- gasseri, 92 strains of L. - gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. - paragasseri had an open pan-genome. - Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. - Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species.. - paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.. - Lactobacillus gasseri, as one of the autochthonous microorganism colonizes the oral cavity, gastrointestinal tract and vagina of humans, has a variety of probiotic properties [1]. - ANI values were considered as a useful approach to evaluate the genetic distance, based on genomes [12, 13].. - paragasseri, based on whole- genome analysis [16].. - Pan-genome is a collection of. - 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. - Full list of author information is available at the end of the article. - The core genome consists of genes presented in all strains and is generally associated with biological functions and major phenotypic characteristics, reflect- ing the stability of the species. - And variable genome consists of genes that exist only in a single strain or a portion of strains, and is generally related to adaptation to particular environments or to unique biological char- acteristics, reflecting the characteristics of the species [17]. - Based on 16S rDNA sequencing, 92 L. - All of the 94 strains were classified into two groups, with 80 strains including L. - paragasseri strain) showing an ANI value range 97–99%, and the other group consisted of 14 strains including the type strain L. - paragasseri based on whole-genome analyses [16], therefore, other 79 strains on the same group with L. - A robust phylogenetic tree based on 1282 ortho- logues proteins was constructed (Fig. - paragasseri K7 and the other 14 strains were on the cluster with L. - 3), which was consistent with phylogenetic data based on orthologous genes. - The general information of the 80 genomes of L. - para- gasseri strains and 14 genomes of L .gasseri strains are summarized in Table 1. - para- gasseri ranged from 1.87 to 2.14 Mb, with a mean size of 1.97 Mb, and all 14 L. - sequence length of 1.94 Mb with a range of 1.87–2.01 Mb. - To further determine the function of each gene, non-redundant protein databases based on NCBI database were created, which revealed that average. - The preference of the two species codons for the start codon were predicted, and the re- sults showed that ATG, TTG and CTG in L. - According to the results of the COG an- notation, the genes were divided into 20 groups, and the details are shown in (Additional file 1: Table S1) and (Additional file 2: Table S2). - To analyze the overall approximation of the gene repertoire for L. - The results showed that the pan- genome size of all 80 strains of L. - The pan-genome size of the 14 strains of L. - gasseri was 2834 genes, and the exponential value of deduced mathematical function is <. - The number of conserved gene families constituting the core genome decreased slightly, and the extrapola- tion of the curve indicated that the core genome reached a minimum of 1256 genes in L. - gasseri, and the curve of L. - 2 The phylogenetic tree based on orthologous genes. - gasseri cluster and the blue area was the L. - The purple circle indicated the strains isolated from infant feces and the gray indicated strains isolated from adults. - The pink indicated strains from female and the green represent strains from male subjects. - 3 Neighbor-joining tree based on groEL (a) and pheS (b) gene. - paragasseri, and 13 strains of L. - gasseri consisted of two Cas1 genes, and the second Cas1 gene was located in a different region constituting a second putative CRISPR locus. - According to previous method of classification of the CRISPR subtypes, 52 Type II-A systems were detected in all the strains of L.. - 4 Pan-genome and core-genome curve of the L. - Strikingly, phylogenetic tree based on Cas1 and Cas2 proteins re- vealed that clusters consisted of only the second Cas1 and Cas2 proteins in Type I-E systems in L. - gasseri, and the Cas1 and Cas2 proteins in subtype II-A systems in both L. - paragasseri were composed of G (T/C) TTT and the DRs were weakly palindromic. - The putative RNA sec- ondary structure of the DRs in L. - paragasseri shared two variable nucleotides at the 2nd and 29th site (C/T), and the difference affected the RNA secondary structures (Fig. - Class II bac- teriocins are small heat stable peptides further subdi- vided IIa, IIb, IIc and IId based on the structure and activity of the peptides [25]. - a Phylogenetic tree based on the Ca1 protein, b Phylogenetic tree based on the Cas2 protein, c Phylogenetic tree based on the Cas9 protein. - The earliest classifications of lactobacilli were based on their carbohydrate utilization patterns. - each genome, and the distribution and abundance of GH, GT, CE family genes across the L. - paragasseri, GH137 (β-L-arabinofuranosidase) was only predicted in 5 strains, GH65, GH73, GH8, CE9 and GT51 families showed exactly same and CE12 was detected in most of the strains except L. - Notably, 12 strains of L.. - Twelve strains of L. - The height of the letters indicates the frequency of the corresponding base at that position. - f – g Predicted RNA secondary structures of the CRISPR DR in L. - paragasseri showed high diversity, but the difference was not a result of gender and age difference, and may be associated with diet habits of the host individual. - Di- versity do not correlate with gender and age and could be result of sugar diet habits of the host individual.. - through pairwise comparison at the 95% threshold, to- gether with phylogenetic analysis based on orthologous genes and house-keeping genes (pheS and groEL) were performed to ensure the species affiliations and elimi- nated the mislabeled genomes only using ANI [30].. - paragasseri, and the remained 13 (14%) strains were L. - paragasseri based on whole-genome sequence analyses as well. - paragesseri are sister taxon with high similarity but not the same species, and the cultivable “L.. - paragasseri had no preference to colonize the female or male subjects, and the strains distribution had no trend on age neither infants nor adults. - rhamnosus [33], and the average G + C content among lactobacilli genera is estimated at 42.4%. - gasseri were ana- lysed, and the pan-genome size of the 80 strains among L. - paragasseri and 14 strains of L. - paragasseri K7 were 6535 and 2834 genes, respectively, and the core genomes were 1256 and 1375 genes, re- spectively, suggesting that open pan-genome within the. - gasseri species, and the L. - In the current study, most of the L. - gasseri by 16S rDNA sequencing, while based on whole-genome analyses they were reclas- sified. - According to ANI values and phylogenetic analysis based on both orthologous genes and house- keeping genes, 13 strains and 79 strains were reclassified as L. - Pan-genome structure for L. - gasseri K7 [27]) from National Centre for Biotechnology Infor- mation (https://www.ncbi.nlm.nih.gov/) were used for comparison and the latter one has recently been re- classified as L. - and phylogenetic trees were constructed using the py- thon script (https://github.com/jvollme/fasta2phylip) and the supertree was modified using Evolgenius (http://. - The house-keeping genes, pheS [46] and groEL [47], were extracted from the genomes using BLAST (Version and the multiple alignments were carried out through Cluster-W (default parameters), and the single gene neighbor- joining trees were built by MEGA 6.0 [49], with boot- strap by a self-test of 1000 resampling.. - Open Reading Frame (ORF) prediction was performed with Glim- mer3.02 and ORFs were annotated by BLASTP analysis against the non-redundant protein databases created by BLASTP based on NCBI. - Functions of the genome- encoded proteins were categorized based on clusters of orthologous groups (COG) (http://www.ncbi.nlm.nih.. - Pan-genome computation for L. - gas- seri genomes was performed using the PGAP-1.2.1, which analysed multiple genomes based on protein se- quences, nucleotide sequences and annotation informa- tion, and performed the analysis according to the Heap’s law pan-genome model [17, 52]. - (https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder), and the CRISPR subtypes designation was based on the signature of Cas proteins [54]. - MEGA6.0 was used to perform multiple sequence alignments, and neighbor- joining trees based on Cas1, Cas2 and Cas9 were bulit.. - Analysis of the families of carbohydrate-active enzymes was carried out by using HMMER-3.1 (http://hmmer.. - The copy number of the verified enzymes were summarized in a heatmap with hierarchical clustering method and Pearson distance [35].. - CRISPR-Cas systems in L. - Functional assignment of the L. - gasseri core genome based on the COG database. - JUSRP11733), National Firs-Class Dis- cipline Program of Food Science and Technology (JUFSTR20180102) and the Jiangsu Province “ Collaborative Innovation Center for Food Safety and Qual- ity Control. - The funding body only provided research funds without any contribution in the design of the study and collection, analysis, and interpret- ation of data and in writing the manuscript.. - simulator of the human colonic microbiota. - nov., a new species of the subgenus Thermobacterium. - Use of the DNA sequence of variable regions of the 16S rRNA gene for rapid and accurate identification of bacteria in the Lactobacillus acidophilus complex. - nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses. - Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. - Comparative genomics of the lactic acid bacteria. - Comparative and functional genomics of the Lactococcus lactis taxon. - Comparative genomics of the Bifidobacterium breve taxon.. - Identification of phenotypically and genotypically related Lactobacillus strains based on nucleotide sequence analysis of the groEL, rpoB, rplB, and 16S rRNA genes. - Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt