Abstract:
:Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and de novo assemble the genomes of three Lactobacillus helveticus starter strains, raising the number of completely sequenced strains to 12. The first comparative genomics study for L. helveticus-to our knowledge-identified a core genome of 988 genes and sets of unique, strain-specific genes ranging from about 30 to more than 200 genes. Importantly, the comparison of MiSeq- and PacBio-based assemblies uncovered that not only accessory but also core genes can be missed in incomplete genome assemblies based on short reads. Analysis of the three genomes revealed that a large number of pseudogenes were enriched for functional Gene Ontology categories such as amino acid transmembrane transport and carbohydrate metabolism, which is in line with a reductive genome evolution in the rich natural habitat of L. helveticus. Notably, the functional Clusters of Orthologous Groups of proteins categories "cell wall/membrane biogenesis" and "defense mechanisms" were found to be enriched among the strain-specific genes. A genome mining effort uncovered examples where an experimentally observed phenotype could be linked to the underlying genotype, such as for cell envelope proteinase PrtH3 of strain FAM8627. Another possible link identified for peptidoglycan hydrolases will require further experiments. Of note, strain FAM22155 did not harbor a CRISPR/Cas system; its loss was also observed in other L. helveticus strains and lactobacillus species, thus questioning the value of the CRISPR/Cas system for diagnostic purposes. Importantly, the complete genome sequences proved to be very useful for the analysis of natural whey starter cultures with metagenomics, as a larger percentage of the sequenced reads of these complex mixtures could be unambiguously assigned down to the strain level.
journal_name
Front Microbioljournal_title
Frontiers in microbiologyauthors
Schmid M,Muri J,Melidis D,Varadarajan AR,Somerville V,Wicki A,Moser A,Bourqui M,Wenzel C,Eugster-Meier E,Frey JE,Irmler S,Ahrens CHdoi
10.3389/fmicb.2018.00063subject
Has Abstractpub_date
2018-01-30 00:00:00pages
63issn
1664-302Xjournal_volume
9pub_type
杂志文章abstract::This study used 16S rRNA high-throughput sequencing technology to examine the differences in gut microbiota between the Père David's deer populations in the Beijing and Shishou areas of China in order to understand the effects of ex situ conservation on the intestinal microflora in the Père David's deer. Results: On t...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.01258
更新日期:2018-06-12 00:00:00
abstract::Combatting antimicrobial resistant (AMR) using a One-Health approach is essential as various bacteria, including Escherichia coli, a common bacteria, are becoming increasingly resistant and livestock may be a reservoir. The AMR gene content of 492 E. coli, isolated from 56 pig farms across Great Britain in 2014-2015, ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.00861
更新日期:2020-05-25 00:00:00
abstract::The alarming spread of bacterial resistance to traditional antibiotics has warranted the study of alternative antimicrobial agents. Quorum sensing (QS) is a chemical cell-to-cell communication mechanism utilized by bacteria to coordinate group behaviors and establish infections. QS is integral to bacterial survival, a...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2015.00189
更新日期:2015-03-10 00:00:00
abstract::The vertebrate gut teems with a large, diverse, and dynamic bacterial community that has pervasive effects on gut physiology, metabolism, and immunity. Under natural conditions, these microbes share their habitat with a similarly dynamic community of eukaryotes (helminths, protozoa, and fungi), many of which are well-...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2018.00843
更新日期:2018-05-14 00:00:00
abstract::Traditionally, the shelf-life and safety of foods have been achieved by thermal processing. Low temperature long time and high temperature short time treatments are the most commonly used hurdles for the pasteurization of fluid foods and raw materials. However, the thermal treatments can reduce the product quality and...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2016.01132
更新日期:2016-08-03 00:00:00
abstract::Plants shape distinct, species-specific microbiomes in their rhizospheres. A main premise for evaluating microbial communities associated with root-soil compartments is their successful separation into the rhizosphere (soil-root interface), the rhizoplane (root surface), and the endosphere (inside roots). We evaluated...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.00773
更新日期:2016-05-24 00:00:00
abstract::In this study, Taisui TS-2007S, a previously unidentified biological object discovered in soil in China, was identified. TS-2007S was shown to contain abundant carbohydrates but a scarcity of protein, fat, and minerals. The exopolymers of TS-2007S showed FT-IR spectra that were similar to those of xanthan gum (XG) but...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.592034
更新日期:2020-11-11 00:00:00
abstract::To estimate and predict the transmission dynamics of respiratory viruses, the estimation of the basic reproduction number, R0, is essential. Recently, approximate Bayesian computation methods have been used as likelihood free methods to estimate epidemiological model parameters, particularly R0. In this paper, we expl...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00343
更新日期:2018-03-02 00:00:00
abstract::Vanillin is a potent fermentation inhibitor derived from the lignocellulosic biomass in biofuel production, and high concentrations of vanillin result in the pronounced repression of bulk translation in Saccharomyces cerevisiae. Studies on genes that are efficiently translated even in the presence of high concentratio...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.01059
更新日期:2016-07-06 00:00:00
abstract::Omeprazole was shown to improve the anti-cancer effects of the nucleoside analogue 5-fluorouracil. Here, we combined omeprazole with the antiviral nucleoside analogues ribavirin and acyclovir. Omeprazole did not affect the antiviral effects of ribavirin in non-toxic concentrations up to 80 μg/mL but increased the acyc...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.02790
更新日期:2019-12-03 00:00:00
abstract::Although canine adenovirus (CAdV) is highly prevalent in dogs, there is currently a lack of a quick diagnostic method. In this study, we developed a rapid immunochromatographic strip (ICS) assay using colloidal gold coupled to CAdV-2-specific monoclonal antibodies (mAbs). BALB/c mice were immunized with a purified CAd...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.02882
更新日期:2019-12-11 00:00:00
abstract::Staphylococcus epidermidis is one of the most prevalent pathogens implicated in catheter-related bloodstream infections (CRBSI) at an academic hospital in Pretoria, South Africa. Little is known about the clonality and the prevalence of antibiotic resistance and virulence genes in S. epidermidis (e.g., icaAB, IS256, m...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00417
更新日期:2018-03-07 00:00:00
abstract::The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chai...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2015.00152
更新日期:2015-03-03 00:00:00
abstract::Alternative sigma factors have led the core RNA polymerase (RNAP) to recognize different sets of promoters to those recognized by the housekeeping sigma A-directed RNAP. This change in RNAP promoter selectivity allows a rapid and flexible reformulation of the genetic program to face environmental and metabolic stimuli...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2020.01761
更新日期:2020-09-15 00:00:00
abstract::Non-Saccharomyces yeasts are a heterogeneous microbial group involved in the early stages of wine fermentation. The high enzymatic potential of these yeasts makes them a useful tool for increasing the final organoleptic characteristics of wines in spite of their low fermentative power. Their physiology and contributio...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.00012
更新日期:2016-01-20 00:00:00
abstract::Label-free bacterial colony phenotyping technology called BARDOT (Bacterial Rapid Detection using Optical scattering Technology) provided successful classification of several different bacteria at the genus, species, and serovar level. Recent experiments with colonies of Bacillus species provided strikingly different ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2014.00537
更新日期:2014-10-14 00:00:00
abstract::Genome duplication requires the coordinated activity of a multi-component machine, the replisome. In contrast to the background of metabolic diversity across the bacterial domain, the composition and architecture of the bacterial replisome seem to have suffered few changes during evolution. This immutability underline...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2015.00562
更新日期:2015-06-05 00:00:00
abstract::Bacteria are the highest abundant microorganisms in the soil. To investigate bacteria community structures, diversity, and functions, contrasting them in four different seasons all the year round with/within two different forest type soils of China. We analyzed soil bacterial community based on 16S rRNA gene sequencin...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.01693
更新日期:2018-07-31 00:00:00
abstract::Klebsiella pneumoniae (K. pneumoniae) spp. are important nosocomial and community-acquired opportunistic pathogens, which cause various infections. We observed that K. pneumoniae strain K7 abruptly mutates to rough-type phage-resistant phenotype upon treatment with phage GH-K3. In the present study, the rough-type pha...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.01189
更新日期:2019-05-28 00:00:00
abstract::The intention of this study was to investigate the inactivation of endospores by a combined thermal and pulsed electric field (PEF) treatment. Therefore, self-cultivated spores of Bacillus subtilis and commercial Geobacillus stearothermophilus spores with certified heat resistance were utilized. Spores of both strains...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2015.00400
更新日期:2015-05-06 00:00:00
abstract::Acinetobacter baumannii is emerging as a challenging nosocomial pathogen due to its rapid evolution of antibiotic resistance. We report characterization of two novel bacteriophages, PBAB08 and PBAB25, infecting clinically isolated, multidrug-resistant (MDR) A. baumannii strains. Both phages belonged to Myoviridae of C...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00696
更新日期:2018-04-10 00:00:00
abstract::Molecular signaling networks in the actinorhizal rhizosphere select host-compatible Frankia strains, trigger the infection process and eventually the genesis of nitrogen-fixing nodules. The molecular triggers involved remain difficult to ascertain. Root exudates (RE) are highly dynamic substrates that play key roles i...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.00720
更新日期:2017-05-02 00:00:00
abstract::In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between di...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2016.01234
更新日期:2016-08-08 00:00:00
abstract::Two-component regulatory systems (TCSSs) are key regulatory elements responsible for the adaptation of bacteria to environmental stresses. A classical TCSS is typically comprised of a sensory histidine kinase and a corresponding response regulator. Here, we used homologous recombination to construct a Mycobacterium sm...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.02145
更新日期:2017-11-03 00:00:00
abstract::In this study we investigated how the source of organic carbon (Corg) and nitrogen (Norg) affects the interactions between fungi of the genus Morchella and bacteria dispersing along their hyphae (fungal highways; FH). We demonstrated that bacteria using FH increase the hydrolysis of an organic nitrogen source that onl...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.00124
更新日期:2019-03-01 00:00:00
abstract::Rapidly changing concentrations of substrates frequently occur during large-scale microbial cultivations. These changing conditions, caused by large mixing times, result in a heterogeneous population distribution. Here, we present a powerful and efficient modeling approach to predict the influence of varying substrate...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.01195
更新日期:2017-06-28 00:00:00
abstract::The yeast cell is surrounded by a cell wall conferring protection and resistance to environmental conditions that can be harmful. Identify the molecular cues (genes) which shape the biochemical composition and the nanomechanical properties of the cell wall and the links between these two parameters represent a major i...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.01806
更新日期:2017-09-27 00:00:00
abstract::The purpose of present study was the simulation of an oil spill accompanied by burial of significant amount of petroleum hydrocarbons (PHs) in coastal sediments. Approximately 1000 kg of sediments collected in Messina harbor were spiked with Bunker C furnace fuel oil (6500 ppm). The rapid consumption of oxygen by aero...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2014.00162
更新日期:2014-04-14 00:00:00
abstract::Bacterial microcompartments (BMCs) are proteinaceous organelles that optimize specific metabolic pathways referred to as metabolosomes involving transient production of toxic volatile metabolites such as aldehydes. Previous bioinformatics analysis predicted the presence of BMCs in 23 bacterial phyla including foodborn...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.02660
更新日期:2019-11-15 00:00:00
abstract::Staphylococcus aureus (S.aureus) resistance, considered a dilemma for the clinical treatment of this bacterial infection, is becoming increasingly intractable. Novel anti-virulence strategies will undoubtedly provide a path forward in combating these resistant bacterial infections. Sortase A (SrtA), an enzyme responsi...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.01715
更新日期:2017-09-06 00:00:00