Abstract Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up optimal sampling and DNA isolation procedures is crucial for robustness reproducibility results. We performed a systematic comparison several kits, quantified their effect on bacterial gDNA quality composition estimates at all taxonomic levels. Sixteen volunteers tested three kits. All samples were consequently processed two found that choice both...

Bacteriocin production is an important characteristic of E. coli strains human origin. To date, 26 colicin and 9 microcin types have been analyzed on a molecular level allowing detection the corresponding genes. The incidence 29 bacteriocin phylogroups were tested in set 361 isolated from urinary tract infections (UTI) 411 control feces patients without bacterial gut infection. Production 17 20 individual was found UTI strains, respectively. Microcin H47 encoding determinants more often...

The study used a set of 407 human extraintestinal pathogenic E. coli strains (ExPEC) isolated from (1) skin and soft tissue infections, (2) respiratory (3) intra-abdominal (4) genital smears. was tested for bacteriocin production, prevalence virulence determinants, phylogenetic typing. Results obtained the group ExPEC were compared to data our previously published analyses 1283 fecal commensal strains. frequency bacteriocinogeny significantly higher in (63.1 %), (54.2 %; p < 0.01). Microcin...

A set of 1181 E. coli strains human fecal origin isolated in the South Moravia region Czech Republic was collected during years 2007–2010. Altogether, 17 virulence determinants and 31 bacteriocin-encoding genes were tested each them. The occurrence found to be positively correlated with factors. Based on presence factors their combinations, classified as non-pathogenic (n = 399), diarrhea-associated 179) ExPEC 603). Non-pathogenic had a low frequency bacteriocinogeny (32.6% 36.9%,...

Abstract Escherichia coli strains are classified into four main phylogenetic groups (A, B1, B2, and D) of these phylogroups differ in a number characteristics. This study tested whether human fecal E. isolates belonging to different prevalence bacteriocinogenic individual determinants. A set 1283 from patients with diseases was for the presence DNA regions allowing classification ability produce bacteriocins (23 colicins 7 microcins). Of tested, most common phylogroup B2 (38.3%) followed by...

Escherichia coli sequence type 131 (ST131) is currently one of the leading causes multidrug-resistant extraintestinal infections globally. Here, we analyzed phenotypic and genotypic characteristics 169 ST131 isolates from various sources (wildlife, wastewater, companion animals, community, hospitals) to determine whether wildlife environment share similar strains with humans, supporting transmission between different ecological niches. Susceptibility 32 antimicrobials was tested by disc...

Butyrate produced by the intestinal microbiota is essential for proper functioning of immune system. Total dependence on parenteral nutrition (PN) associated with numerous adverse effects, including severe microbial dysbiosis and loss important butyrate producers. We hypothesised that a lack gut may be compensated its supplementation in PN mixtures. tested whether i.v. administration would (a) positively modulate defence mechanisms (b) counteract PN-induced dysbiosis. Male Wistar rats were...

Abstract Colicin production in Escherichia coli ( E . ) strains represents an important trait with regard to microbial survival and competition the complex intestinal environment. A novel colicin type, Z (26.3 kDa), was described as a product of original producer, extraintestinal B1356 strain, isolated from anorectal abscess 17 years-old man. The 4,007 bp plasmid (pColZ) completely sequenced activity cza immunity czi genes were identified. are transcribed opposite directions encode for 237...

Common variable immunodeficiency (CVID) is a clinically and genetically heterogeneous disorder with inadequate antibody responses low levels of immunoglobulins including IgA that involved in the maintenance intestinal homeostasis. In this study, we analyzed taxonomical functional metagenome fecal microbiota stool metabolome cohort six CVID patients without gastroenterological symptomatology their healthy housemates. The microbiome contained higher numbers bacterial species altered abundance...

Cytokinin (CK) signalling is known to play key roles in the regulation of plant growth and development, crop yields, tolerance both abiotic stress pathogen defences, but mechanisms involved are poorly characterized dicotyledonous crops. Here identification functional characterization sensor histidine kinases homologous Arabidopsis CK receptors AHK2 AHK3 winter oilseed rape presented. Five CHASE-containing His were identified Brassica napus var. Tapidor (BnCHK1–BnCHK5) by heterologous...

Abstract Microbial communities in the active layer play a crucial role biogeochemical cycles of Antarctic pristine ecosystems. Here, 16S rRNA gene sequencing was used to investigate bacterial five different geological sites related compositional variation bedrock, including Neogene volcanic or Cretaceous rocks and marine sediments areas distinct elevation. Local variations thickness (50–80 cm) were observed on Ulu Peninsula, James Ross Island, southwest coast Vega Antarctica during sampling...

Human and animal skin is colonized by a complex microbial population. An imbalance of these microorganisms often associated with dermatological diseases. The aim this work was to describe the bacterial microbiota composition healthy dogs inflammatory lesions. Genomic DNA sequenced using primers that target V4 region 16S rRNA gene. Superficial swabs were collected from eight body areas six (n = 48) directly altered canine 16). predominantly phylum Bacillota (34.4 ± 27.2%), followed...

Escherichia albertii is a recently discovered species with limited number of well characterized strains.The aim this study was to characterize four the E. strains, which were among 41 identified strains isolated from feces living animals on James Ross Island, Antarctica, and Isla Magdalena, Patagonia.Sequencing 16S rDNA, automated ribotyping, rep-PCR used identify isolates.Phylogenetic analyses based multi-locus sequence typing showed these isolates be genetically most similar members...

Yersiniosis belongs to the common foodborne diseases around world, and frequently manifests as diarrhea that can be treated with probiotics. Colicin FY is an antibacterial agent produced by bacteria it capable of specific growth inhibition Yersinia enterocolitica, causative gastrointestinal yersiniosis. In this study, recombinant E. coli producing colicin were constructed, using both known probiotic strains EcH22 EcColinfant, newly isolated murine Ec1127 Ec1145. All inhibited pathogenic Y....

Increasing levels of antibiotic resistance among bacteria also increase the need for alternatives to conventional treatment. Pathogenic Escherichia coli represents a major diarrheic infectious agent piglets in their postweaning period; however, available measures control these infections are limited.

Abstract In the first days of life, newborns’ intestinal microbiota develops simultaneously with gut barrier and follows immunity. The mode delivery shows significant impact on microbial development and, thus, initiation tryptophan catabolism pathway. Further antibiotics (ATB) treatment mothers before or during affects metabolite composition stool caesarean- vaginal-delivered newborns. determination microbiome levels metabolites in meconium can characterize colonization a newborn. From 134...

A taxonomic study of two fluorescent Pseudomonas strains (HJ/4 T and SJ/9/1 ) isolated from calcite moonmilk samples obtained caves in the Moravian Karst Czech Republic was carried out. Results initial 16S rRNA gene sequence analysis assigned both into genus showed yamanorum 8H1 as their closest neighbour with 99.8 99.7 % similarities to HJ/4 , respectively. Subsequent rpoD rpoB gyrB housekeeping genes confirmed highest similarity isolates P. but phylogeny sequences implied that they are...

A group of four psychrotrophic bacterial strains was isolated on James Ross Island (Antarctica) in 2013. All isolates, originating from different soil samples, were collected the ice-free northern part island. They rod-shaped, Gram-stain-negative, and produced moderately slimy red-pink pigmented colonies R2A agar. polyphasic taxonomic approach based 16S rRNA gene sequencing, whole-genome MALDI-TOF MS, rep-PCR analyses, chemotaxonomic methods extensive biotyping used to clarify position these...

Long-term dysbiosis of the gut microbiome has a significant impact on colorectal cancer (CRC) progression and explains part observed heterogeneity disease. Even though shifts in normal-adenoma-carcinoma sequence were described, landscape within CRC its associations with clinical variables remain under-explored. We performed 16S rRNA gene sequencing paired tumour tissue, adjacent visually normal mucosa stool swabs 178 patients stage 0-IV to describe association variables. identified new...

The purpose of this study was to characterize the extended-spectrum β-lactamase (ESBL)-producing uropathogenic Escherichia coli (UPEC) strains isolated in South Moravia region Czech Republic.Out 109 ESBL-producing UPEC isolates, CTX-M-15-producing E. O25b-ST131 detected 55 (50.5%) and CTX-M-27-producing 40 isolates (36.7%). Most were distributed among three pulsed-field gel electrophoresis clusters characterized by low variability relative antibiotic resistance patterns, phylogroups...