The biodiversity of microorganisms is maintained by intricate nets of interactions between competing species. Impaired functionality of human microbiomes correlates with their reduced biodiversity ...originating from aseptic environmental conditions and antibiotic use. Microbiomes of wild animals are free of these selective pressures. Microbiota provides a protecting shield from invasion by pathogens in the wild, outcompeting their growth in specific ecological niches. We applied ultrahigh-throughput microfluidic technologies for functional profiling of microbiomes of wild animals, including the skin beetle, Siberian lynx, common raccoon dog, and East Siberian brown bear. Single-cell screening of the most efficient killers of the common human pathogen
resulted in repeated isolation of
strains. While isolated strains had different phenotypes, all of them displayed a similar set of biosynthetic gene clusters (BGCs) encoding antibiotic amicoumacin, siderophore bacillibactin, and putative analogs of antimicrobials including bacilysin, surfactin, desferrioxamine, and class IId cyclical bacteriocin. Amicoumacin A (Ami) was identified as a major antibacterial metabolite of these strains mediating their antagonistic activity. Genome mining indicates that Ami BGCs with this architecture subdivide into three distinct families, characteristic of the
,
, and
species. While Ami itself displays mediocre activity against the majority of Gram-negative bacteria, isolated
strains efficiently inhibit the growth of both Gram-positive
and Gram-negative
in coculture. We believe that the expanded antagonistic activity spectrum of Ami-producing
can be attributed to the metabolomic profile predetermined by their biosynthetic fingerprint. Ultrahigh-throughput isolation of natural probiotic strains from wild animal microbiomes, as well as their metabolic reprogramming, opens up a new avenue for pathogen control and microbiome remodeling in the food industry, agriculture, and healthcare.
In order to address the upcoming crisis in the treatment of
infections, caused by an increasing proportion of resistant isolates, new approaches to antimicrobial therapy must be developed. One ...approach would be to use (bacterio)phages and/or phage derivatives for therapy. In this study, we present a description of the first
phage from the
family. The vB_KpnP_Klyazma podovirus, which forms translucent halos around the plaques, was isolated from river water. The phage genome is composed of 82 open reading frames, which are divided into two clusters located on opposite strands. Phylogenetic analysis revealed that the phage belongs to the
family, although its identity with the closest member of this family was not higher than 5%. The bacteriophage demonstrated lytic activity against all (
= 11)
strains with the KL20 capsule type, but only the host strain was lysed effectively. The receptor-binding protein of the phage was identified as a polysaccharide depolymerase with a pectate lyase domain. The recombinant depolymerase protein showed concentration-dependent activity against all strains with the KL20 capsule type. The ability of a recombinant depolymerase to cleave bacterial capsular polysaccharides regardless of a phage's ability to successfully infect a particular strain holds promise for the possibility of using depolymerases in antimicrobial therapy, even though they only make bacteria sensitive to environmental factors, rather than killing them directly.
Lactic acid bacteria (LAB) bacteriocins can be considered as a bio-preservatives and an alternative to antibiotics, but the high manufacturing costs limit their commercial application. The screening ...of LAB strains for bacteriocinogenic activity was carried out and the effect of rye bran enzymatic hydrolysate (RBEH) on gene expression and bacteriocin production was evaluated. qPCR and RT-PCR was applied for bacteriocin gene detection and their expression quantification. The agar diffusion technique with the test strains of Bacillus spp., Staphylococcus spp. and Salmonella enterica was performed for antimicrobial activity assessment of LAB cultivated in MRS broth and RBEH (processed with proteases and cellulases). The genes of different bacteriocins were revealed for thirteen out of eighteen LAB strains, while the antimicrobial activity was detected only for four of them. The strains of Lactobacillus paracasei VKPM B-11657 and L. salivarius VKPM B-2214 with unnamed class IIb bacteriocin gene demonstrated the widest spectrum of activity. The growth patterns and bacteriocin gene expression differed between both strains and media. The activity of cell-free supernatants after cultivation in RBEH was slightly lower. However, the test strain of S. epidermidis was inhibited by L. paracasei cultivated in RBEH but not in MRS. Thus, rye bran can be applied as a sole source of nutrients for LAB fermentation and bacteriocin production.
A number of mechanisms have been proposed explaining probiotics and prebiotics benefit human health, in particular, probiotics have a suppression effect on pathogen growth that can be enhanced with ...the introduction of prebiotics. In vitro models enhanced with computational biology can be useful for selecting a composition with prebiotics from new plant sources with the greatest synergism. Water extracts from burdock root and Jerusalem artichoke tubers were purified by ultrafiltration and activated charcoal and concentrated on a rotary evaporator. Fructans were precipitated with various concentrations of ethanol.
8 VKPM AC-2136 and
ATCC 43300 strains were applied to estimate the synbiotic effect. The growth of bifidobacteria and staphylococci in monocultures and cocultures in broths with glucose, commercial prebiotics, as well as isolated fructans were studied. The minimum inhibitory concentrations (MICs) of lactic and acetic acids for the
strain were determined. A quantitative model joining the formation of organic acids by probiotics as antagonism factors and the MICs of pathogens (as the measure of their inhibition) was tested in cocultures and showed a high predictive value (R
≥ 0.86). The synbiotic factor obtained from the model was calculated based on the experimental data and obtained constants. Fructans precipitated with 20% ethanol and
have the greater synergism against
.
Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we ...developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE–FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus, and predicted which genera were associated with inhibitory activity.
Microbiome spectra serve as critical clues to elucidate the evolutionary biology pathways, potential pathologies, and even behavioral patterns of the host organisms. Furthermore, exotic sources of ...microbiota represent an unexplored niche to discover microbial secondary metabolites. However, establishing the bacterial functionality is complicated by an intricate web of interactions inside the microbiome. Here we apply an ultrahigh-throughput (uHT) microfluidic droplet platform for activity profiling of the entire oral microbial community of the Siberian bear to isolate Bacillus strains demonstrating antimicrobial activity against Staphylococcus aureus. Genome mining allowed us to identify antibiotic amicoumacin A (Ami) as responsible for inhibiting the growth of S. aureus. Proteomics and metabolomics revealed a unique mechanism of Bacillus self-resistance to Ami, based on a subtle equilibrium of its deactivation and activation by kinase AmiN and phosphatase AmiO, respectively. We developed uHT quantitative single-cell analysis to estimate antibiotic efficacy toward different microbiomes and used it to determine the activity spectra of Ami toward human and Siberian bear microbiota. Thus, uHT microfluidic droplet platform activity profiling is a powerful tool for discovering antibiotics and quantifying external influences on a microbiome.
Traumatic eyeball damages is a topical issue in present-day ophthalmology as they constitute one of the main causes of vision loss in people of working age.
Purpose:
to assess the feasibilty, ...effectiveness and safety of one-time early-stage microinvasive optical reconstructive surgery of a patient with traumatic eyeball damage consequences: a swelling cataract, lens ligamentous apparatus defect, iridodialysis, and traumatic mydriasis.
Material and methods.
Patient V., 27, was under observation with the following diagnosis: “OS — condition after a contusion damage to the eyeball: traumatic swelling cataract; stage II subluxation of the lens; traumatic mydriasis, iridodialysis of 180 degrees”. OS visual acuity — correct light projection. The patient underwent an ORO of the left eye: phacoaspiration of a swelling cataract with implantation of an intracapsular ring and an intraocular lens in combination with closed iridoplasty.
Results.
No intraoperative complications took place. In the postoperative period, the best corrected visual acuity was 0.6, IOP remained stable, the lens was centered in the capsular bag, the iris sutures were consistent, the pupil rounded, centered, 4 mm in diameter. The patient felt satisfied with the cosmetic and functional result of surgery.
Conclusion.
One-time iridoplasty in combination with cataract surgery is an effective and safe method of surgical treatment of traumatically damaged iris and lens.
Currently, the search for new therapy options for infectious diseases caused by multidrug-resistant Staphylococcus aureus is a priority. Combining antibiotics with virulent (lytic) bacteriophages may ...be considered a viable alternative to conventional antibiotic therapy. The study was aimed to assess the combined effects of the lytic bacteriophage vB_SauM-515A1 of Herelleviridae family and antibiotics of various classes on the Staphylococcus aureus clinical strains. Strains (n = 4) belong to the clinically significant sequence types ST1, ST8, ST121 and are characterized by multidrug resistance. Efficiency of the combination use of two antibacterial agents was assessed by comparison of optical densities of the test samples and controls after 24 hrs. of incubation. Mutually enhancing activities of bacteriophage used in combination with oxacillin, tetracycline and linezolid were revealed, in contrast to the separate use of each agent. Efficiency generally increased with the selected optimum multiplicity of infection values. No antagonism was revealed when combining the phage with antibiotics. Thus, virulent bacteriophage vB_SauM515A1 can be considered as a possible auxiliary therapeutic agent for antimicrobial-resistant strains of Staphylococcus aureus.
In order to address the upcoming crisis in the treatment of Klebsiella pneumoniae infections, caused by an increasing proportion of resistant isolates, new approaches to antimicrobial therapy must be ...developed. One approach would be to use (bacterio)phages and/or phage derivatives for therapy. In this study, we present a description of the first K. pneumoniae phage from the Zobellviridae family. The vB_KpnP_Klyazma podovirus, which forms translucent halos around the plaques, was isolated from river water. The phage genome is composed of 82 open reading frames, which are divided into two clusters located on opposite strands. Phylogenetic analysis revealed that the phage belongs to the Zobellviridae family, although its identity with the closest member of this family was not higher than 5%. The bacteriophage demonstrated lytic activity against all (n = 11) K. pneumoniae strains with the KL20 capsule type, but only the host strain was lysed effectively. The receptor-binding protein of the phage was identified as a polysaccharide depolymerase with a pectate lyase domain. The recombinant depolymerase protein showed concentration-dependent activity against all strains with the KL20 capsule type. The ability of a recombinant depolymerase to cleave bacterial capsular polysaccharides regardless of a phage's ability to successfully infect a particular strain holds promise for the possibility of using depolymerases in antimicrobial therapy, even though they only make bacteria sensitive to environmental factors, rather than killing them directly.
PDF
