MOESM1 of Phenotypic and genetic changes in the life cycle of small colony variants of Salmonella enterica serotype Typhimurium induced by streptomycin

Additional file 1: Figure S1. Dendrograms of wide-type, SCVs and revertants evaluated by MLVA and PFGE. Figure S2. Representative data on transmission electron microscopy analysis of strain morphology and the number of flagella. Figure S3. Ability of biofilm formation of revertants and WT strain

Characterization of Chinese <i>Haemophilus parasuis</i> Isolates by Traditional Serotyping and Molecular Serotyping Methods

<div><p><i>Haemophilus parasuis</i> is classified mainly through serotyping, but traditional serotyping always yields non-typable (NT) strains and unreliable results via cross-reactions. Here, we surveyed the serotype prevalence of Chinese <i>H</i>. <i>parasuis</i> isolates using traditional serotyping (gel immuno-diffusion test, GID) and molecular serotyping (multiplex PCR, mPCR). We also investigated why discrepant results between these methods were obtained, and investigated mPCR failure through whole-genome sequencing. Of the 100 isolate tested, 73 (73%) and 93 (93%) were serotyped by the GID test and mPCR, respectively, with a concordance rate of 66% (66/100). Additionally, mPCR reduced the number of NT isolates from 27 (27%) for the GID testing, to seven (7%). Eleven isolates were sequenced, including nine serotype-discrepant isolates from mPCR and GID typing (excluding strains that were NT by GID only) and two NT isolates from both methods, and their <i>in silico</i> serotypes were obtained from genome sequencing based on their capsule loci. The mPCR results were supported by the <i>in silico</i> serotyping of the seven serotype-discrepant isolates. The discrepant results and NT isolates determined by mPCR were attributed to deletions and unknown sequences in the serotype-specific region of each capsule locus. Compared with previous investigations, this study found a similar predominant serotype profile, but a different prevalence frequency for <i>H</i>. <i>parasuis</i>, and the five most prevalent serotypes or strain groups were serotypes 5, 4, NT, 7 and 13 for mPCR, and serotypes 5, NT, 4, 7 and 13/10/14 for GID. Additionally, serotype 7 was recognized as a principal serotype in this work.</p></div

General genome features of the sequenced <i>H</i>. <i>parasuis</i> isolates.

<p>General genome features of the sequenced <i>H</i>. <i>parasuis</i> isolates.</p

Summary of the capsule loci of the serotype-discrepant isolates and common NT isolates from the mPCR and GID tests.

<p>Summary of the capsule loci of the serotype-discrepant isolates and common NT isolates from the mPCR and GID tests.</p

Features of Variable Number of Tandem Repeats in <i>Yersinia pestis</i> and the Development of a Hierarchical Genotyping Scheme

<div><p>Background</p><p>Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of <i>Yersinia pestis</i> proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the <i>Y. pestis</i> genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.</p><p>Methodology/Principal Findings</p><p>Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 <i>Y. pestis</i> strains. The general features and genetic diversities of 88 VNTR loci in <i>Y. pestis</i> were analyzed with BioNumerics, and a “14+12” loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.</p><p>Conclusions/Significance</p><p>Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized “14+12” loci are highly discriminative in genotyping and source-tracing <i>Y. pestis</i> for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of <i>Y. pestis.</i></p></div

Data_Sheet_1_Genomic Variations in Probiotic Lactobacillus plantarum P-8 in the Human and Rat Gut.docx

<p>The effects of probiotics on host gastrointestinal health have become an area of particular interest in the field of probiotic research. However, the impact of the host intestinal environment on genomic changes in probiotic organisms remains largely unknown. To investigate, Lactobacillus plantarum P-8, a well-studied probiotic bacterium, was consumed by healthy human volunteers and rats. Then, the persistence and genomic stability of P-8 in the host gut were surveyed. qPCR results revealed that after the consumption of one dose, P-8 could be detected in the host gastrointestinal tract for 4–5 weeks. By contrast, after 4 successive weeks of consumption, P-8 could be detected for up to 17 weeks after consumption ceased. In total, 92 P-8 derived strains were isolated from fecal samples and their genomes were sequenced and analyzed. Comparative genomic analysis detected 19 SNPs, which showed the characteristics of neutral evolution in the core genome. In nearly half of samples (n = 39, 42%), the loss of one to three plasmids was observed. The frequent loss of plasmids indicated reductive evolution in the accessory genome under selection pressure within the gastrointestinal tract. We also observed a 609-bp 23S rRNA homologous fragment that may have been acquired from other species after intake. Our findings offer insight into the complex reactions of probiotics to the gut environment during survival in the host. The in vivo genomic dynamics of L. plantarum P-8 observed in this study will aid the commercial development of probiotics with more stable characteristics.</p

Serotype distribution of 100 Chinese isolates as determined by GID (blue) and mPCR (red).

<p>Serotype distribution of 100 Chinese isolates as determined by GID (blue) and mPCR (red).</p

Test results comparison for GID, mPCR and <i>in silico</i> serotyping of the serotype-discrepant isolates.

<p>Test results comparison for GID, mPCR and <i>in silico</i> serotyping of the serotype-discrepant isolates.</p

Comparison of the results for mPCR and GID for 100 <i>H</i>. <i>parasuis</i> isolates.

<p>Comparison of the results for mPCR and GID for 100 <i>H</i>. <i>parasuis</i> isolates.</p

Genotyping results of 97<i>Y. pestis</i> and four <i>Y. pseudotuberculosis</i> strains based on 14+12 VNTRs.

<p>The trees were built by Ward. The twelve VNTRs used for defining the sub-populations were indicated on the arrows.</p