Genome-wide evidence of positive selection in Bacteroides fragilis

Yoshizaki, Sumio; Umemura, Toshiaki; Tanaka, Kaori; Watanabe, Kunitomo; Hayashi, Masahiro; Muto, Yoshinori

doi:10.1016/j.compbiolchem.2014.09.001

Cited by 8 publications

(3 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Advantageous point mutations enhance bacterial physiological fitness or virulence factor profiles appropriate to survival under various conditions [11]. Genome-wide analyses of positive selection associated with increased rates of point mutations in specific genes has been reported for several bacteria, including Bacteroides fragilis [12] , Escherichia coli [13, 14], Mycobacterium tuberculosis [15] , Salmonella serotypes [16] and Pasteurella multocida [17]. To date reports of positive selection in Leptospira remain scarce, and there is still a lack of genomic information for Leptospira isolates recovered from asymptomatic animals.…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

et al. 2019

View full text Add to dashboard Cite

Background Leptospirosis is an emerging infectious disease worldwide that can cause high morbidity and mortality rates in humans and animals. The causative spirochetes have reservoirs in mammalian hosts, but there has been limited analysis of the genomes of isolates recovered from animals. The aims of this study were to characterize genomic features of two Leptospira interrogans strains recently isolated from asymptomatic dogs in Thailand (strains CUDO5 and CDUO8), and to perform comparative genome analyses with other strains. Molecular adaptive evolution in L. interrogans as signaled by positive selection also was analyzed. Results Whole genome sequence analysis revealed that strains CUDO5 and CUDO8 had genome sizes of approximately 4.9 Mbp with 35.1% GC contents. Using monoclonal antibodies, strains CUDO5 and CUDO8 were identified as serovars Paidjan and Dadas, respectively. These strains harbored genes known to be associated with acute and chronic infections. Using Single Nucleotide Polymorphisms phylogeny (SNPs) with 97 L. interrogans strains, CUDO5 and CUDO8 had closest genetic relatedness with each other. Nevertheless, the serovar determinant region ( rfb locus) showed variations in the genes encoding sugar biosynthesis. Amongst 13 representative L. interrogans strains examined for molecular adaptive evolution through positive selection under the site-model of Phylogenetic Analysis of Maximum Likelihood, genes responsible for iron acquisition ( tlyA and hbpA ), motility ( fliN2 , flgK , and flhB ) and thermal adaptation ( lpxD1 ) were under increased selective pressure. Conclusions L. interrogans serovar Paidjan strain CUDO5 and serovar Dadas strain CUDO8 had close genetic relatedness as analyzed by SNPs phylogeny. They contained genes with established roles in acute and chronic leptospirosis. The rfb locus in both serovars showed gene variation associated with sugar biosynthesis. Positive selection analysis indicated that genes encoding factors involved in motility, temperature adaptation, and iron acquisition were under strong positive selection in L. interrogans . These may be associated with adaptation in the early stages of infection. Electronic supplementary material The online version of this article (10.1186/s12864-019-5562-z) contains supplementary material, which is available to authorized users.

show abstract

Section: Introductionmentioning

confidence: 99%

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Further studies will be required to determine if the association holds in a larger study population and if they are direct associations driven by individual species or indirectly driven by alterations in networks of bacterial communities. It will also be important to evaluate if, like enterotoxigenic strains of E. coli and B. fragilis , certain species traditionally considered to reflect a healthy microbiome, have undergone adaptive evolution due to environmental pressures (i.e., bacterial community changes or interactions with host immune system) resulting in positive selection of virulence genes [[103], [104], [105]].…”

Section: Discussionmentioning

confidence: 99%

Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus

et al. 2019

View full text Add to dashboard Cite

BackgroundHIV-1 infection and physiological aging are independently linked to elevated systemic inflammation and changes in enteric microbial communities (dysbiosis). However, knowledge of the direct effect of HIV infection on the aging microbiome and potential links to systemic inflammation is lacking.MethodsIn a cross-sectional study of older people living with HIV (PLWH) (median age 61.5 years, N = 14) and uninfected controls (median 58 years, n = 22) we compared stool microbiota, levels of microbial metabolites (short-chain fatty acid levels, SCFA) and systemic inflammatory biomarkers by HIV serostatus and age.FindingsHIV and age were independently associated with distinct changes in the stool microbiome. For example, abundances of Enterobacter and Paraprevotella were higher and Eggerthella and Roseburia lower among PLWH compared to uninfected controls. Age-related microbiome changes also differed by HIV serostatus. Some bacteria with inflammatory potential (e.g. Escherichia) increased with age among PLWH, but not controls. Stool SCFA levels were similar between the two groups yet patterns of associations between individual microbial taxa and SCFA levels differed. Abundance of various genera including Escherichia and Bifidobacterium positively associated with inflammatory biomarkers (e.g. soluble Tumor Necrosis Factor Receptors) among PLWH, but not among controls.InterpretationThe age effect on the gut microbiome and associations between microbiota and microbial metabolites or systemic inflammation differed based on HIV serostatus, raising important implications for the impact of therapeutic interventions, dependent on HIV serostatus or age.

show abstract

“…We executed the GARD analysis using the general reversible model (GTR), and we employed a general discrete distribution that has four rate classes. We performed the Kishino-Hasegawa test [ 41 ] as it is used in the GARDProcess.bf batch file of the HYPHY package, as described [ 42 ] to identify the statistically significant recombination breakpoints.…”

Section: Methodsmentioning

confidence: 99%

Molecular Evolution of the TET Gene Family in Mammals

Akahori

Guindon

Yoshizaki

et al. 2015

IJMS

Self Cite

View full text Add to dashboard Cite

Ten-eleven translocation (TET) proteins, a family of Fe2+- and 2-oxoglutarate-dependent dioxygenases, are involved in DNA demethylation. They also help regulate various cellular functions. Three TET paralogs have been identified (TET1, TET2, and TET3) in humans. This study focuses on the evolution of mammalian TET genes. Distinct patterns in TET1 and TET2 vs. TET3 were revealed by codon-based tests of positive selection. Results indicate that TET1 and TET2 genes have experienced positive selection more frequently than TET3 gene, and that the majority of codon sites evolved under strong negative selection. These findings imply that the selective pressure on TET3 may have been relaxed in several lineages during the course of evolution. Our analysis of convergent amino acid substitutions also supports the different evolutionary dynamics among TET gene subfamily members. All of the five amino acid sites that are inferred to have evolved under positive selection in the catalytic domain of TET2 are localized at the protein’s outer surface. The adaptive changes of these positively selected amino acid sites could be associated with dynamic interactions between other TET-interacting proteins, and positive selection thus appears to shift the regulatory scheme of TET enzyme function.

show abstract

Genome-wide evidence of positive selection in Bacteroides fragilis

Cited by 8 publications

References 47 publications

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus

Molecular Evolution of the TET Gene Family in Mammals

Contact Info

Product

Resources

About