scholarly journals Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 70 ◽  
Author(s):  
Shuo Wang ◽  
Bo Yang ◽  
R. Paul Ross ◽  
Catherine Stanton ◽  
Jianxin Zhao ◽  
...  
Keyword(s):  
Intestinal Tract ◽  
Great Influence ◽  
Gc Content ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Carbohydrate Utilization ◽  
Comparative Genomics Analysis ◽  
Lactobacillus Ruminis ◽  
Gains And Losses

Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.

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

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.

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

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9171 ◽  
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.

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

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.

Molecular detection of the index case of a subclinical Salmonella Kentucky epidemic on a dairy farm

2014 ◽  
Vol 143 (4) ◽  
pp. 682-686 ◽  
Author(s):  
B. J. HALEY ◽  
M. ALLARD ◽  
E. BROWN ◽  
E. HOVINGH ◽  
J. S. KARNS ◽  
...  
Keyword(s):  
Intestinal Tract ◽  
Molecular Detection ◽  
Index Case ◽  
Dairy Farm ◽  
Genomic Analysis ◽  
Pcr Primers ◽  
Comparative Genomic Analysis ◽  
Foodborne Illness ◽  
Comparative Genomic ◽  
Epidemic Strain

SUMMARYSalmonella enterica commonly colonizes the intestinal tract of cattle and is a leading cause of foodborne illness. A previously described investigation into the prevalence of S. enterica on a dairy farm revealed an 8-year-long asymptomatic S. enterica epidemic caused by serotypes Cerro and Kentucky in the lactating herd. To investigate the source of the S. Kentucky strains, the genomes of two S. Kentucky isolates were sequenced; one collected prior to the epidemic (2004) and one collected during the epidemic (2010). Comparative genomic analysis demonstrated significant polymorphisms between the two strains. PCR primers targeting unique and strain-specific regions were developed, and screening of the archived isolates identified the index case of the asymptomatic S. Kentucky epidemic as a heifer that was raised off-site and transported onto the study farm in 2005. Analysis of isolates collected from all heifers brought onto the farm demonstrated frequent re-introduction of clones of the epidemic strain suggesting transmission of pathogens between farms might occur repeatedly.

scholarly journals Comparative genomic analysis demonstrates that true reinfection following SARS-CoV-2 infection is possible

2021 ◽  
pp. 100015
Author(s):  
Eamon O. Murchu ◽  
Sinead O'Neill ◽  
Paula Byrne ◽  
Cillian De Gascun ◽  
Michelle O'Neill ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

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

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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