Studying permafrost in Antarctica provides insights into climate history, soil and rock structure, and a unique biodiversity with potential impact on ecosystems. Although a great deal of effort has been devoted to the microbiological composition of permafrost soils, the objective pursued in this study is, for the first time, to examine soil and rock samples collected from a 350 cm deep core drilled near the Johann Gregor Mendel Czech Antarctic Station on the Ulu Peninsula of James Ross Island, to study the effect of geochemical properties on microbial composition and diversity and vice versa. We collected samples from the profile starting on the ground surface down to 350 cm depth and correlated information from metagenomic 16S rRNA gene analysis and geochemical data. The 80-cm-thick active layer had a distinct bacterial composition different from the Pseudomonadota-rich permafrost layer, with Actinomycetota, Acidobacteriota, Chloroflexota, and Verrucomicrobiota being the prevalent phyla. Throughout the core, the higher bacterial diversity was positively associated with the sand fraction and intensive weathering. The highest identified diversity in the deepest part of the active layer (transient active layer) suggests that the bacteria here have been gradually cryopreserved, possibly accumulating from the upper layers. In summary, the identified interface between the active layer and permafrost, as well as the transition within the permafrost from Holocene marine sediments to underlying Cretaceous sedimentary rocks (deeper than similar to 260 cm), had the greatest influence on the bacterial composition. Decadal records of soil temperature and active layer thickness predict more significant interactions in the future between bacterial communities in the current active layer and mineral weathering bacteria that are typical of permafrost.

IntroductionHuman and animal skin is colonized by a complex microbial population. An imbalance of these microorganisms is often associated with dermatological diseases.MethodsThe aim of this work was to describe the skin bacterial microbiota composition of healthy dogs and dogs with inflammatory skin lesions. Genomic DNA was sequenced using primers that target the V4 region of the bacterial 16S rRNA gene. Superficial skin swabs were collected from eight body areas of six healthy dogs (n = 48) and directly from inflammatory altered canine skin (n = 16).ResultsThe skin of healthy dogs was predominantly colonized by phylum Bacillota (34.4 ± 27.2%), followed by Actinomycetota (32.2 ± 20.3%), Pseudomonadota (16.4 ± 12.2%), and Bacteroidota (8.7 ± 11.6%). At the level of genera, Streptococcus spp. (19.4 ± 26.1%) was the most abundant genus across all samples collected from healthy skin, followed by Curtobacterium (5.4 ± 12.1%), Bacteroides (5.2 ± 11.1%) and Corynebacterium_1 (4.3 ± 13.2%). More specifically, Streptococcus spp. was the most abundant on the chin (49.0 ± 35.5%), nose (37.9 ± 32.1%), perianal region (21.1 ± 28.2%), abdomen (11.0 ± 12.8%), dorsal back (12.4 ± 10.3%) and interdigital area (5.5 ± 2.2%). Curtobacterium spp. was predominant on inner pinna (17.8 ± 24.8%) and axilla (6.7 ± 10.8%). Alpha diversity analysis (Shannon index) showed maximum on interdigital area but minimum on a chin (p-value: 0.0416). Beta diversity analysis showed clustering across samples from the individual skin sites but also across samples collected from individual dogs. Staphylococcus spp. was the most abundant genus in 12/16 samples collected from inflammatory skin. In addition, a lower bacterial diversity was observed in samples from skin lesions compared to samples from healthy canine skin.DiscussionThe results confirm the fact that the microbiome of healthy skin is very diverse. Compared to other studies, streptococci predominated on healthy canine skin. Shannon index showed only minor differences in diversity between different parts of canine skin. Results of beta-diversity showed the fact that the main force driving the skin microbiota composition is the individual, followed by the skin site. On the area of skin lesions, dysbiosis was observed with a significant predominance of staphylococci.

Early life events significantly influence the developing gut microbiome, yet the response time and duration of microbiome changes to specific factors, such as vaccination or solid food introduction, remain unclear. Consequently, determining the optimal sampling frequency to monitor gut microbiome development is challenging. This study monitored gut microbiome plasticity using 16S rRNA gene sequencing almost daily in one infant (A) and weekly in 12 others (B-M) during their first year. Changes were linked to external factors and their duration analyzed. Three bacterial colonization groups emerged: "Early-life colonizers," "Re-appearing colonizers," and "Later-colonizers." Weekly sampling underestimated microbiome variability, as individual samples within the same week differed by over 1 Shannon index, and most of the weekly coefficients of variation of different alpha diversity indices in the first 23 weeks were higher than 10 %. Alpha diversity variability decreased with age, but beta diversity variability remained high. Key events like solid food introduction and probiotics caused gradual but significant bacterial composition changes, with effects varying among infants. Sparse weekly sampling hindered a detailed understanding of the impact of maternal microbiome, diet, probiotics, vaccinations, and unforeseen variables. Analysis of weekly variability in alpha and beta diversity suggests that such rare sampling may not be sufficient in terms of the outcomes of interest.

Microbial communities in the active layer play a crucial role in the biogeochemical cycles of Antarctic pristine ecosystems. Here, 16S rRNA gene sequencing was used to investigate bacterial communities in active layer of five different geological sites related to the compositional variation of the geological bedrock, including Neogene volcanic or Cretaceous rocks and or marine sediments areas of distinct elevation. Local variations in the thickness of the active layer (50–80 cm) were observed on the Ulu Peninsula, James Ross Island, and the southwest coast of Vega Island, Antarctica during sampling in 2019. High bacterial diversity was detected in all sampling sites. Significant site effects on bacterial composition with increased Chloroflexota and decreased Flavobacteriaceae were only observed between the highest elevation Johnson Mesa 2 plateau and coastal areas. The overall effect of the depth was reflected by the increased of e.g., Cyanobacteria , Propionibacterium , Staphylococcus in the upper surface and Chloroflexota , Acidobacteriota , Actinomycetota at depths below 30 cm. The huge number of unassigned bacteria indicated a potential source of new bacterial species and their ecological role in this extreme environment. For the first time, we showed that the effect of depth on bacterial composition was more significant than the effect of geological bedrock from these previously unexplored regions.

In the first days of life, the newborns’ intestinal microbiota develops simultaneously with the intestinal gut barrier and follows intestinal immunity. The mode of delivery shows significant impact on microbial development and, thus, the initiation of the tryptophan catabolism pathway. Further antibiotics (ATB) treatment of mothers before or during delivery affects the microbial and tryptophan metabolite composition of stool of the caesarean- and vaginal-delivered newborns. The determination of microbiome and levels of tryptophan microbial metabolites in meconium and stool can characterize intestinal colonization of a newborn. From 134 samples from the Central European Longitudinal Studies of Parents and Children: The Next Generation (CELSPAC: TNG) cohort study, 16S rRNA gene sequencing was performed, and microbial tryptophan metabolites were quantified using ultra-high-performance liquid chromatography with triple-quadrupole mass spectrometry. Microbial diversity and concentrations of tryptophan metabolites were significantly higher in stool compared to meconium. Treatment of mothers with ATB before or during delivery affects metabolite composition and microbial diversity in stool of vaginal- and caesarean-delivered newborns. Correlation of microbial and metabolite composition shows significant positive correlations of indol-3-lactic acid, N-acetyl-tryptophan and indol-3-acetic acid with Bifidobacterium, Bacteroides and Peptoclostridium. The positive effect of vaginal delivery on newborns’ microbiome development is degraded when mother is treated with ATB before or during delivery. • Antibiotic treatment diminishes the positive effects of vaginal delivery. • Antibiotic treatment affects metabolite and microbial composition in newborns. • Bifidobacterium and Peptoclostridium could be the producer of indole-lactic acid.

The complete genome sequences of five Escherichia coli strains with probiotic attributes were determined, including strain A0 34/86, a component of the probiotic product Colinfant New Born, and strains H22, 582, B771, and B1172 with published probiotic potential. The size of sequenced genomes ranged from 5,092 to 5,408 kb.

The purpose of this experiment was to determine the impact of feed supplementation with organic zinc and/or a medicinal plants mixture on the composition and enzymatic activity of intestinal microflora as well as on the duodenal and jejunal barrier integrity in lambs. A total of 28 lambs were randomly allocated into 4 dietary treatments (n = 7) and were fed an unsupplemented basal diet (BD), or the BD enriched with organic Zn (Zn, 70 mg/kg diet), an herbal mixture (Herbmix, 100 g/day) or a combination of both additives (Zn+Herbmix). The Herbmix contained 33% each of Fumaria officinalis, Malva sylvestris, Matricaria chamomilla and 1% Artemisia absinthium. No significant effect on the fecal microbiota composition was observed due to the 35-day or 70-day dietary treatment. The intake of Zn alone resulted in decreased bacterial enzyme activities, such as β-glucuronidase, N-acetyl-glucosaminidase, β-galactosidase and β-glucosidase. The transepithelial electrical resistance of the small intestinal mucosa was not influenced by the dietary treatment, whereas simultaneous feeding of Zn and Herbmix exhibited higher claudin-1 and occludin levels in the jejunal mucosa. These results indicate that dietary intake of organic zinc and/or medicinal plants in the mentioned dosage did not alter the diversity of intestinal bacteria in growing lambs but did significantly influence bacterial enzyme activity. Supplementing the zinc and herbs combination showed the potential to regulate intestinal permeability by increasing the level of tight junction proteins in the jejunal mucosa.

Modulation of the intestinal microbiota through the application of probiotic bacteria is currently one possible way to improve gastrointestinal health in dogs. Knowledge on the efficacy of lactic acid bacteria in a diarrhoeic disorder of dogs is still spreading; however, the used or commercialized strains are often not of canine origin. In this study, E. faecium DSM 32820 strain (a canine isolate selected in our laboratory based on safety and probiotic criteria) was fed to nine dogs suffering from acute non-haemorrhagic diarrhoea at a dose of 1×109 CFU/ml for 7 days. Samples of feces and blood were taken on day 0 and 7. Evaluation of the CIBDAI (Canine Intestinal Bowel Disease activity index) score showed significantly lower vomiting frequency, stool frequency, stool consistency and weight loss at day 7 compared to day 0 (P<0.05). The 16S rRNA gene analysis revealed Firmicutes as the predominant phylum on both sampling days (72.0% vs. 67.9%, day 0 and 7) followed by Proteobacteria (13.4% vs. 6.0%), Actinobacteria (10.0% vs 13.5%), Fusobacteria (4.2% vs. 2.3%) and Bacteroidetes (0.4% vs. 10.4%). The abundance of family Erysipelotrichiaceae was higher on day 7 compared to the initial levels (P<0.05). Among 19 detected fecal enzymatic activities, five (α-chymotrypsin, β-glucuronidase, α-fucosidase, β-galactosidase, N-acetyl-glucosaminidase) were changed (P<0.05). After the application of the DSM 32820 strain, mean fecal dry matter was significantly higher on day 7 compared to baseline (P< 0.05). Although hematological and biochemical parameters in the blood were not significantly different on average, individual values of certain parameters in several dogs were improved.

In Slovakia, goat milk production for direct consumption and cheese processing has attracted growing interest. However, there is a lack of information regarding the microbial consortium in Slovak raw goat milk analyzed by next-generation sequencing and trace elements and vitamin E as well. A randomly selected samples (G24-G50) of raw goat milk from different animals at farms in Slovakia were analyzed. The phylum Actinobacteria dominated (62.8%), followed by the phyla Firmicutes (20.5%), Proteobacteria (7.4%), and Bacteroidetes (6.4%). The family Microbacteriaceae was detected in the highest percentage (60.2%) followed by Staphylococcaceae, Bacteroidaceae, Streptococcaceae, Lactobacillaceae, Enterobacteriaceae, and others. Regarding the genera, the most prevalent was genus Curtobacterium (47.4%) followed by the genera such as Staphylococcus (8.3%) and Bifidobacterium (4%). The genera Streptococcus, Lactococcus, Enterococcus, Lactobacillus, and Lacticaseibacillus were evaluated in abundance percentage in range 1%-3.2%. The genus Veillonella reached abundance 3.2%. The genera Enterobacter, Pseudomonas (1.3% and 0.5%), and Bacteroides (6.4%) were evaluated in small percentage abundance too. Zinc was detected with the highest mean value (2.561 ± 0.6823 mg/L) in raw goat milk, followed by iron (1.383 ± 0.5087 mg/L). The mean value of copper and manganese was 0.1746 ± 0.0463 mg/L and 0.051 ± 0.0238 mg/L. The vitamin E reached the mean value 0.3783 ± 0.1976 mg/L. This study is an original contribution showing microbial consortium in raw goat milk from Slovak farms. It also contributes to trace elements and vitamin E status in raw goat milk showing it as a nutritionally healthy food.

Young rabbits are susceptible to gastrointestinal diseases caused by bacteria. Enterococcus hirae can be associated with diseases. But enterocins produced by some enterococcal species can prevent/reduce this problem. Therefore, the interaction of enterocin M with a biofilm-forming, autochthonous E. hirae Kr8+ strain was tested in rabbits to assess enterocin potential in vivo. Rabbits (96), aged 35 days, both sexes, meat line M91 breed were divided into four groups, control C and three experimental groups. The rabbits in C received the standard diet, rabbits in experimental group 1 (E1) received 108 CFU/mL of Kr8+, a dose 500 µL/animal/day, E2 received Ent M (50 µL/animal/day), and E3 received both Kr8+ and Ent M in their drinking water over 21 days. The experiment lasted 42 days. Feces and blood were sampled at day 0/1 (at the start of the experiment, fecal mixture of 96 animals, n = 10), at day 21 (five fecal mixtures per group, n = 5), and at day 42 (21 days after additives cessation, the same). At days 21 and 42, four rabbits from each group were slaughtered, and cecum and appendix were sampled for standard microbial analysis. Ent M showed decreased tendency of Kr8+. Using next-generation sequencing, the phyla detected with the highest abundance were Firmicutes, Verrucomicrobia, Bacteroidetes, Tenericutes, Proteobacteria, Cyanobacteria, Saccharibacteria, and Actinobacteria. Interaction of Ent M with some phyla resulted in reduced abundance percentage. At day 21, significantly increased phagocytic activity (PA) was found in E1 and E2 (p < 0.001). Kr8+ did not attack PA and did not stimulate oxidative stress. But Ent M supported PA. The prospective importance of this study lies in beneficial interaction of enterocin in host body.

The beneficial influence of bacteriocin-producing, probiotic, mostly non-autochthonous bacteria has already been reported in various animals. However, their use in horses provides limited information, and results with autochthonous bacteria have not been reported. Therefore, the main objective of this model study was to test the effect of autochthonous, bacteriocin-producing faecal strain Enterococcus faecium EF 412 application in horses. One gram of freeze-dried EF 412 strain (109 CFU/mL for 21 days) was applied to horses in a small feed ball. Clinically healthy horses (12), Slovak warm-blood breed of various ages (5–13 years), were involved in a 35-day-long experiment, also functioning as control for themselves. They were stabled in separate boxes (university property), fed twice a day (hay, whole oats or grazed) with water access ad libitum. Sampling was performed at the start of the experiment, i.e. at days 0/1, 21 (3 weeks of EF 412 application) and at day 35 (2 weeks of EF 412 cessation). EF 412 colonized GIT of horses was 3.54 ± 0.75 CFU/g (log 10) at day 21. The eggs of the nematode Strongylus spp. were not found in horses after EF 412 application, and Eimeria spp. oocysts were similarly not found. The other microbiota were not reduced as evaluated by the use of standard method. Using next-generation sequencing, at phylum level, phyla Bacteroidetes and Firmicutes dominated and at family level, they were Bacteroidales BS11 and S24-7 gut goups and Lentisphaerae. In horses, the increasing tendency in phagocytic activity was noted after EF 412 application. Biochemical parameters were in the physiological range. Total protein value was significantly decreased at day 21 compared with day 0/1 as well as with day 35 (P < 0.05). Cholesterol and triglycerides were influenced (decreased) at day 21 compared with day 0/1 and day 35. Neither nematode eggs Strongylus spp. nor Eimeria spp. oocysts were found in faeces after EF 412 application. Autochthonous, faecal strain E. faecium EF 412 showed promising application potential.

Worldwide consumers increasingly demand traditional/local products, to which those made from ewe's milk belong. In Slovakia, dairy products made from ewe's milk have a long tradition. A total of seventeen farmhouse fresh ewe's milk lump cheeses from various local farm producers in central Slovakia were sampled at farms and then analyzed. Based on the sequencing data analysis, the phylum Firmicutes dominated (60.92%) in ewe's lump cheeses, followed with the phylum Proteobacteria (38.23%), Actinobacteria (0.38%) and Bacteroidetes (0.35%). The phylum Firmicutes was represented by six genera, among which the highest amount possessed the genus Streptococcus (41.13%) followed with the genus Lactococcus (8.54%), Fructobacillus (3.91%), Enterococcus (3.18%), Staphylococcus (1.80%) and the genus Brochotrix (0.08%). The phylum Proteobacteria in ewe's lump cheeses involved eight Gram-negative genera: Pseudomonas, Acinetobacter, Enterobacter, Ewingella, Escherichia-Shigella, Pantoea and Moraxella. The phylum Bacteroidetes involved three genera: Bacteroides, Sphingobacterium and Chrysobacterium. Results presented are original; the microbiome of Slovak ewe's milk lump cheese has been not analyzed at those taxonomic levels up to now.

Common variable immunodeficiency (CVID) is a clinically and genetically heterogeneous disorder with inadequate antibody responses and low levels of immunoglobulins including IgA that is involved in the maintenance of the intestinal homeostasis. In this study, we analyzed the taxonomical and functional metagenome of the fecal microbiota and stool metabolome in a cohort of six CVID patients without gastroenterological symptomatology and their healthy housemates. The fecal microbiome of CVID patients contained higher numbers of bacterial species and altered abundance of thirty-four species. Hungatella hathewayi was frequent in CVID microbiome and absent in controls. Moreover, the CVID metagenome was enriched for low-abundance genes likely encoding nonessential functions, such as bacterial motility and metabolism of aromatic compounds. Metabolomics revealed dysregulation in several metabolic pathways, mostly associated with decreased levels of adenosine in CVID patients. Identified features have been consistently associated with CVID diagnosis across the patients with various immunological characteristics, length of treatment, and age. Taken together, this initial study revealed expansion of bacterial diversity in the host immunodeficient conditions and suggested several bacterial species and metabolites, which have potential to be diagnostic and/or prognostic CVID markers in the future.

Enterotoxigenic Escherichia coli (ETEC) and Shiga toxin-producing E. coli (STEC) strains are the causative agents of severe foodborne diseases in both humans and animals. In this study, porcine pathogenic E. coli strains (n =277) as well as porcine commensal strains (n = 188) were tested for their susceptibilities to 34 bacteriocin monoproducers to identify the most suitable bacteriocin types inhibiting porcine pathogens. Under in vitro conditions, the set of pathogenic E. coli strains was found to be significantly more susceptible to the majority of tested bacteriocins than commensal E. coli. Based on the production of bacteriocins with specific activity against pathogens, three potentially probiotic commensal E. coli strains of human origin were selected. These strains were found to be able to outcompete ETEC strains expressing F4 or F18 fimbriae in liquid culture and also decreased the severity and duration of diarrhea in piglets during experimental ETEC infection as well as pathogen numbers on the last day of in vivo experimentation. While the extents of the probiotic effect were different for each strain, the cocktail of all three strains showed the most pronounced beneficial effects, suggesting synergy between the tested E. coli strains. IMPORTANCE Increasing levels of antibiotic resistance among bacteria also increase the need for alternatives to conventional antibiotic treatment. Pathogenic Escherichia coli represents a major diarrheic infectious agent of piglets in their postweaning period; however, available measures to control these infections are limited. This study describes three novel E. coli strains producing antimicrobial compounds (bacteriocins) that actively inhibit a majority of toxigenic E. coli strains. The beneficial effect of three potentially probiotic E. coli strains was demonstrated under both in vitro and in vivo conditions. The novel probiotic candidates may be used as prophylaxis during piglets' postweaning period to overcome common infections caused by E. coli.

Long-term dysbiosis of the gut microbiome has a significant impact on colorectal cancer (CRC) progression and explains part of the observed heterogeneity of the disease. Even though the shifts in gut microbiome in the normal-adenoma-carcinoma sequence were described, the landscape of the microbiome within CRC and its associations with clinical variables remain under-explored. We performed 16S rRNA gene sequencing of paired tumour tissue, adjacent visually normal mucosa and stool swabs of 178 patients with stage 0–IV CRC to describe the tumour microbiome and its association with clinical variables. We identified new genera associated either with CRC tumour mucosa or CRC in general. The tumour mucosa was dominated by genera belonging to oral pathogens. Based on the tumour microbiome, we stratified CRC patients into three subtypes, significantly associated with prognostic factors such as tumour grade, sidedness and TNM staging, BRAF mutation and MSI status. We found that the CRC microbiome is strongly correlated with the grade, location and stage, but these associations are dependent on the microbial environment. Our study opens new research avenues in the microbiome CRC biomarker detection of disease progression while identifying its limitations, suggesting the need for combining several sampling sites (e.g., stool and tumour swabs).

Introduction The emergence and spread of antibiotic resistance among pathogenic bacteria drives the search for alternative antimicrobial therapies. Bacteriocins represent a potential alternative to antibiotic treatment. In contrast to antibiotics, bacteriocins are peptides or proteins that have relatively narrow spectra of antibacterial activities and are produced by a wide range of bacterial species. Bacteriocins ofEscherichia coliare historically classified as microcins and colicins, and, until now, more than 30 different bacteriocin types have been identified and characterized. Areas covered We performed bibliographical searches of online databases to review the literature regarding bacteriocins produced byE. coliwith respect to their occurrence, bacteriocin role in bacterial colonization and pathogenicity, and application of their antimicrobial effect. Expert opinion The potential use of bacteriocins for applications in human and animal medicine and the food industry includes (i) the use of bacteriocin-producing probiotic strains, (ii) recombinant production in plants and application in food, and (iii) application of purified bacteriocins.

Background Long-term dysbiosis of the gut microbiome has a significant impact on the development, progression and the aggressiveness of colorectal cancer (CRC) and may explain part of the observed heterogeneity of the disease from phenotypic, prognostic and response to treatment perspectives. Although the shifts in gut microbiome in the normal-adenoma-carcinoma sequence have been described, the landscape of microbiome within CRC and its associations with clinical variables remain under-explored. Results We performed 16S rRNA gene sequencing of paired tumour tissue, adjacent visually-normal mucosa and stool swabs of N=186 patients with stage 0-IV CRC to describe the tumour microbiome and its association with clinical variable and to derive tumour microbial subtypes.We identified new genera never previously associated with CRC tumour mucosa ( Flavonifractor, Haemophilus, Howardella, Pseudomonas, Sutterella, Treponema 2 ) or CRC ( Actinobacillus, Aggregatibacter, Bergeyella, Phocaeiola, Defluviitaleaceae UCG-011, Massilia, Tyzzerella 4 ). The bacteria residing on tumour-mucosa were dominated by genera belonging to (potential) oral pathogens. Based on tumour microbial profiles, we stratified CRC patients into three subtypes. The subtypes were significantly associated with prognostic factors such as tumor grade, primary tumour sidedness and TNM staging, with one subtype enriched in tumours with poor prognosis. Further, we inspected the associations of microbiome with clinical variables in a subtype-agnostic setting. The primary tumour-associated clinical variables predominantly correlated with tumour mucosal microbiome, while the presence of local and distant metastases was mostly associated with the stool microbiome. Conclusions Understanding the interactions of the bacteria residing on tumour mucosa within different CRC tumour microbiome subtypes will help to better understand the underlying biological background of the heterogeneity of this disease. Indeed, the tumour microbiome is a possible source of additional integrative markers of CRC patients’ survival and prognosis. We found that CRC microbiome is strongly correlated with clinical variables, but these associations are dependent on the microbial environment (tumour mucosa, normal mucosa, stool). Our study thus identifies limitations of the usage of microbiome composition as marker of CRC progression, suggesting the need of combining several sampling sites (e.g. stool and tumour swabs).

A taxonomic study of two fluorescent Pseudomonas strains (HJ/4T and SJ/9/1T) isolated from calcite moonmilk samples obtained from two caves in the Moravian Karst in the Czech Republic was carried out. Results of initial 16S rRNA gene sequence analysis assigned both strains into the genus Pseudomonas and showed Pseudomonas yamanorum 8H1T as their closest neighbour with 99.8 and 99.7 % 16S rRNA gene similarities to strains HJ/4T and SJ/9/1T, respectively. Subsequent sequence analysis of rpoD, rpoB and gyrB housekeeping genes confirmed the highest similarity of both isolates to P. yamanorum 8H1T, but phylogeny and sequences similarities implied that they are representatives of two novel species within the genus Pseudomonas. Further study comprising whole-genome sequencing followed by average nucleotide identity and digital DNA-DNA hybridization calculations, repetitive sequence-based PCR fingerprinting with the REP and ERIC primers, automated ribotyping with the EcoRI restriction endonuclease, cellular fatty acid analysis, quinone and polar lipid characterization, and extensive biotyping confirmed clear separation of both analysed strains from the remaining Pseudomonas species and showed that they represent two novel species within the genus Pseudomonas for which the names Pseudomonas karstica sp. nov. (type strain HJ/4T=CCM 7891T=LMG 27930T) and Pseudomonas spelaei sp. nov. (type strain SJ/9/1T=CCM 7893T=LMG 27931T) are suggested.

Colinfant New Born (CNB) is an orally administered probiotic preparation containing the Escherichia coli strain A0 34/86, which is specially marketed for use in newborns and infants. Although the impact of different probiotics on the composition of the human gut microbiota has been previously described, the effects of E. coli probiotic consumption during infancy on the development of intestinal microbiota are not known. The effect of oral administration of CNB on the Enterobacteriaceae population was mapped using 16S rRNA gene sequencing in DNA samples isolated from the stools of one infant collected at 177 different time points during the first year of life. E. coli strains turnover was analyzed based on the detection of 26 genetic determinants, phylogroups, and pulsed-field gel electrophoresis (PFGE) analysis. Administration of CNB during the second and third month of life introduced the Escherichia genus to the infant’s intestinal tract, and Escherichia became dominant among the Enterobacteriaceae family (p < 0.01). Genetic determinants, typical for probiotic E. coli A0 34/86 strain, were detected on the first day after application of CNB and persisted all year. In addition, nine transient E. coli strains were identified; these strains harbored different genetic determinants and showed different PFGE profiles. Transient strains were detected from 2 to 24 days in the stool samples. The first Escherichia colonizer originated from the application of the CNB probiotic preparation. Probiotic E. coli A0 34/86 successfully colonized the intestinal tract of an infant and became resident during the first year of life.

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 from the ice-free northern part of the island. They were rod-shaped, Gram-stain-negative, and produced moderately slimy red-pink pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, MALDI-TOF MS, rep-PCR analyses, chemotaxonomic methods and extensive biotyping was used to clarify the taxonomic position of these isolates. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to the genus Hymenobacter. The closest relative was Hymenobacter humicola CCM 8763T, exhibiting 98.3 and 98.9% 16S rRNA pairwise similarity with the reference isolates P5342T and P5252T, respectively. Average nucleotide identity, digital DNA-DNA hybridization and core gene distances calculated from the whole-genome sequencing data confirmed that P5252T and P5342T represent two distinct Hymenobacter species. The menaquinone systems of both strains contained MK-7 as the major respiratory quinone. The predominant polar lipids for both strains were phosphatidylethanolamine and one unidentified glycolipid. The major components in the cellular fatty acid composition were summed feature 3 (C16:1ω7c/C16:1ω6c), C16:1ω5c, summed feature 4 (anteiso-C17:1 B/iso-C17:1 I), anteiso-C15:0 and iso-C15 : 0 for all isolates. Based on the obtained results, two novel species are proposed, for which the names Hymenobacter terrestris sp. nov. (type strain P5252T=CCM 8765T=LMG 31495T) and Hymenobacter lapidiphilus sp. nov. (type strain P5342T=CCM 8764T=LMG 30613T) are suggested.