogenetic position, and its potential pathogenicity. However, further understanding of the pathogenesis of this potentially pathogenic bacterium is required, which might help to manage H. himalayensis-induced diseases.

Download Full-text

Genomic analysis of Helicobacter himalayensis sp. nov. isolated from Marmota himalayana

BMC Genomics ◽

10.1186/s12864-020-07245-y ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Shoukui Hu ◽

Lina Niu ◽

Lei Wu ◽

Xiaoxue Zhu ◽

Yu Cai ◽

...

Keyword(s):

Gc Content ◽

Genomic Analysis ◽

Tibet Plateau ◽

Phylogenetic Position ◽

Comparative Genomic ◽

Low Degree ◽

Membrane Envelope ◽

H Pylori ◽

Potential Pathogenicity ◽

Qinghai Tibet Plateau

Abstract Background Helicobacter himalayensis was isolated from Marmota himalayana in the Qinghai-Tibet Plateau, China, and is a new non-H. pylori species, with unclear taxonomy, phylogeny, and pathogenicity. Results A comparative genomic analysis was performed between the H. himalayensis type strain 80(YS1)T and other the genomes of Helicobacter species present in the National Center for Biotechnology Information (NCBI) database to explore the molecular evolution and potential pathogenicity of H. himalayensis. H. himalayensis 80(YS1)T formed a clade with H. cinaedi and H. hepaticus that was phylogenetically distant from H. pylori. The H. himalayensis genome showed extensive collinearity with H. hepaticus and H. cinaedi. However, it also revealed a low degree of genome collinearity with H. pylori. The genome of 80(YS1)T comprised 1,829,936 bp, with a 39.89% GC content, a predicted genomic island, and 1769 genes. Comparatively, H. himalayensis has more genes for functions in “cell wall/membrane/envelope biogenesis” and “coenzyme transport and metabolism” sub-branches than the other compared helicobacters, and its genome contained 42 virulence factors genes, including that encoding cytolethal distending toxin (CDT). Conclusions We characterized the H. himalayensis 80(YS1)T genome, its phylogenetic position, and its potential pathogenicity. However, further understanding of the pathogenesis of this potentially pathogenic bacterium is required, which might help to manage H. himalayensis-induced diseases.

Download Full-text

Genomic and Histological Analysis of Helicobacter Himalayensis Sp. Nov. Isolated From Marmota Himalayana to Discovery the Potential Human Pathogen

10.21203/rs.3.rs-55448/v1 ◽

2020 ◽

Author(s):

Shouhui Hu ◽

Lina Niu ◽

Lei Wu ◽

Xiaoxue Zhu ◽

Yu Cai ◽

...

Keyword(s):

Gc Content ◽

Genomic Analysis ◽

Tibet Plateau ◽

Phylogenetic Position ◽

Comparative Genomic ◽

Tissue Samples ◽

Membrane Envelope ◽

Gastrointestinal Tissue ◽

H Pylori ◽

Potential Pathogenicity

Abstract Background: Helicobacter himalayensis was isolated from Marmota himalayana in the Qinghai-Tibet Plateau, China, and is a new non-H. pylori species, with unclear taxonomy, phylogeny, and pathogenicity. Methods and results: A comparative genomic analysis was performed between the H. himalayensis type strain 80(YS1) and other the genomes of Helicobacter species present in the National Center for Biotechnology Information (NCBI) database to explore the molecular evolution and potential pathogenicity of H. himalayensis. We also compared the lesions of gastrointestinal tissue samples from H. himalayensis-positive Marmota himalayana with H. himalayensis-negative Marmota himalayana using histology. H. himalayensis 80(YS1)T formed a clade with H. cinaedi and H. hepaticus that was phylogenetically distant from H. pylori. The genome of 80(YS1)T comprised 1,829,936 bp, with a 39.9% GC content, a predicted genomic island, and 1,910 predicted proteins. Comparatively, H. himalayensis has more genes for functions in “cell wall/membrane/envelope biogenesis” and “nucleotide transport and metabolism” sub-branches than the other compared helicobacters, and its genome contained 42 virulence factors genes, including that encoding cytolethal distending toxin (CDT). Histologically, the gastrointestinal mucosa of H. himalayensis-infected Marmota himalayana showed obvious lesions, implying that H. himalayensis is pathogenic to its host. Conclusions: We characterized the H. himalayensis 80(YS1)T genome, its phylogenetic position, and its potential pathogenicity. 80(YS1)T may be pathogenic to animals or humans; however, further understanding of the pathogenesis of this potentially pathogenic bacterium is required, which might help to manage H. himalayensis-induced diseases.

Download Full-text

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.

Download Full-text

Biology and Genome Sequence of Streptococcus mutans Phage M102AD

Applied and Environmental Microbiology ◽

10.1128/aem.07726-11 ◽

2012 ◽

Vol 78 (7) ◽

pp. 2264-2271 ◽

Cited By ~ 12

Author(s):

Allan L. Delisle ◽

Ming Guo ◽

Natalia I. Chalmers ◽

Gerard J. Barcak ◽

Geneviève M. Rousseau ◽

...

Keyword(s):

Streptococcus Mutans ◽

Genome Sequence ◽

Gc Content ◽

Genomic Analysis ◽

Streptococcus Thermophilus ◽

Open Reading Frames ◽

Comparative Genomic ◽

Content Type ◽

Close Relationship ◽

Virion Structure

ABSTRACTM102AD is the new designation for aStreptococcus mutansphage described in 1993 as phage M102. This change was necessitated by the genome analysis of anotherS. mutansphage named M102, which revealed differences from the genome sequence reported here. Additional host range analyses confirmed thatS. mutansphage M102AD infects only a few serotype c strains. Phage M102AD adsorbed very slowly to its host, and it cannot adsorb to serotype e and f strains ofS. mutans. M102AD adsorption was blocked by c-specific antiserum. Phage M102AD also adsorbed equally well to heat-treated and trypsin-treated cells, suggesting carbohydrate receptors. Saliva and polysaccharide production did not inhibit plaque formation. The genome of this siphophage consisted of a linear, double-stranded, 30,664-bp DNA molecule, with a GC content of 39.6%. Analysis of the genome extremities indicated the presence of a 3′-overhangcossite that was 11 nucleotides long. Bioinformatic analyses identified 40 open reading frames, all in the same orientation. No lysogeny-related genes were found, indicating that phage M102AD is strictly virulent. No obvious virulence factor gene candidates were found. Twelve proteins were identified in the virion structure by mass spectrometry. Comparative genomic analysis revealed a close relationship betweenS. mutansphages M102AD and M102 as well as withStreptococcus thermophilusphages. This study also highlights the importance of conducting research with biological materials obtained from recognized microbial collections.

Download Full-text

Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

10.21203/rs.3.rs-822059/v1 ◽

2021 ◽

Author(s):

Jiaxin Yang ◽

Guoxiong Hu ◽

Guangwan Hu

Keyword(s):

Endangered Species ◽

Chloroplast Genome ◽

Genome Size ◽

Gc Content ◽

Genomic Analysis ◽

Single Copy ◽

Comparative Genomic ◽

Eurycorymbus Cavaleriei ◽

Cp Genome ◽

Relationship Of

Abstract Background Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. Results The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisted of Aesculus chinensis and A. wangii, strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. Conclusion This study revealed that the cp genome size of the Hippocastanoideae was generally smaller across Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.

Download Full-text

Comparative Genomic Analysis of Limosilactobacillus Pontis Reveals Genetic Characteristics of High GC Content and Potential Niches Adaptations

10.21203/rs.3.rs-969439/v1 ◽

2021 ◽

Author(s):

Qing Liu ◽

Chen Liu ◽

Weicheng Li ◽

Wenjun Liu ◽

Qing Liu

Keyword(s):

Broiler Chickens ◽

Gc Content ◽

Genomic Analysis ◽

Fermented Milk ◽

Evolutionary Strategies ◽

Comparative Genomic ◽

Genetic Characteristics ◽

Genomic Approach ◽

Application Potential ◽

Carbohydrate Enzymes

Abstract Limosilactobacillus pontis is a species of lactic acid bacteria (LAB) found in fermented milk, sourdough and broiler chickens gastrointestinal tract and so on. However, the evolutionary strategies and genomic characteristics of the species remain unknown, which limits its application. In this study, whole genome sequencing was combined with a comparative genomic approach to investigate genomic characteristics and evolutionary strategies of L. pontis; this includes three published genomic sequences and two strains isolated from fermented milk in Inner Mongolia, China. The mean genome size and GC content of L. pontis was 1.70 Mb and 53.06%, respectively. Within the LAB L. pontis has a high GC content. The phylogenetic tree based on 1,281 core genomes showed that strains from the same sources aggregated together in clusters. Genome information, average nucleotide identity values, and phylogenetic relationships amongst L. pontis from different sources indicated that strains have potential niche adaptability. Functional genomic aspects, GT2 and GT4 (glycosyltransferases, GTs) involved in the synthesis of cellulose and sucrose were the family with the largest number of carbohydrate enzymes in L. pontis, particularly strains isolated from fermented milk. It is worth mentioning that the ability of L. pontis to produce bacteriocin may increase its application potential. This study provides new insight into the genetic characteristics and potential niche adaptations of L. pontis.

Download Full-text

Comparative Genomic Analysis of Bifidobacterium Catenulatum Reveal the Genetic Divergence of its Two Subspecies from Infant and Adult Gut

10.21203/rs.3.rs-957925/v1 ◽

2021 ◽

Author(s):

Jiaqi Liu ◽

Weicheng Li ◽

Caiqing Yao ◽

Jie Yu ◽

Heping Zhang

Keyword(s):

Genetic Divergence ◽

Gc Content ◽

Genomic Analysis ◽

Glycoside Hydrolases ◽

Comparative Genomic ◽

Carbohydrate Binding ◽

Functional Difference ◽

Carbohydrate Utilization ◽

Carbohydrate Binding Modules ◽

Genomic Studies

Abstract Background: Bifidobacterium catenulatum, which includes two subspecies that B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum are usually from infant and adult gut respectively, while the genomic studies of functional difference and genetic divergence in them have been rarely reported. In this study, we analyzed 16 B. catenulatum strains through comparative genomics, including two novel sequenced strains. Results: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated and confirmed their colonizing bias in infants and adults. Comparison of general genomic characteristics revealed that the two subspecies had significantly different genomic sizes but similar GC content. Functional annotations found that they peculiarly differ in utilization of carbohydrates and amino acid. Among them, we found that carbohydrate metabolism seems to play an important role in the divergence because of their carbohydrate-active enzymes (CAZyme) present two different clustering patterns. B. catenulatum subsp. kashiwanohense have functional genes that specifically adapted to the infant gut for glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51), which specifically participated in the metabolism of Human Milk Oligosaccharides (HMOs), and specific genes fuc that related to HMOs were also detected. While B. catenulatum subsp. catenulatum rich in GH3 and glycosyltransferases 4 (GT4) tended to metabolize plant-derived glycan that may help it metabolize more complex carbohydrates (eg. xylan) in the adult intestine. Conclusions: Our findings revealed genomic evidence of carbohydrate utilization bias which may be a key leading to the genetic divergence of two subspecies of B. catenulatum.

Download Full-text

Recombination Drives Emergence of Orf Virus Diversity: Evidence From the First Complete Genome of Indian Orf Virus and Comparative Genomic Analysis

10.21203/rs.3.rs-1119090/v1 ◽

2021 ◽

Author(s):

Debasis Nayak ◽

Basanta Sahu ◽

Prativa Majee ◽

Ravi Singh ◽

Niranjan Sahoo

Keyword(s):

Complete Genome ◽

Phylogenetic Trees ◽

Small Ruminants ◽

Gc Content ◽

Genomic Analysis ◽

Central India ◽

Purifying Selection ◽

Orf Virus ◽

Comparative Genomic ◽

Virus Diversity

Abstract Contagious pustular dermatitis is a disease that primarily infects small ruminants and has the zoonotic potential evoked by a Parapoxvirus, Orf virus (ORFV). This study evaluated an ORFV outbreak in goats that arose in Madhya Pradesh, a state of central India, during 2017 by constructing phylogenetic trees and unveiling its transboundary potential. Thereafter, the complete genome of an ORFV strain named Ind/MP has revealed the presence of 139,807bp nucleotide sequences, GC content 63.7%, 132 open reading frames (ORFs) circumscribed by inverted terminal repeats (ITRs) of 3,910bp. Evolutionary parameters such as selection pressure (θ=dN/dS), nucleotide diversity (π), etc., demonstrate the ORFV exhibit purifying selection. A total of forty recombination events were observed, out of which Ind/MP strains were engaged in twenty-one recombination events indicating this strain can recombine for the generation of new variants.

Download Full-text

Isolation, characterization, and comparative genomic analysis of a phage infecting high-level aminoglycoside-resistant (HLAR) Enterococcus faecalis

PeerJ ◽

10.7717/peerj.9171 ◽

2020 ◽

Vol 8 ◽

pp. e9171 ◽

Cited By ~ 1

Author(s):

Danial Nasr Azadani ◽

Daiyuan Zhang ◽

J. Robert Hatherill ◽

David Silva ◽

Jeffrey W. Turner

Keyword(s):

Genome Sequencing ◽

Large Subunit ◽

Gc Content ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Single Locus ◽

Comparative Genomic ◽

Antibiotic Resistant ◽

High Level ◽

High Degree

Enterococcus is a genus of Gram-positive bacteria that are commensal to the gastrointestinal tracts of humans but some species have been increasingly implicated as agents of nosocomial infections. The increase in infections and the spread of antibiotic-resistant strains have contributed to renewed interest in the discovery of Enterococcus phages. The aims of this study were (1) the isolation, characterization, and genome sequencing of a phage capable of infecting an antibiotic-resistant E. faecalis strain, and (2) the comparative genomic analysis of publicly-available Enterococcus phages. For this purpose, multiple phages were isolated from wastewater treatment plant (WWTP) influent using a high-level aminoglycoside-resistant (HLAR) E. faecalis strain as the host. One phage, phiNASRA1, demonstrated a high lytic efficiency (∼97.52%). Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) showed that phiNASRA1 belongs to the Siphoviridae family of double-stranded DNA viruses. The phage was approximately 250 nm in length and its complete genome (40,139 bp, 34.7% GC) contained 62 open reading frames (ORFs). Phylogenetic comparisons of phiNASRA1 and 31 publicly-available Enterococcus phages, based on the large subunit terminase and portal proteins, grouped phage by provenance, size, and GC content. In particular, both phylogenies grouped phages larger than 100 kbp into distinct clades. A phylogeny based on a pangenome analysis of the same 32 phages also grouped phages by provenance, size, and GC content although agreement between the two single-locus phylogenies was higher. Per the pangenome phylogeny, phiNASRA1 was most closely related to phage LY0322 that was similar in size, GC content, and number of ORFs (40,139 and 40,934 bp, 34.77 and 34.80%, and 60 and 64 ORFs, respectively). The pangenome analysis did illustrate the high degree of sequence diversity and genome plasticity as no coding sequence was homologous across all 32 phages, and even ‘conserved’ structural proteins (e.g., the large subunit terminase and portal proteins) were homologous in no more than half of the 32 phage genomes. These findings contribute to a growing body of literature devoted to understanding phage biology and diversity. We propose that this high degree of diversity limited the value of the single-locus and pangenome phylogenies. By contrast, the high degree of homology between phages larger than 100 kbp suggests that pangenome analyses of more similar phages is a viable method for assessing subclade diversity. Future work is focused on validating phiNASRA1 as a potential therapeutic agent to eradicate antibiotic-resistant E. faecalis infections in an animal model.

Download Full-text