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A reliable and standardized classification of Listeria monocytogenes is important for accurate strain identification during outbreak investigations. Current whole-genome sequencing (WGS) based approaches for strain characterization are either difficult to standardize, rendering them less suitable for data exchange, or are not freely available. Thus, we developed a portable and open-source tool Haplo-ST to improve standardization and provide maximum discriminatory potential to WGS data tied to a multi-locus sequence typing (MLST) framework. Haplo-ST performs whole-genome MLST (wgMLST) for L. monocytogenes while allowing for data exchangeability worldwide. This tool takes in (i) raw WGS reads as input, (ii) cleans the raw data according to us.
All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feeding termite species using 16S rRNA gene amplicon sequencing. We found that the composition of bacterial communities differs among termite bodies, termite galleries, and control wood fragments devoid of termite activities, in a species-specific manner. Termite galleries were enriched in bacterial OTUs belonging to Rhizobiales and Actinobacteria, which were often shared by several termite species. Th.
Rumen-protected glucose (RPG) plays an important role in alleviating the negative energy balance of dairy cows. This study used a combination of rumen microbes 16S and metabolomics to elucidate the changes of rumen microbial composition and rumen metabolites of different doses of RPG's rumen degradation part in early lactation dairy cows. Twenty-four multiparous Holstein cows in early lactation were randomly allocated to control (CON), low RPG (LRPG), medium RPG (MRPG) or high RPG (HRPG) groups in a randomized block design. The cows were fed a basal total mixed ration diet with 0, 200, 350 and 500 g RPG per cow per day, respectively. Rumen fluid samples were analyzed using Illumina MiSeq sequencing and ultrahigh-performance liquid chromatog.
Stenotrophomonas maltophilia is one of the most frequently isolated multidrug resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis patients and is frequently isolated from wounds, infected tissues or catheter surfaces. On these diverse surfaces S. maltophilia lives in single or multi-species biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4 and Sm2 - Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variab.
KfrA of the broad host range RA3 plasmid is an alpha-helical DNA-binding protein that acts as a transcriptional autoregulator. KfrA RA3 operator site overlaps the kfrA promoter and is composed of five 9 bp repeats (DR). Here, the biological properties of KfrA were studied using both in vivo and in vitro approaches. Localization of DNA binding helix-turn-helix motif (HTH) was mapped to the N29-R52 region by protein structure modelling and confirmed by the alanine scanning. KfrA repressor ability depended on the number and orientation of DRs in the operator, as well as the ability of the protein to oligomerize. Long alpha-helical tail of residues 54-355, was shown to be involved in the self-interactions whereas 54-177 region was involved in h.
The atmosphere contains diverse living microbes, of which the heterotrophic community has been the most studied. Microbes with other trophic modes, such as photoautotrophy, have received much less attention. Here, culture-independent and dependent methods were used to examine the presence and diversity of oxygenic photoautotrophic microbes in clouds and rain collected at or around puy de Dôme Mountain, central France. Cloud water was collected from the summit of puy de Dôme (1465 m above sea level (a.s.l.)) for cultivation and metagenomic analysis. Cyanobacteria, diatoms, green algae, and other oxygenic photoautotrophs were found to be recurrent members of clouds, while green algae affiliated with the Chlorellaceae were successfully culture.
The occurrence of viable but nonculturable (VBNC) bacteria poses potential risk to food safety due to failure in conventional colony detection. In this study, the induction of VBNC Staphylococcus aureus was conducted by exposure to an atmospheric-pressure air dielectric barrier discharge-nonthermal plasma (DBD-NTP) treatment with an applied energy of 8.1 KJ. The stress resistance profiles and pathogenicity of VBNC S. aureus were further evaluated. We found that VBNC S. aureus showed comparable tolerance towards heat, acid and osmosis challenges compared with culturable S. aureus . While VBNC S. aureus exhibited enhanced resistance to oxidative and antibiotic stress, relating to the mechanisms of cellular energy depletion, antioxidant respon.
Bacteria can survive antibiotic treatment both by acquiring antibiotic resistance genes, and through mechanisms of tolerance that are based on phenotypic changes and the formation of metabolically inactive cells. Here, we report an Enterococcus faecalis strain ( E. faecalis UM001B) isolated from a cystic fibrosis patient that has no increase in resistance but extremely high-level tolerance to ampicillin, vancomycin, and tetracycline. Specifically, the percentage of cells that survive 3.5-h antibiotic treatment (at 100 μg ⋅mL -1 ) is 25.4 ± 4.3% and 51.9 ± 4.0% for ampicillin and tetracycline, respectively; and vancomycin does not exhibit any significant killing. Consistent with the change in antibiotic susceptibility, UM001B is found to hav.
Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhance natural microbial degradation in soils. However, little is known about how this initial microbiota influences the rhizodegradation outcome in a context of different soil microbiotas. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this, we planted ℗ or not (NP) balsam poplars ( Populus balsamifera ) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg -1 of phenanthr.
Hexachlorobenzene (HCB), as one of the persistent organic pollutants (POPs) and a possible human carcinogen, is especially resistant to biodegradation. In this study, HcbA1A3, a distinct flavin-N5-peroxide utilizing enzyme and the sole known naturally occurring aerobic HCB dechlorinase, was biochemically characterized. Its apparent preference for HCB in binding affinity determined that HcbA1 could only oxidize HCB rather than less chlorinated benzenes such as pentachlorobenzene and tetrachlorobenzenes. In addition, the crystal structure of HcbA1 and its complex with FMN were resolved, revealing HcbA1 as a new member of the bacterial luciferase-like family. Compared with its close homologues, a much smaller substrate-binding pocket of HcbA1
Waterborne pathogenic diseases are public health issues, especially for people staying in a remote environment such as Antarctica. After repeated detection of Legionella by PCR from the shower room of Syowa Station, the Japanese Antarctic research station, we wanted to understand the occurrence of waterborne pathogens, especially Legionella , in the station and their potential sources. In this study, we analyzed water and biofilm samples collected from the water facilities of Syowa Station, as well as water samples from surrounding glacier lakes, by 16S rRNA gene-based amplicon sequencing. For Legionella spp., we further attempted to obtain a detailed community structure by using genus-specific primers. The results showed that potential pat.
Heterotrophic microbes play a key role in remineralizing organic material in the coastal ocean. While there is a significant body of literature examining heterotrophic bacterioplankton and phytoplankton communities, much less is known about the diversity, dynamics, and ecology of eukaryotic heterotrophs. Here we focus on the Labyrinthulomycetes, a fungus-like protistan group whose biomass can exceed that of the bacterioplankton in coastal waters. We examined their diversity and community structure in a weekly temperate coastal ocean time series. Their seasonal community patterns were related to temperature, insolation, dissolved inorganic carbon, fungal abundance, ammonia, chlorophyll a , pH, and other environmental variables. Similar to th.
In recent years, community-acquired Clostridium difficile infection (CA-CDI) has emerged as a significant health problem, accounting for ~50% of all CDI cases. We hypothesised that the home garden environment could contribute to the dissemination of C. difficile spores in the community and investigated 23 homes in 22 suburbs of Perth, Western Australia. We identified a high prevalence of toxigenic C. difficile in this environment. In total, 97 samples consisting of soil (n=48), compost (n=15), manure (n=12) and shoe sole swabs (n= 22) were collected. All samples were cultured anaerobically on C. difficile ChromID agar and enriched in brain heart infusion broth, and isolates were characterised by toxin gene PCR and PCR ribotyping. Two-thirds.
Phosphorus ℗ is an essential nutrient for the gut bacteria and the host. Nevertheless, little information exists to what extent an improved P availability in the small intestine leads to functional adaptations in bacterial metabolic pathways in the large intestine. Therefore, we investigated the changes in the taxonomic and functional bacterial metagenome in cecal digesta of growing pigs fed diets containing phytase and/or cereals treated with 2.5% lactic acid (LA) for 19 days (n=8/diet) using shotgun metagenome sequencing. Especially the phytase supplementation resulted in distinct bacterial communities, affecting almost all major bacterial families, whereas functional changes were less dramatic among feeding groups. While phytase decrease.
Listeria monocytogenes is a foodborne pathogen that causes high rates of hospitalization and mortality in people infected. Contamination of fresh, ready to eat produce by this pathogen is especially troubling because of the ability of this bacterium to grow on produce under refrigeration temperatures. In this study, we created a library of over 8,000 plant phyllosphere associated bacteria (PPAB) and screened them for the ability to inhibit the growth of L. monocytogenes in an in vitro fluorescence based assay. One isolate, later identified as Bacillus amyloliquefaciens ALB65, was able to inhibit the fluorescence of L. monocytogenes by > 30-fold in vitro . B. amyloliquefaciens ALB65 was also able to grow, persist and reduce the growth of L.
Gardnerella vaginalis is described as a common anaerobic vaginal bacterium whose presence may correlate with vaginal dysbiotic conditions. In the current study, we performed phylogenomic analyses of 72 G. vaginalis genome sequences, revealing noteworthy genome differences underlying a polyphyletic organization of this taxon. Particularly, the genomic survey revealed that this species may actually include nine distinct genotypes (GGtype1-9). Furthermore, the observed link among sialidase encoded protein and phylogenomic grouping, provided clues of a connection between virulence potential and the evolutionary history of this microbial taxon. In detail, based on the outcomes of these in silico analyses, GGtype3, GGtype7, GGtype8, and GGtype9 a.
Genomic data reveal single nucleotide polymorphism (SNPs) which may carry in- formation about the evolutionary history of bacteria. However, it remains unclear what inferences about selection can be made from genomic SNP data. Bacterial species are often sampled during epidemic outbreaks, or within hosts through the course of chronic infections. SNPs obtained from genomic analysis of this data are not necessarily fixed. Treating them as fixed during analysis by using measures such as dN/dS may lead to incorrect inferences about the strength and direction of se- lection. In this study, we consider data from a range of whole genome sequencing studies of bacterial pathogens, and explore patterns of non-synonymous variation to assess whether ev.
The ‘lactobacilli’ to date encompass more than 270 closely related species that were recently re-classified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related, yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA-based amplicon sequencing have significant limitations (high cost, low resolution, etc.). Here, we generated a lactobacilli phylogeny based on phenylalanyl-tRNA synthetase ( pheS ) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of.
Methomyl [Bis [1-methylthioacetaldehyde-O-( N -methylcarbamoyl) oximino] sulfide] is a highly toxic oxime carbamate insecticide. Several methomyl-degrading microorganisms have been reported so far, but the role of specific enzymes and genes in this process is still unexplored. In this study, a protein annotated as a carbamate C-N hydrolase was identified in the methomyl-degrading strain Aminobacter aminovorans MDW-2, and the encoding gene was termed as ameH . A comparative analysis between the mass fingerprints of AmeH and deduced proteins of strain MDW-2 genome revealed AmeH to be a key enzyme of the detoxification degradation step of methomyl. The results also demonstrated that AmeH was a functional homodimer with a subunit molecular mass.
Environmental sanitation in food manufacturing plants promotes food safety and product microbial quality. However, the development of experimental models remains a challenge due to the complex nature of the commercial cleaning processes, which include spraying water and sanitizer on equipment and structural surfaces within manufacturing space. Although simple in execution, the physical driving forces are difficult to simulate in a controlled laboratory environment. Here, we present a bench-scale bioreactor system which mimics the flow conditions in environmental sanitation programs. We applied computational fluid dynamic (CFD) simulations to obtain fluid flow parameters which better approximate and predict industrial outcomes. According to

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